From 4d7f98a6dd54d9863ba449ec79dcd95d25ed863d Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 10 Sep 2015 04:57:44 +0100 Subject: [PATCH] JAL-1645 source formatting and organise imports --- src/MCview/AppletPDBCanvas.java | 36 +- src/MCview/AppletPDBViewer.java | 29 +- src/MCview/Bond.java | 6 +- src/MCview/PDBCanvas.java | 31 +- src/MCview/PDBChain.java | 29 +- src/MCview/PDBViewer.java | 12 +- src/MCview/PDBfile.java | 50 +- src/MCview/Zsort.java | 3 +- src/com/github/reinert/jjschema/Attributes.java | 39 +- src/com/stevesoft/pat/Any.java | 2 +- src/com/stevesoft/pat/BackG.java | 2 +- src/com/stevesoft/pat/BackMatch.java | 2 +- src/com/stevesoft/pat/Backup.java | 2 +- src/com/stevesoft/pat/Bits.java | 4 +- src/com/stevesoft/pat/Boundary.java | 2 +- src/com/stevesoft/pat/Bracket.java | 3 +- src/com/stevesoft/pat/Ctrl.java | 97 +- src/com/stevesoft/pat/Custom.java | 6 +- src/com/stevesoft/pat/CustomEndpoint.java | 2 +- src/com/stevesoft/pat/DotMulti.java | 2 +- src/com/stevesoft/pat/End.java | 2 +- src/com/stevesoft/pat/FastBracket.java | 3 +- src/com/stevesoft/pat/FastMulti.java | 2 +- src/com/stevesoft/pat/FileRegex.java | 81 +- src/com/stevesoft/pat/Group.java | 2 +- src/com/stevesoft/pat/Multi.java | 8 +- src/com/stevesoft/pat/Multi_stage2.java | 2 +- src/com/stevesoft/pat/NoPattern.java | 2 +- src/com/stevesoft/pat/NullPattern.java | 2 +- src/com/stevesoft/pat/Or.java | 3 +- src/com/stevesoft/pat/OrMark.java | 2 +- src/com/stevesoft/pat/Pattern.java | 6 +- src/com/stevesoft/pat/Pthings.java | 2 +- src/com/stevesoft/pat/PushRule.java | 5 +- src/com/stevesoft/pat/Range.java | 2 +- src/com/stevesoft/pat/RegOpt.java | 4 +- src/com/stevesoft/pat/RegRes.java | 4 +- src/com/stevesoft/pat/Regex.java | 77 +- src/com/stevesoft/pat/RegexReader.java | 5 +- src/com/stevesoft/pat/RegexTokenizer.java | 3 +- src/com/stevesoft/pat/ReplaceRule.java | 2 +- src/com/stevesoft/pat/Replacer.java | 6 +- src/com/stevesoft/pat/Skip.java | 4 +- src/com/stevesoft/pat/SkipBMH.java | 10 +- src/com/stevesoft/pat/Skipped.java | 6 +- src/com/stevesoft/pat/Start.java | 2 +- src/com/stevesoft/pat/StringLike.java | 8 +- src/com/stevesoft/pat/Transformer.java | 6 +- src/com/stevesoft/pat/lookAhead.java | 2 +- src/com/stevesoft/pat/oneChar.java | 2 +- .../stevesoft/pat/wrap/CharArrayBufferWrap.java | 3 +- src/com/stevesoft/pat/wrap/CharArrayWrap.java | 3 +- .../stevesoft/pat/wrap/RandomAccessFileWrap.java | 17 +- src/com/stevesoft/pat/wrap/StringBufferWrap.java | 3 +- src/com/stevesoft/pat/wrap/StringWrap.java | 3 +- src/com/stevesoft/pat/wrap/WriterWrap.java | 6 +- src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java | 1678 +++--- src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java | 554 +- .../edu/ucsf/rbvi/strucviz2/ChimeraManager.java | 23 +- src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java | 987 ++-- .../edu/ucsf/rbvi/strucviz2/ChimeraResidue.java | 752 +-- .../rbvi/strucviz2/ChimeraStructuralObject.java | 120 +- .../edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java | 306 +- .../edu/ucsf/rbvi/strucviz2/StructureManager.java | 14 +- .../edu/ucsf/rbvi/strucviz2/StructureSettings.java | 35 +- src/ext/vamsas/IRegistryServiceLocator.java | 10 +- src/ext/vamsas/JpredServiceLocator.java | 10 +- src/ext/vamsas/JpredSoapBindingStub.java | 14 +- src/ext/vamsas/MuscleWSServiceLocator.java | 10 +- src/ext/vamsas/MuscleWSSoapBindingStub.java | 15 +- src/ext/vamsas/RegistryServiceSoapBindingStub.java | 3 +- src/ext/vamsas/SeqSearchServiceLocator.java | 10 +- .../vamsas/SeqSearchServiceSoapBindingStub.java | 18 +- src/jalview/analysis/AAFrequency.java | 19 +- src/jalview/analysis/AlignSeq.java | 44 +- src/jalview/analysis/AlignmentAnnotationUtils.java | 8 +- src/jalview/analysis/AlignmentSorter.java | 16 +- src/jalview/analysis/AlignmentUtils.java | 84 +- src/jalview/analysis/AnnotationSorter.java | 9 +- src/jalview/analysis/Conservation.java | 33 +- src/jalview/analysis/CrossRef.java | 13 +- src/jalview/analysis/Dna.java | 20 +- src/jalview/analysis/Finder.java | 2 +- src/jalview/analysis/Grouping.java | 4 +- src/jalview/analysis/NJTree.java | 3 +- src/jalview/analysis/PCA.java | 8 +- src/jalview/analysis/ParseProperties.java | 9 +- src/jalview/analysis/Rna.java | 33 +- src/jalview/analysis/SeqsetUtils.java | 13 +- src/jalview/analysis/SequenceIdMatcher.java | 4 +- src/jalview/analysis/StructureFrequency.java | 19 +- .../scoremodels/PairwiseSeqScoreModel.java | 1 - src/jalview/api/AlignViewControllerGuiI.java | 4 +- src/jalview/api/AlignViewControllerI.java | 14 +- src/jalview/api/AlignViewportI.java | 9 +- src/jalview/api/AlignmentViewPanel.java | 2 +- src/jalview/api/FeatureRenderer.java | 4 +- src/jalview/api/FeatureSettingsControllerI.java | 2 +- src/jalview/api/ViewStyleI.java | 2 +- src/jalview/api/analysis/ViewBasedAnalysisI.java | 2 +- .../api/structures/JalviewStructureDisplayI.java | 2 + src/jalview/appletgui/APopupMenu.java | 116 +- src/jalview/appletgui/AlignFrame.java | 103 +- src/jalview/appletgui/AlignViewport.java | 7 +- src/jalview/appletgui/AlignmentPanel.java | 62 +- src/jalview/appletgui/AnnotationColumnChooser.java | 3 +- src/jalview/appletgui/AnnotationLabels.java | 62 +- src/jalview/appletgui/AnnotationRowFilter.java | 6 - src/jalview/appletgui/AppletJmol.java | 10 +- src/jalview/appletgui/CutAndPasteTransfer.java | 29 +- src/jalview/appletgui/EditNameDialog.java | 7 +- src/jalview/appletgui/EmbmenuFrame.java | 7 +- src/jalview/appletgui/FeatureColourChooser.java | 36 +- src/jalview/appletgui/FeatureRenderer.java | 19 +- src/jalview/appletgui/FeatureSettings.java | 50 +- src/jalview/appletgui/Finder.java | 7 +- src/jalview/appletgui/FontChooser.java | 6 +- src/jalview/appletgui/IdCanvas.java | 18 +- src/jalview/appletgui/JVDialog.java | 10 +- src/jalview/appletgui/OverviewPanel.java | 4 +- src/jalview/appletgui/PCAPanel.java | 26 +- src/jalview/appletgui/PaintRefresher.java | 12 +- src/jalview/appletgui/RedundancyPanel.java | 9 +- src/jalview/appletgui/RotatableCanvas.java | 26 +- src/jalview/appletgui/ScalePanel.java | 24 +- src/jalview/appletgui/SeqCanvas.java | 14 +- src/jalview/appletgui/SeqPanel.java | 53 +- src/jalview/appletgui/SequenceRenderer.java | 16 +- src/jalview/appletgui/SliderPanel.java | 9 +- src/jalview/appletgui/SplitFrame.java | 10 +- src/jalview/appletgui/Tooltip.java | 19 +- src/jalview/appletgui/UserDefinedColours.java | 21 +- src/jalview/bin/BuildDetails.java | 3 - src/jalview/bin/Cache.java | 41 +- src/jalview/bin/Jalview.java | 43 +- src/jalview/bin/JalviewLite.java | 35 +- src/jalview/binding/Alignment.java | 305 +- src/jalview/binding/Annotation.java | 837 +-- src/jalview/binding/AnnotationElement.java | 546 +- src/jalview/binding/Colour.java | 939 ++-- src/jalview/binding/Feature.java | 544 +- src/jalview/binding/FeatureSettings.java | 464 +- src/jalview/binding/Features.java | 178 +- src/jalview/binding/JGroup.java | 1457 +++--- src/jalview/binding/JSeq.java | 1226 ++--- src/jalview/binding/JalviewModel.java | 409 +- src/jalview/binding/JalviewModelSequence.java | 1835 +++---- src/jalview/binding/JalviewUserColours.java | 618 +-- src/jalview/binding/Pdbentry.java | 614 +-- src/jalview/binding/PdbentryItem.java | 344 +- src/jalview/binding/Pdbids.java | 178 +- src/jalview/binding/Property.java | 305 +- src/jalview/binding/Sequence.java | 178 +- src/jalview/binding/SequenceSet.java | 1010 ++-- src/jalview/binding/SequenceType.java | 356 +- src/jalview/binding/Setting.java | 462 +- src/jalview/binding/Tree.java | 1621 +++--- src/jalview/binding/UserColourScheme.java | 179 +- src/jalview/binding/UserColours.java | 306 +- src/jalview/binding/VAMSAS.java | 1141 ++-- src/jalview/binding/VamsasModel.java | 177 +- src/jalview/binding/Viewport.java | 2793 +++++----- src/jalview/commands/EditCommand.java | 25 +- src/jalview/commands/RemoveGapColCommand.java | 6 +- src/jalview/commands/RemoveGapsCommand.java | 10 +- src/jalview/controller/AlignViewController.java | 44 +- .../controller/FeatureSettingsController.java | 6 +- src/jalview/datamodel/AlignedCodonFrame.java | 14 +- src/jalview/datamodel/Alignment.java | 75 +- src/jalview/datamodel/AlignmentAnnotation.java | 28 +- src/jalview/datamodel/AlignmentExportData.java | 1 - src/jalview/datamodel/AlignmentI.java | 5 +- src/jalview/datamodel/AlignmentView.java | 47 +- src/jalview/datamodel/BinarySequence.java | 3 +- src/jalview/datamodel/CigarArray.java | 10 +- src/jalview/datamodel/CigarBase.java | 56 +- src/jalview/datamodel/ColumnSelection.java | 24 +- src/jalview/datamodel/DBRefSource.java | 22 +- src/jalview/datamodel/Mapping.java | 25 +- src/jalview/datamodel/PDBEntry.java | 11 +- src/jalview/datamodel/Provenance.java | 2 +- src/jalview/datamodel/RnaViewerModel.java | 4 +- src/jalview/datamodel/SearchResults.java | 3 +- src/jalview/datamodel/SeqCigar.java | 57 +- src/jalview/datamodel/Sequence.java | 11 +- src/jalview/datamodel/SequenceCollectionI.java | 10 +- src/jalview/datamodel/SequenceDummy.java | 3 +- src/jalview/datamodel/SequenceGroup.java | 29 +- src/jalview/datamodel/SequenceI.java | 5 +- src/jalview/datamodel/SequenceNode.java | 2 +- src/jalview/datamodel/StructureViewerModel.java | 1 + src/jalview/datamodel/xdb/embl/EmblEntry.java | 33 +- src/jalview/datamodel/xdb/embl/EmblFeature.java | 4 +- src/jalview/datamodel/xdb/embl/EmblFile.java | 5 +- src/jalview/ext/jmol/JalviewJmolBinding.java | 30 +- src/jalview/ext/jmol/PDBFileWithJmol.java | 8 +- src/jalview/ext/paradise/Annotate3D.java | 14 +- src/jalview/ext/rbvi/chimera/ChimeraCommands.java | 25 +- src/jalview/ext/rbvi/chimera/ChimeraListener.java | 6 +- src/jalview/gui/AlignExportSettings.java | 4 +- src/jalview/gui/AlignFrame.java | 263 +- src/jalview/gui/AlignViewport.java | 33 +- src/jalview/gui/AlignmentPanel.java | 66 +- src/jalview/gui/AnnotationChooser.java | 23 +- src/jalview/gui/AnnotationColourChooser.java | 18 +- src/jalview/gui/AnnotationColumnChooser.java | 56 +- src/jalview/gui/AnnotationExporter.java | 27 +- src/jalview/gui/AnnotationLabels.java | 94 +- src/jalview/gui/AnnotationPanel.java | 12 +- src/jalview/gui/AnnotationRowFilter.java | 2 - src/jalview/gui/AppJmol.java | 38 +- src/jalview/gui/AppJmolBinding.java | 10 +- src/jalview/gui/AppVarna.java | 10 +- src/jalview/gui/AppVarnaBinding.java | 17 +- src/jalview/gui/AssociatePdbFileWithSeq.java | 4 +- src/jalview/gui/BlogReader.java | 13 +- src/jalview/gui/ChimeraViewFrame.java | 38 +- src/jalview/gui/Console.java | 26 +- src/jalview/gui/CutAndPasteHtmlTransfer.java | 31 +- src/jalview/gui/CutAndPasteTransfer.java | 15 +- src/jalview/gui/DasSourceBrowser.java | 27 +- src/jalview/gui/Desktop.java | 102 +- src/jalview/gui/EPSOptions.java | 19 +- src/jalview/gui/EditNameDialog.java | 11 +- src/jalview/gui/FeatureColourChooser.java | 33 +- src/jalview/gui/FeatureRenderer.java | 26 +- src/jalview/gui/FeatureSettings.java | 74 +- src/jalview/gui/Finder.java | 14 +- src/jalview/gui/FontChooser.java | 15 +- src/jalview/gui/HTMLOptions.java | 3 +- src/jalview/gui/Help.java | 4 +- src/jalview/gui/IdCanvas.java | 19 +- src/jalview/gui/IdPanel.java | 14 +- src/jalview/gui/IdwidthAdjuster.java | 4 +- src/jalview/gui/JDatabaseTree.java | 17 +- src/jalview/gui/Jalview2XML.java | 15 +- src/jalview/gui/Jalview2XML_V1.java | 25 +- src/jalview/gui/JalviewChimeraBindingModel.java | 21 +- src/jalview/gui/JvSwingUtils.java | 6 +- src/jalview/gui/OOMWarning.java | 11 +- src/jalview/gui/OptsAndParamsPage.java | 57 +- src/jalview/gui/OverviewPanel.java | 6 +- src/jalview/gui/PCAPanel.java | 56 +- src/jalview/gui/PDBSearchPanel.java | 2 - src/jalview/gui/PopupMenu.java | 107 +- src/jalview/gui/Preferences.java | 49 +- src/jalview/gui/ProgressBar.java | 15 +- src/jalview/gui/PromptUserConfig.java | 2 +- src/jalview/gui/RedundancyPanel.java | 21 +- src/jalview/gui/RestInputParamEditDialog.java | 14 +- src/jalview/gui/RestServiceEditorPane.java | 6 +- src/jalview/gui/RotatableCanvas.java | 35 +- src/jalview/gui/SVGOptions.java | 3 +- src/jalview/gui/ScalePanel.java | 16 +- src/jalview/gui/SeqCanvas.java | 33 +- src/jalview/gui/SeqPanel.java | 84 +- src/jalview/gui/SequenceFetcher.java | 59 +- src/jalview/gui/SequenceRenderer.java | 5 +- src/jalview/gui/SliderPanel.java | 9 +- src/jalview/gui/SplitFrame.java | 8 +- src/jalview/gui/StructureChooser.java | 102 +- src/jalview/gui/StructureViewer.java | 15 +- src/jalview/gui/StructureViewerBase.java | 54 +- src/jalview/gui/TextColourChooser.java | 25 +- src/jalview/gui/TreeCanvas.java | 15 +- src/jalview/gui/TreePanel.java | 25 +- src/jalview/gui/UserDefinedColours.java | 112 +- src/jalview/gui/UserQuestionnaireCheck.java | 7 +- src/jalview/gui/VamsasApplication.java | 28 +- src/jalview/gui/ViewSelectionMenu.java | 4 +- src/jalview/gui/WebserviceInfo.java | 16 +- src/jalview/gui/WsJobParameters.java | 33 +- src/jalview/gui/WsParamSetManager.java | 11 +- src/jalview/gui/WsPreferences.java | 28 +- src/jalview/httpserver/HttpServer.java | 6 +- src/jalview/io/AMSAFile.java | 3 +- src/jalview/io/AlignFile.java | 41 +- src/jalview/io/AlignmentProperties.java | 6 +- src/jalview/io/AnnotationFile.java | 29 +- src/jalview/io/AppletFormatAdapter.java | 60 +- src/jalview/io/BLCFile.java | 2 +- src/jalview/io/BioJsHTMLOutput.java | 18 +- src/jalview/io/ClustalFile.java | 14 +- src/jalview/io/FastaFile.java | 8 +- src/jalview/io/FeaturesFile.java | 58 +- src/jalview/io/FileLoader.java | 8 +- src/jalview/io/FileParse.java | 40 +- src/jalview/io/FormatAdapter.java | 14 +- src/jalview/io/Gff3File.java | 4 +- src/jalview/io/HTMLOutput.java | 22 +- src/jalview/io/HtmlFile.java | 4 +- src/jalview/io/HtmlSvgOutput.java | 55 +- src/jalview/io/IdentifyFile.java | 9 +- src/jalview/io/JPredFile.java | 25 +- src/jalview/io/JalviewFileChooser.java | 6 +- src/jalview/io/JalviewFileFilter.java | 6 +- src/jalview/io/JalviewFileView.java | 9 +- src/jalview/io/JnetAnnotationMaker.java | 3 +- src/jalview/io/ModellerDescription.java | 19 +- src/jalview/io/NewickFile.java | 18 +- src/jalview/io/PIRFile.java | 7 +- src/jalview/io/PfamFile.java | 15 +- src/jalview/io/PhylipFile.java | 4 +- src/jalview/io/PileUpfile.java | 6 +- src/jalview/io/RnamlFile.java | 18 +- src/jalview/io/SequenceAnnotationReport.java | 32 +- src/jalview/io/SimpleBlastFile.java | 14 +- src/jalview/io/StockholmFile.java | 27 +- src/jalview/io/TCoffeeScoreFile.java | 3 +- src/jalview/io/VamsasAppDatastore.java | 44 +- src/jalview/io/WSWUBlastClient.java | 35 +- src/jalview/io/vamsas/Datasetsequence.java | 1 + src/jalview/io/vamsas/DatastoreItem.java | 43 +- src/jalview/io/vamsas/DatastoreRegistry.java | 3 +- src/jalview/io/vamsas/Dbref.java | 3 +- src/jalview/io/vamsas/Rangetype.java | 19 +- src/jalview/io/vamsas/Sequencefeature.java | 6 +- src/jalview/io/vamsas/Sequencemapping.java | 3 +- src/jalview/io/vamsas/Tree.java | 19 +- src/jalview/javascript/JSFunctionExec.java | 3 +- src/jalview/javascript/JsSelectionSender.java | 12 +- src/jalview/javascript/MouseOverListener.java | 6 +- .../javascript/MouseOverStructureListener.java | 11 +- src/jalview/jbgui/GAlignExportSettings.java | 5 +- src/jalview/jbgui/GAlignFrame.java | 15 +- src/jalview/jbgui/GAlignmentPanel.java | 13 +- src/jalview/jbgui/GCutAndPasteHtmlTransfer.java | 20 +- src/jalview/jbgui/GCutAndPasteTransfer.java | 18 +- src/jalview/jbgui/GDasSourceBrowser.java | 29 +- src/jalview/jbgui/GDesktop.java | 9 +- src/jalview/jbgui/GFinder.java | 1 - src/jalview/jbgui/GFontChooser.java | 9 +- src/jalview/jbgui/GPDBSearchPanel.java | 29 +- src/jalview/jbgui/GPairwiseAlignPanel.java | 10 +- src/jalview/jbgui/GPreferences.java | 37 +- src/jalview/jbgui/GRestInputParamEditDialog.java | 15 +- src/jalview/jbgui/GRestServiceEditorPane.java | 18 +- src/jalview/jbgui/GRnaStructureViewer.java | 2 +- src/jalview/jbgui/GSequenceLink.java | 27 +- src/jalview/jbgui/GSliderPanel.java | 19 +- src/jalview/jbgui/GSplitFrame.java | 6 +- src/jalview/jbgui/GStructureChooser.java | 20 +- src/jalview/jbgui/GStructureViewer.java | 9 +- src/jalview/jbgui/GUserDefinedColours.java | 45 +- src/jalview/jbgui/GWebserviceInfo.java | 18 +- src/jalview/jbgui/PDBDocFieldPreferences.java | 25 +- .../json/binding/biojs/BioJSRepositoryPojo.java | 4 +- .../biojson/v1/AlignmentAnnotationPojo.java | 10 +- .../json/binding/biojson/v1/AlignmentPojo.java | 22 +- .../json/binding/biojson/v1/AnnotationPojo.java | 14 +- .../binding/biojson/v1/SequenceFeaturesPojo.java | 22 +- .../json/binding/biojson/v1/SequenceGrpPojo.java | 35 +- .../json/binding/biojson/v1/SequencePojo.java | 28 +- src/jalview/math/Matrix.java | 13 +- src/jalview/renderer/AnnotationRenderer.java | 58 +- .../renderer/seqfeatures/FeatureRenderer.java | 6 +- src/jalview/rest/RestHandler.java | 4 +- src/jalview/schemabinding/version2/AlcodMap.java | 332 +- src/jalview/schemabinding/version2/Alcodon.java | 484 +- .../schemabinding/version2/AlcodonFrame.java | 828 +-- src/jalview/schemabinding/version2/Annotation.java | 2701 +++++----- .../version2/AnnotationColourScheme.java | 934 ++-- .../schemabinding/version2/AnnotationColours.java | 183 +- .../schemabinding/version2/AnnotationElement.java | 652 +-- .../schemabinding/version2/CalcIdParam.java | 546 +- src/jalview/schemabinding/version2/Colour.java | 940 ++-- src/jalview/schemabinding/version2/DBRef.java | 408 +- src/jalview/schemabinding/version2/Feature.java | 1025 ++-- .../schemabinding/version2/FeatureSettings.java | 824 +-- src/jalview/schemabinding/version2/Features.java | 178 +- src/jalview/schemabinding/version2/Group.java | 369 +- .../schemabinding/version2/HiddenColumns.java | 399 +- src/jalview/schemabinding/version2/JGroup.java | 2460 ++++----- src/jalview/schemabinding/version2/JSeq.java | 1972 +++---- .../schemabinding/version2/JalviewModel.java | 412 +- .../version2/JalviewModelSequence.java | 1869 +++---- .../schemabinding/version2/JalviewUserColours.java | 621 +-- .../schemabinding/version2/MapListFrom.java | 399 +- src/jalview/schemabinding/version2/MapListTo.java | 399 +- .../schemabinding/version2/MapListType.java | 1135 ++-- src/jalview/schemabinding/version2/Mapping.java | 290 +- .../schemabinding/version2/MappingChoice.java | 308 +- src/jalview/schemabinding/version2/OtherData.java | 307 +- src/jalview/schemabinding/version2/Pdbentry.java | 671 +-- .../schemabinding/version2/PdbentryItem.java | 352 +- src/jalview/schemabinding/version2/Pdbids.java | 481 +- src/jalview/schemabinding/version2/Property.java | 307 +- src/jalview/schemabinding/version2/RnaViewer.java | 1271 ++--- .../schemabinding/version2/SecondaryStructure.java | 534 +- src/jalview/schemabinding/version2/Sequence.java | 579 ++- .../schemabinding/version2/SequenceSet.java | 1637 +++--- .../version2/SequenceSetProperties.java | 309 +- .../schemabinding/version2/SequenceType.java | 409 +- src/jalview/schemabinding/version2/Setting.java | 1335 ++--- .../schemabinding/version2/StructureState.java | 1771 +++---- .../schemabinding/version2/ThresholdLine.java | 452 +- src/jalview/schemabinding/version2/Tree.java | 1695 +++--- .../schemabinding/version2/UserColourScheme.java | 182 +- .../schemabinding/version2/UserColours.java | 308 +- src/jalview/schemabinding/version2/VAMSAS.java | 813 +-- .../schemabinding/version2/VamsasModel.java | 178 +- src/jalview/schemabinding/version2/Viewport.java | 5427 ++++++++++---------- .../version2/WebServiceParameterSet.java | 819 ++- .../version2/descriptors/AlcodMapDescriptor.java | 431 +- .../version2/descriptors/AlcodonDescriptor.java | 523 +- .../descriptors/AlcodonFrameDescriptor.java | 443 +- .../AnnotationColourSchemeDescriptor.java | 974 ++-- .../descriptors/AnnotationColoursDescriptor.java | 261 +- .../version2/descriptors/AnnotationDescriptor.java | 2220 ++++---- .../descriptors/AnnotationElementDescriptor.java | 789 +-- .../descriptors/CalcIdParamDescriptor.java | 520 +- .../version2/descriptors/ColourDescriptor.java | 1042 ++-- .../version2/descriptors/DBRefDescriptor.java | 567 +- .../version2/descriptors/FeatureDescriptor.java | 963 ++-- .../descriptors/FeatureSettingsDescriptor.java | 443 +- .../version2/descriptors/FeaturesDescriptor.java | 260 +- .../version2/descriptors/GroupDescriptor.java | 426 +- .../descriptors/HiddenColumnsDescriptor.java | 439 +- .../version2/descriptors/JGroupDescriptor.java | 2177 ++++---- .../version2/descriptors/JSeqDescriptor.java | 1116 ++-- .../descriptors/JalviewModelDescriptor.java | 581 ++- .../JalviewModelSequenceDescriptor.java | 796 +-- .../descriptors/JalviewUserColoursDescriptor.java | 506 +- .../descriptors/MapListFromDescriptor.java | 441 +- .../version2/descriptors/MapListToDescriptor.java | 441 +- .../descriptors/MapListTypeDescriptor.java | 635 +-- .../descriptors/MappingChoiceDescriptor.java | 423 +- .../version2/descriptors/MappingDescriptor.java | 354 +- .../version2/descriptors/OtherDataDescriptor.java | 431 +- .../version2/descriptors/PdbentryDescriptor.java | 588 ++- .../descriptors/PdbentryItemDescriptor.java | 370 +- .../version2/descriptors/PdbidsDescriptor.java | 373 +- .../version2/descriptors/PropertyDescriptor.java | 431 +- .../version2/descriptors/RnaViewerDescriptor.java | 1083 ++-- .../descriptors/SecondaryStructureDescriptor.java | 584 ++- .../version2/descriptors/SequenceDescriptor.java | 432 +- .../descriptors/SequenceSetDescriptor.java | 798 +-- .../SequenceSetPropertiesDescriptor.java | 423 +- .../descriptors/SequenceTypeDescriptor.java | 577 ++- .../version2/descriptors/SettingDescriptor.java | 1279 ++--- .../descriptors/StructureStateDescriptor.java | 1238 +++-- .../descriptors/ThresholdLineDescriptor.java | 519 +- .../version2/descriptors/TreeDescriptor.java | 1702 +++--- .../descriptors/UserColourSchemeDescriptor.java | 261 +- .../descriptors/UserColoursDescriptor.java | 428 +- .../version2/descriptors/VAMSASDescriptor.java | 454 +- .../descriptors/VamsasModelDescriptor.java | 260 +- .../version2/descriptors/ViewportDescriptor.java | 4756 +++++++++-------- .../WebServiceParameterSetDescriptor.java | 676 +-- src/jalview/schemes/AnnotationColourGradient.java | 10 +- src/jalview/schemes/BuriedColourScheme.java | 2 +- src/jalview/schemes/ColourSchemeI.java | 8 +- src/jalview/schemes/CovariationColourScheme.java | 6 +- src/jalview/schemes/HelixColourScheme.java | 2 +- src/jalview/schemes/HydrophobicColourScheme.java | 2 +- .../schemes/PurinePyrimidineColourScheme.java | 2 +- src/jalview/schemes/RNAHelicesColour.java | 1 - src/jalview/schemes/ResidueColourScheme.java | 4 +- src/jalview/schemes/ResidueProperties.java | 118 +- src/jalview/schemes/StrandColourScheme.java | 2 +- src/jalview/schemes/TCoffeeColourScheme.java | 5 +- src/jalview/schemes/TurnColourScheme.java | 2 +- src/jalview/schemes/UserColourScheme.java | 8 +- src/jalview/structure/SequenceListener.java | 1 - src/jalview/structure/StructureListener.java | 4 +- .../structure/StructureSelectionManager.java | 5 +- .../structures/models/AAStructureBindingModel.java | 30 +- src/jalview/util/AWTConsole.java | 23 +- src/jalview/util/BrowserLauncher.java | 155 +- src/jalview/util/Comparison.java | 16 +- src/jalview/util/DBRefUtils.java | 14 +- src/jalview/util/GroupUrlLink.java | 44 +- src/jalview/util/ImageMaker.java | 33 +- src/jalview/util/MapList.java | 66 +- src/jalview/util/MappingUtils.java | 31 +- src/jalview/util/ParseHtmlBodyAndLinks.java | 3 +- src/jalview/util/QuickSort.java | 11 +- src/jalview/util/ReverseListIterator.java | 1 + src/jalview/util/ShiftList.java | 6 +- src/jalview/util/StringUtils.java | 18 +- src/jalview/util/TableSorter.java | 30 +- src/jalview/util/UrlLink.java | 15 +- src/jalview/viewmodel/AlignmentViewport.java | 68 +- src/jalview/viewmodel/PCAModel.java | 6 +- .../AnnotationFilterParameter.java | 1 + .../seqfeatures/FeatureRendererModel.java | 21 +- .../seqfeatures/FeatureRendererSettings.java | 2 +- src/jalview/viewmodel/styles/ViewStyle.java | 9 +- src/jalview/workers/AlignCalcWorker.java | 4 +- src/jalview/workers/ComplementConsensusThread.java | 6 +- src/jalview/workers/ConsensusThread.java | 7 +- src/jalview/ws/AWSThread.java | 7 +- src/jalview/ws/DBRefFetcher.java | 21 +- src/jalview/ws/DasSequenceFeatureFetcher.java | 30 +- src/jalview/ws/HttpClientUtils.java | 3 +- src/jalview/ws/SequenceFetcher.java | 24 +- src/jalview/ws/WSClient.java | 2 +- .../ws/dbsources/EbiFileRetrievedProxy.java | 4 +- src/jalview/ws/dbsources/EmblCdsSouce.java | 4 +- src/jalview/ws/dbsources/EmblSource.java | 4 +- src/jalview/ws/dbsources/EmblXmlSource.java | 15 +- src/jalview/ws/dbsources/GeneDbSource.java | 4 +- src/jalview/ws/dbsources/PDBRestClient.java | 1 - src/jalview/ws/dbsources/Pdb.java | 8 +- src/jalview/ws/dbsources/Pfam.java | 4 +- src/jalview/ws/dbsources/Rfam.java | 4 +- src/jalview/ws/dbsources/Uniprot.java | 3 +- .../ws/dbsources/das/api/jalviewSourceI.java | 4 +- .../dbsources/das/datamodel/DasSequenceSource.java | 28 +- .../ws/dbsources/das/datamodel/JalviewSource.java | 12 +- src/jalview/ws/ebi/EBIFetchClient.java | 4 +- src/jalview/ws/io/mime/MimeTypes.java | 4 +- src/jalview/ws/jws1/Annotate3D.java | 5 +- src/jalview/ws/jws1/Discoverer.java | 23 +- src/jalview/ws/jws1/JPredClient.java | 29 +- src/jalview/ws/jws1/JPredThread.java | 61 +- src/jalview/ws/jws1/JWS1Thread.java | 5 +- src/jalview/ws/jws1/MsaWSClient.java | 38 +- src/jalview/ws/jws1/MsaWSThread.java | 50 +- src/jalview/ws/jws1/SeqSearchWSClient.java | 42 +- src/jalview/ws/jws1/SeqSearchWSThread.java | 51 +- src/jalview/ws/jws1/WS1Client.java | 4 +- src/jalview/ws/jws2/AADisorderClient.java | 72 +- src/jalview/ws/jws2/AbstractJabaCalcWorker.java | 10 +- src/jalview/ws/jws2/JPred301Client.java | 8 +- src/jalview/ws/jws2/JWs2Job.java | 4 +- src/jalview/ws/jws2/JabaParamStore.java | 58 +- src/jalview/ws/jws2/JabaPreset.java | 15 +- src/jalview/ws/jws2/JabaWsServerQuery.java | 27 +- src/jalview/ws/jws2/JabawsCalcWorker.java | 5 +- .../ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java | 34 +- src/jalview/ws/jws2/Jws2Client.java | 19 +- src/jalview/ws/jws2/Jws2Discoverer.java | 34 +- src/jalview/ws/jws2/MsaWSClient.java | 50 +- src/jalview/ws/jws2/MsaWSThread.java | 54 +- src/jalview/ws/jws2/ParameterUtils.java | 17 +- src/jalview/ws/jws2/RNAalifoldClient.java | 3 +- .../ws/jws2/SequenceAnnotationWSClient.java | 40 +- src/jalview/ws/jws2/dm/AAConSettings.java | 19 +- src/jalview/ws/jws2/dm/JabaOption.java | 4 +- src/jalview/ws/jws2/dm/JabaParameter.java | 1 + src/jalview/ws/jws2/dm/JabaValueConstrain.java | 10 +- src/jalview/ws/jws2/dm/JabaWsParamSet.java | 18 +- src/jalview/ws/jws2/jabaws2/Jws2Instance.java | 4 +- .../ws/jws2/jabaws2/Jws2InstanceFactory.java | 2 + src/jalview/ws/params/simple/BooleanOption.java | 7 +- src/jalview/ws/rest/HttpResultSet.java | 6 +- src/jalview/ws/rest/InputType.java | 3 +- src/jalview/ws/rest/RestClient.java | 67 +- src/jalview/ws/rest/RestJob.java | 14 +- src/jalview/ws/rest/RestJobThread.java | 13 +- src/jalview/ws/rest/RestServiceDescription.java | 33 +- src/jalview/ws/rest/params/Alignment.java | 3 +- src/jalview/ws/rest/params/AnnotationFile.java | 13 +- src/jalview/ws/rest/params/JobConstant.java | 3 +- .../ws/rest/params/SeqGroupIndexVector.java | 26 +- src/jalview/ws/rest/params/SeqIdVector.java | 7 +- src/jalview/ws/rest/params/SeqVector.java | 7 +- src/jalview/ws/rest/params/Tree.java | 7 +- src/jalview/ws/seqfetcher/ASequenceFetcher.java | 23 +- src/jalview/ws/uimodel/AlignAnalysisUIText.java | 1 - src/jalview/ws/uimodel/PDBRestRequest.java | 1 - src/jalview/ws/uimodel/PDBRestResponse.java | 7 +- src/org/jibble/epsgraphics/EpsDocument.java | 13 +- src/org/jibble/epsgraphics/EpsGraphics2D.java | 73 +- src/uk/ac/ebi/www/WSWUBlastServiceLocator.java | 5 +- src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java | 26 +- .../AccessionMapperBindingStub.java | 14 +- .../AccessionMapperServiceLocator.java | 10 +- src/vamsas/IMsaWS.java | 5 +- 570 files changed, 56516 insertions(+), 51586 deletions(-) diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java index dc69f43..7f87326 100644 --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -20,6 +20,18 @@ */ package MCview; +import jalview.analysis.AlignSeq; +import jalview.appletgui.AlignmentPanel; +import jalview.appletgui.FeatureRenderer; +import jalview.appletgui.SequenceRenderer; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.structure.AtomSpec; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + import java.awt.Color; import java.awt.Dimension; import java.awt.Event; @@ -37,18 +49,6 @@ import java.io.PrintStream; import java.util.List; import java.util.Vector; -import jalview.analysis.AlignSeq; -import jalview.appletgui.AlignmentPanel; -import jalview.appletgui.FeatureRenderer; -import jalview.appletgui.SequenceRenderer; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.structure.AtomSpec; -import jalview.structure.StructureListener; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; - public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotionListener, StructureListener { @@ -189,11 +189,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { mappingDetails.append("\n\nPDB Sequence is :\nSequence = " - + pdb.chains.elementAt(i).sequence - .getSequenceAsString()); + + pdb.chains.elementAt(i).sequence.getSequenceAsString()); mappingDetails.append("\nNo of residues = " - + pdb.chains.elementAt(i).residues.size() - + "\n\n"); + + pdb.chains.elementAt(i).residues.size() + "\n\n"); // Now lets compare the sequences to get // the start and end points. @@ -201,8 +199,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, // TODO: DNa/Pep switch AlignSeq as = new AlignSeq(sequence, pdb.chains.elementAt(i).sequence, - pdb.chains.elementAt(i).isNa ? AlignSeq.DNA - : AlignSeq.PEP); + pdb.chains.elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP); as.calcScoreMatrix(); as.traceAlignment(); PrintStream ps = new PrintStream(System.out) @@ -1113,8 +1110,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, // /StructureListener public String[] getPdbFile() { - return new String[] - { pdbentry.getFile() }; + return new String[] { pdbentry.getFile() }; } String lastMessage; diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java index ed13578..8233ac3 100644 --- a/src/MCview/AppletPDBViewer.java +++ b/src/MCview/AppletPDBViewer.java @@ -20,14 +20,31 @@ */ package MCview; -import java.awt.*; -import java.awt.event.*; - -import jalview.appletgui.*; -import jalview.datamodel.*; -import jalview.schemes.*; +import jalview.appletgui.AlignmentPanel; +import jalview.appletgui.EmbmenuFrame; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.ZappoColourScheme; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.CheckboxGroup; +import java.awt.CheckboxMenuItem; +import java.awt.Frame; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; + public class AppletPDBViewer extends EmbmenuFrame implements ActionListener, ItemListener { diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java index 1f2edd2..371ccd5 100755 --- a/src/MCview/Bond.java +++ b/src/MCview/Bond.java @@ -38,10 +38,8 @@ public class Bond public Bond(Atom at1, Atom at2) { - this.start = new float[] - { at1.x, at1.y, at1.z }; - this.end = new float[] - { at2.x, at2.y, at2.z }; + this.start = new float[] { at1.x, at1.y, at1.z }; + this.end = new float[] { at2.x, at2.y, at2.z }; this.startCol = at1.color; this.endCol = at2.color; this.at1 = at1; diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java index 406d9f1..ac1ba06 100644 --- a/src/MCview/PDBCanvas.java +++ b/src/MCview/PDBCanvas.java @@ -20,6 +20,17 @@ */ package MCview; +import jalview.analysis.AlignSeq; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignmentPanel; +import jalview.gui.FeatureRenderer; +import jalview.gui.SequenceRenderer; +import jalview.structure.AtomSpec; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; + import java.awt.Color; import java.awt.Dimension; import java.awt.Event; @@ -41,17 +52,6 @@ import java.util.Vector; import javax.swing.JPanel; import javax.swing.ToolTipManager; -import jalview.analysis.AlignSeq; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.gui.AlignmentPanel; -import jalview.gui.FeatureRenderer; -import jalview.gui.SequenceRenderer; -import jalview.structure.AtomSpec; -import jalview.structure.StructureListener; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; - public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListener, StructureListener { @@ -188,11 +188,9 @@ public class PDBCanvas extends JPanel implements MouseListener, { mappingDetails.append("\n\nPDB Sequence is :\nSequence = " - + pdb.chains.elementAt(i).sequence - .getSequenceAsString()); + + pdb.chains.elementAt(i).sequence.getSequenceAsString()); mappingDetails.append("\nNo of residues = " - + pdb.chains.elementAt(i).residues.size() - + "\n\n"); + + pdb.chains.elementAt(i).residues.size() + "\n\n"); // Now lets compare the sequences to get // the start and end points. @@ -1069,8 +1067,7 @@ public class PDBCanvas extends JPanel implements MouseListener, // /StructureListener public String[] getPdbFile() { - return new String[] - { pdbentry.getFile() }; + return new String[] { pdbentry.getFile() }; } String lastMessage; diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 0e486ac..6d5f9fe 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -20,10 +20,6 @@ */ package MCview; -import java.awt.Color; -import java.util.List; -import java.util.Vector; - import jalview.analysis.AlignSeq; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; @@ -35,6 +31,10 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.StructureMapping; +import java.awt.Color; +import java.util.List; +import java.util.Vector; + public class PDBChain { /** @@ -193,10 +193,10 @@ public class PDBChain if (features[i].getFeatureGroup().equals(pdbid)) { SequenceFeature tx = new SequenceFeature(features[i]); - tx.setBegin(1 + residues.elementAt(tx.getBegin() - - offset).atoms.elementAt(0).alignmentMapping); - tx.setEnd(1 + residues.elementAt(tx.getEnd() - - offset).atoms.elementAt(0).alignmentMapping); + tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms + .elementAt(0).alignmentMapping); + tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms + .elementAt(0).alignmentMapping); tx.setStatus(status + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? "" : ":" + tx.getStatus())); @@ -409,8 +409,7 @@ public class PDBChain AlignmentAnnotation tfactorann = new AlignmentAnnotation( "Temperature Factor", "Temperature Factor for " + pdbid + id, - annots, 0, max, - AlignmentAnnotation.LINE_GRAPH); + annots, 0, max, AlignmentAnnotation.LINE_GRAPH); tfactorann.setSequenceRef(sequence); sequence.addAlignmentAnnotation(tfactorann); } @@ -474,12 +473,10 @@ public class PDBChain { try { - index = ResidueProperties.aa3Hash.get(b.at1.resName) - .intValue(); + index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue(); b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); - index = ResidueProperties.aa3Hash.get(b.at2.resName) - .intValue(); + index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue(); b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); } catch (Exception e) @@ -508,8 +505,8 @@ public class PDBChain * @param sqmpping * - mapping between destination sequence and local chain */ - public void transferResidueAnnotation( - StructureMapping mapping, jalview.datamodel.Mapping sqmpping) + public void transferResidueAnnotation(StructureMapping mapping, + jalview.datamodel.Mapping sqmpping) { SequenceI sq = mapping.getSequence(); SequenceI dsq = sq; diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index 12367b2..e1324d2 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.java @@ -329,7 +329,8 @@ public class PDBViewer extends JInternalFrame implements Runnable } }); viewMenu.setText(MessageManager.getString("action.view")); - background.setText(MessageManager.getString("action.background_colour")); + background + .setText(MessageManager.getString("action.background_colour")); background.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -523,15 +524,14 @@ public class PDBViewer extends JInternalFrame implements Runnable if (type == jalview.util.ImageMaker.TYPE.PNG) { im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.PNG, - "Make PNG image from view", width, height, null, null); + jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", + width, height, null, null); } else if (type == jalview.util.ImageMaker.TYPE.EPS) { im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.EPS, - "Make EPS file from view", width, height, null, - this.getTitle()); + jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view", + width, height, null, this.getTitle()); } else { diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 58991f3..c1018a3 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -63,8 +63,8 @@ public class PDBfile extends jalview.io.AlignFile */ private boolean externalSecondaryStructure = false; - public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure, - boolean externalSecStr) + public PDBfile(boolean addAlignmentAnnotations, + boolean predictSecondaryStructure, boolean externalSecStr) { super(); this.visibleChainAnnotation = addAlignmentAnnotations; @@ -72,9 +72,9 @@ public class PDBfile extends jalview.io.AlignFile this.externalSecondaryStructure = externalSecStr; } - public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure, - boolean externalSecStr, String file, String protocol) - throws IOException + public PDBfile(boolean addAlignmentAnnotations, + boolean predictSecondaryStructure, boolean externalSecStr, + String file, String protocol) throws IOException { super(false, file, protocol); this.visibleChainAnnotation = addAlignmentAnnotations; @@ -83,8 +83,9 @@ public class PDBfile extends jalview.io.AlignFile doParse(); } - public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure, - boolean externalSecStr, FileParse source) throws IOException + public PDBfile(boolean addAlignmentAnnotations, + boolean predictSecondaryStructure, boolean externalSecStr, + FileParse source) throws IOException { super(false, source); this.visibleChainAnnotation = addAlignmentAnnotations; @@ -252,8 +253,7 @@ public class PDBfile extends jalview.io.AlignFile processPdbFileWithAnnotate3d(rnaSequences); } catch (Exception x) { - System.err - .println("Exceptions when dealing with RNA in pdb file"); + System.err.println("Exceptions when dealing with RNA in pdb file"); x.printStackTrace(); } @@ -339,7 +339,8 @@ public class PDBfile extends jalview.io.AlignFile public static String relocateCalcId(String calcId, Hashtable alreadyLoadedPDB) throws Exception { - int s = CALC_ID_PREFIX.length(), end = calcId.indexOf(CALC_ID_PREFIX, s); + int s = CALC_ID_PREFIX.length(), end = calcId + .indexOf(CALC_ID_PREFIX, s); String between = calcId.substring(s, end - 1); return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":" + calcId.substring(end); @@ -374,16 +375,15 @@ public class PDBfile extends jalview.io.AlignFile Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol"); if (cl != null) { - final Constructor constructor = cl.getConstructor(new Class[] - { FileParse.class }); - final Object[] args = new Object[] - { new FileParse(getDataName(), type) }; + final Constructor constructor = cl + .getConstructor(new Class[] { FileParse.class }); + final Object[] args = new Object[] { new FileParse(getDataName(), + type) }; Object jmf = constructor.newInstance(args); AlignmentI al = new Alignment((SequenceI[]) cl.getMethod( - "getSeqsAsArray", new Class[] - {}).invoke(jmf)); - cl.getMethod("addAnnotations", new Class[] - { AlignmentI.class }).invoke(jmf, al); + "getSeqsAsArray", new Class[] {}).invoke(jmf)); + cl.getMethod("addAnnotations", new Class[] { AlignmentI.class }) + .invoke(jmf, al); for (SequenceI sq : al.getSequences()) { if (sq.getDatasetSequence() != null) @@ -402,8 +402,8 @@ public class PDBfile extends jalview.io.AlignFile } } - private void replaceAndUpdateChains(List prot, - AlignmentI al, String pep, boolean b) + private void replaceAndUpdateChains(List prot, AlignmentI al, + String pep, boolean b) { List> replaced = AlignSeq .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep, @@ -445,13 +445,11 @@ public class PDBfile extends jalview.io.AlignFile { // TODO: use the PDB ID of the structure if one is available, to save // bandwidth and avoid uploading the whole structure to the service - Object annotate3d = cl.getConstructor(new Class[] - {}).newInstance(new Object[] - {}); + Object annotate3d = cl.getConstructor(new Class[] {}).newInstance( + new Object[] {}); AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", - new Class[] - { FileParse.class }).invoke(annotate3d, new Object[] - { new FileParse(getDataName(), type) })); + new Class[] { FileParse.class }).invoke(annotate3d, + new Object[] { new FileParse(getDataName(), type) })); for (SequenceI sq : al.getSequences()) { if (sq.getDatasetSequence() != null) diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java index 20f034c..6bdbafa 100755 --- a/src/MCview/Zsort.java +++ b/src/MCview/Zsort.java @@ -63,8 +63,7 @@ public class Zsort do { i++; - } while ((i < bonds.size()) - && (bonds.elementAt(i).start[2] < x)); + } while ((i < bonds.size()) && (bonds.elementAt(i).start[2] < x)); if (i < j) { diff --git a/src/com/github/reinert/jjschema/Attributes.java b/src/com/github/reinert/jjschema/Attributes.java index f6a3d47..c3bd6c4 100755 --- a/src/com/github/reinert/jjschema/Attributes.java +++ b/src/com/github/reinert/jjschema/Attributes.java @@ -29,39 +29,40 @@ import java.lang.annotation.Target; * @author reinert */ @Retention(RetentionPolicy.RUNTIME) -@Target({ElementType.METHOD, ElementType.FIELD, ElementType.TYPE}) -public @interface Attributes { - String $ref() default ""; +@Target({ ElementType.METHOD, ElementType.FIELD, ElementType.TYPE }) +public @interface Attributes +{ + String $ref() default ""; - String id() default ""; + String id() default ""; - String title() default ""; + String title() default ""; - String description() default ""; + String description() default ""; - long maximum() default -1l; + long maximum() default -1l; - boolean exclusiveMaximum() default false; + boolean exclusiveMaximum() default false; - int minimum() default -1; + int minimum() default -1; - boolean exclusiveMinimum() default false; + boolean exclusiveMinimum() default false; - String pattern() default ""; + String pattern() default ""; - boolean required() default false; + boolean required() default false; - String[] enums() default {}; + String[] enums() default {}; - int minItems() default 0; + int minItems() default 0; - long maxItems() default -1l; + long maxItems() default -1l; - boolean uniqueItems() default false; + boolean uniqueItems() default false; - int multipleOf() default 0; + int multipleOf() default 0; - int minLength() default 0; + int minLength() default 0; - long maxLength() default -1l; + long maxLength() default -1l; } diff --git a/src/com/stevesoft/pat/Any.java b/src/com/stevesoft/pat/Any.java index c97599c..dbaa961 100755 --- a/src/com/stevesoft/pat/Any.java +++ b/src/com/stevesoft/pat/Any.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * This is the '.' character in a Pattern. It matches any character. diff --git a/src/com/stevesoft/pat/BackG.java b/src/com/stevesoft/pat/BackG.java index 69f7f61..166b58c 100755 --- a/src/com/stevesoft/pat/BackG.java +++ b/src/com/stevesoft/pat/BackG.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** This class represents the \G pattern element. */ class BackG extends Pattern diff --git a/src/com/stevesoft/pat/BackMatch.java b/src/com/stevesoft/pat/BackMatch.java index 1b166e9..1d7499e 100755 --- a/src/com/stevesoft/pat/BackMatch.java +++ b/src/com/stevesoft/pat/BackMatch.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * Provides the ability to match a backreference from within a Pattern. diff --git a/src/com/stevesoft/pat/Backup.java b/src/com/stevesoft/pat/Backup.java index 1986460..6602aca 100755 --- a/src/com/stevesoft/pat/Backup.java +++ b/src/com/stevesoft/pat/Backup.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * Implements the (?<number) Pattern, where number is an integer telling us diff --git a/src/com/stevesoft/pat/Bits.java b/src/com/stevesoft/pat/Bits.java index 05b3d34..b47f794 100755 --- a/src/com/stevesoft/pat/Bits.java +++ b/src/com/stevesoft/pat/Bits.java @@ -60,8 +60,8 @@ public class Bits * StringWriter(); static PrintWriter pw_s = new PrintWriter(sw,true); public * static void test(String var,Tester t) throws Exception { * - * char[] ca = new char[(66536 >> 4)+1]; Bits b = new Bits(ca); FileWriter fw = - * new FileWriter("x.out",true); PrintWriter pw = new PrintWriter(fw); + * char[] ca = new char[(66536 >> 4)+1]; Bits b = new Bits(ca); FileWriter fw + * = new FileWriter("x.out",true); PrintWriter pw = new PrintWriter(fw); * * //pw_s.println(" "+var+"_f();"); pw.println(" public static Bits * "+var+";"); pw.println(" static void "+var+"_f() {"); pw.println(" char[] diff --git a/src/com/stevesoft/pat/Boundary.java b/src/com/stevesoft/pat/Boundary.java index 566b20e..af79f66 100755 --- a/src/com/stevesoft/pat/Boundary.java +++ b/src/com/stevesoft/pat/Boundary.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** This class implements the word boundary pattern element: \b. */ class Boundary extends Pattern diff --git a/src/com/stevesoft/pat/Bracket.java b/src/com/stevesoft/pat/Bracket.java index cec8af4..adbcded 100755 --- a/src/com/stevesoft/pat/Bracket.java +++ b/src/com/stevesoft/pat/Bracket.java @@ -7,7 +7,8 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; +import java.util.Vector; /** * The Bracket is a form of the Or class, implements the pattern element [ ]. diff --git a/src/com/stevesoft/pat/Ctrl.java b/src/com/stevesoft/pat/Ctrl.java index 5d40098..07b9d6d 100755 --- a/src/com/stevesoft/pat/Ctrl.java +++ b/src/com/stevesoft/pat/Ctrl.java @@ -9,53 +9,52 @@ 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 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 61879ac..3251fa3 100755 --- a/src/com/stevesoft/pat/Custom.java +++ b/src/com/stevesoft/pat/Custom.java @@ -7,13 +7,13 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * Simple custom patterns. See deriv2.java and deriv3.java in the - * test directory. + * href="http://javaregex.com/code/deriv3.java.html">deriv3.java in the test + * directory. * * @see com.stevesoft.pat.CustomEndpoint */ diff --git a/src/com/stevesoft/pat/CustomEndpoint.java b/src/com/stevesoft/pat/CustomEndpoint.java index 9608f7e..bf122b7 100755 --- a/src/com/stevesoft/pat/CustomEndpoint.java +++ b/src/com/stevesoft/pat/CustomEndpoint.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * This class is needed internally to make backtracking work correctly in diff --git a/src/com/stevesoft/pat/DotMulti.java b/src/com/stevesoft/pat/DotMulti.java index cc5f094..7fd055b 100755 --- a/src/com/stevesoft/pat/DotMulti.java +++ b/src/com/stevesoft/pat/DotMulti.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * A special optimization of multi that is used when the common subpattern ".*" diff --git a/src/com/stevesoft/pat/End.java b/src/com/stevesoft/pat/End.java index 547f3d6..06aadda 100755 --- a/src/com/stevesoft/pat/End.java +++ b/src/com/stevesoft/pat/End.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; //class AddToEnd extends RegSyntax {}; diff --git a/src/com/stevesoft/pat/FastBracket.java b/src/com/stevesoft/pat/FastBracket.java index a10ec2b..af1bc37 100755 --- a/src/com/stevesoft/pat/FastBracket.java +++ b/src/com/stevesoft/pat/FastBracket.java @@ -7,7 +7,8 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.BitSet; +import java.util.Vector; /** * Uses table lookup to match [] type constructs, but only if it can use a diff --git a/src/com/stevesoft/pat/FastMulti.java b/src/com/stevesoft/pat/FastMulti.java index a8387b4..cad69ee 100755 --- a/src/com/stevesoft/pat/FastMulti.java +++ b/src/com/stevesoft/pat/FastMulti.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * A special case of Multi, implemented when minChars().equals(maxChars()), and diff --git a/src/com/stevesoft/pat/FileRegex.java b/src/com/stevesoft/pat/FileRegex.java index 342d41c..fa57795 100755 --- a/src/com/stevesoft/pat/FileRegex.java +++ b/src/com/stevesoft/pat/FileRegex.java @@ -7,61 +7,65 @@ // package com.stevesoft.pat; -import java.io.*; -import java.util.*; +import java.io.File; +import java.util.StringTokenizer; +import java.util.Vector; /** * This class is a different form of Regex designed to work more like the file * matching utility of a Unix shell. It is implemented by some simple string - * transformations:
+ * transformations:
+ *
* - * - * + * + * * - * - * + * + * * - * - * + * + * * - * - * + * + * * - * - * + * + * * - * - * + * + * * - * - * + * + * * - * - * + * + * * - * - * + * + * * - * - * - *
FileRegex Regex FileRegexRegex
* .* *.*
. \. .\.
{ (?: {(?:
{?! (?! {?!(?!
{?= (?= {?=(?=
{?? (?? {??(??
} ) )
? . ?.
{,} (|)
Note that a FileRegex pattern always ends with the Regex - * pattern element "$". If you like to experiment, try making FileRegex's and - * then printing them out. The toString() method does a decompile of the pattern - * to a standard Regex. Here are some more complete examples:
+ * + * + *
{,}(|)
+ *
Note that a FileRegex pattern always ends with the Regex pattern + * element "$". If you like to experiment, try making FileRegex's and then + * printing them out. The toString() method does a decompile of the pattern to a + * standard Regex. Here are some more complete examples:
+ * * - * - * + * + * * - * - * + * + * * - * - * + * + * * - * - * - *
FileRegex Regex FileRegexRegex
*.java .*\.java$ *.java.*\.java$
*.{java,html} .*\.(java|html)$ *.{java,html}.*\.(java|html)$
foo.[chC] foo.[chC]$
+ * foo.[chC] + * foo.[chC]$ + * + * */ public class FileRegex extends Regex { @@ -82,8 +86,7 @@ public class FileRegex extends Regex * Compile a new pattern. Throws * * @exception com.stevesoft.pat.RegSyntax - * for nonsensical patterns like "[9-0]+" just as Regex - * does. + * 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 diff --git a/src/com/stevesoft/pat/Group.java b/src/com/stevesoft/pat/Group.java index e6f734c..22d9f81 100755 --- a/src/com/stevesoft/pat/Group.java +++ b/src/com/stevesoft/pat/Group.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * This class implements the (?@<>) syntax that matches a balanced parenthesis. diff --git a/src/com/stevesoft/pat/Multi.java b/src/com/stevesoft/pat/Multi.java index 1fe197d..7798d12 100755 --- a/src/com/stevesoft/pat/Multi.java +++ b/src/com/stevesoft/pat/Multi.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * Matches any number of instances of sub Pattern this was the hardest method to @@ -38,11 +38,11 @@ class Multi extends PatternSub /** * @param a - * The fewest number of times the sub pattern can match. + * The fewest number of times the sub pattern can match. * @param b - * The maximum number of times the sub pattern can match. + * The maximum number of times the sub pattern can match. * @param p - * The sub pattern. + * The sub pattern. * @see Multi_stage2 * @see MultiMin */ diff --git a/src/com/stevesoft/pat/Multi_stage2.java b/src/com/stevesoft/pat/Multi_stage2.java index b18ad1c..f5a54db 100755 --- a/src/com/stevesoft/pat/Multi_stage2.java +++ b/src/com/stevesoft/pat/Multi_stage2.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * If Multi were not split into a second stage, then a nested Multi would try to diff --git a/src/com/stevesoft/pat/NoPattern.java b/src/com/stevesoft/pat/NoPattern.java index 444d094..37d6384 100755 --- a/src/com/stevesoft/pat/NoPattern.java +++ b/src/com/stevesoft/pat/NoPattern.java @@ -7,7 +7,7 @@ package // // com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * The idea behind this class is simply to eliminate the need for testing to see diff --git a/src/com/stevesoft/pat/NullPattern.java b/src/com/stevesoft/pat/NullPattern.java index 09460de..accd3f1 100755 --- a/src/com/stevesoft/pat/NullPattern.java +++ b/src/com/stevesoft/pat/NullPattern.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** * This pattern matches nothing -- it is found in patterns like (hello|world|) diff --git a/src/com/stevesoft/pat/Or.java b/src/com/stevesoft/pat/Or.java index 8d405e5..d5ee673 100755 --- a/src/com/stevesoft/pat/Or.java +++ b/src/com/stevesoft/pat/Or.java @@ -7,7 +7,8 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; +import java.util.Vector; /** * This class implements the (?: ... ) extended Pattern. It provides a base diff --git a/src/com/stevesoft/pat/OrMark.java b/src/com/stevesoft/pat/OrMark.java index 89b8869..ce1ecad 100755 --- a/src/com/stevesoft/pat/OrMark.java +++ b/src/com/stevesoft/pat/OrMark.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** Implements the parenthesis pattern subelement. */ class OrMark extends Or diff --git a/src/com/stevesoft/pat/Pattern.java b/src/com/stevesoft/pat/Pattern.java index 3a3462c..1bc74f8 100755 --- a/src/com/stevesoft/pat/Pattern.java +++ b/src/com/stevesoft/pat/Pattern.java @@ -9,7 +9,7 @@ package com.stevesoft.pat; import jalview.util.MessageManager; -import java.util.*; +import java.util.Hashtable; /** Shareware: package pat @@ -261,7 +261,9 @@ public abstract class Pattern */ Pattern clone1(Hashtable h) { - throw new Error(MessageManager.formatMessage("error.no_such_method_as_clone1_for", new String[]{getClass().getName()})); + throw new Error(MessageManager.formatMessage( + "error.no_such_method_as_clone1_for", new String[] { getClass() + .getName() })); } Pattern clone(Hashtable h) diff --git a/src/com/stevesoft/pat/Pthings.java b/src/com/stevesoft/pat/Pthings.java index 69e8fed..8de2748 100755 --- a/src/com/stevesoft/pat/Pthings.java +++ b/src/com/stevesoft/pat/Pthings.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.BitSet; /** * Things that need to be kept track of during a match. Passed along with diff --git a/src/com/stevesoft/pat/PushRule.java b/src/com/stevesoft/pat/PushRule.java index c9aee2b..dd1ac9c 100755 --- a/src/com/stevesoft/pat/PushRule.java +++ b/src/com/stevesoft/pat/PushRule.java @@ -9,9 +9,8 @@ package com.stevesoft.pat; /** * See the example file trans3.java for - * further examples of how this is used. You will probably not want to call it - * directly. + * href="http://javaregex.com/code/trans3.java.html">trans3.java for further + * examples of how this is used. You will probably not want to call it directly. */ public class PushRule extends SpecialRule { diff --git a/src/com/stevesoft/pat/Range.java b/src/com/stevesoft/pat/Range.java index 610a4d5..02c5d3a 100755 --- a/src/com/stevesoft/pat/Range.java +++ b/src/com/stevesoft/pat/Range.java @@ -7,7 +7,7 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Hashtable; /** Thrown when one encounters things like [z-a] */ class BadRangeArgs extends RegSyntax diff --git a/src/com/stevesoft/pat/RegOpt.java b/src/com/stevesoft/pat/RegOpt.java index 0d65139..50d799f 100755 --- a/src/com/stevesoft/pat/RegOpt.java +++ b/src/com/stevesoft/pat/RegOpt.java @@ -7,7 +7,9 @@ // package com.stevesoft.pat; -import java.util.*; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Vector; /** This class is just like oneChar, but doesn't worry about case. */ class FastChar extends oneChar diff --git a/src/com/stevesoft/pat/RegRes.java b/src/com/stevesoft/pat/RegRes.java index a204c47..a963a17 100755 --- a/src/com/stevesoft/pat/RegRes.java +++ b/src/com/stevesoft/pat/RegRes.java @@ -47,9 +47,7 @@ public class RegRes implements Cloneable for (int i = 0; i < numSubs(); i++) { int n = i + 1; - sb - .append(" sub(" + n + ")=" + matchedFrom(n) + ":" - + charsMatched(n)); + sb.append(" sub(" + n + ")=" + matchedFrom(n) + ":" + charsMatched(n)); } return sb.toString(); } diff --git a/src/com/stevesoft/pat/Regex.java b/src/com/stevesoft/pat/Regex.java index 861c33b..c00ddad 100755 --- a/src/com/stevesoft/pat/Regex.java +++ b/src/com/stevesoft/pat/Regex.java @@ -9,10 +9,12 @@ package com.stevesoft.pat; import jalview.util.MessageManager; -import java.io.*; -import java.util.*; +import java.io.File; +import java.io.FilenameFilter; +import java.util.BitSet; +import java.util.Hashtable; -import com.stevesoft.pat.wrap.*; +import com.stevesoft.pat.wrap.StringWrap; /** Matches a Unicode punctuation character. */ class UnicodePunct extends UniValidator @@ -252,7 +254,9 @@ class UnicodeLower extends UniValidator * * 
  * \d+
- *
, but note that the sequence + * + * + * , but note that the sequence * * 
  * (?e=#)
@@ -262,8 +266,8 @@ class UnicodeLower extends UniValidator
  * small differences as well. I will either make my package conform or note them
  * as I become aware of them.
  * 

- * This package supports additional patterns not in perl5: 
 
+ * This package supports additional patterns not in perl5: 

+ * 

  * 
  * 
  * 
@@ -277,8 +281,8 @@ class UnicodeLower extends UniValidator
  * "look behind." It fails if it attempts to move to a position before the
  * beginning of the string. "x(?<1)" is equivalent to "(?=x)". The number, 1
  * in this example, is the number of characters to move backwards.
- * 
(?@())Group
 

- * 
+ * 
+ *  
  * 
  * @author Steven R. Brandt
  * @version package com.stevesoft.pat, release 1.5.3
@@ -627,9 +631,8 @@ public class Regex extends RegRes implements FilenameFilter
    * 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.
+   *              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
    */
@@ -777,7 +780,9 @@ public class Regex extends RegRes implements FilenameFilter
   {
     if (s == null)
     {
-      throw new NullPointerException(MessageManager.getString("exception.null_string_given_to_regex_search"));
+      throw new NullPointerException(
+              MessageManager
+                      .getString("exception.null_string_given_to_regex_search"));
     }
     return _search(s, 0, s.length());
   }
@@ -786,7 +791,9 @@ public class Regex extends RegRes implements FilenameFilter
   {
     if (sl == null)
     {
-      throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search"));
+      throw new NullPointerException(
+              MessageManager
+                      .getString("exception.null_string_like_given_to_regex_search"));
     }
     return _search(sl, 0, sl.length());
   }
@@ -795,7 +802,9 @@ public class Regex extends RegRes implements FilenameFilter
   {
     if (s == null)
     {
-      throw new NullPointerException(MessageManager.getString("exception.null_string_given_to_regex_reverse_search"));
+      throw new NullPointerException(
+              MessageManager
+                      .getString("exception.null_string_given_to_regex_reverse_search"));
     }
     return _reverseSearch(s, 0, s.length());
   }
@@ -804,7 +813,9 @@ public class Regex extends RegRes implements FilenameFilter
   {
     if (sl == null)
     {
-      throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_reverse_search"));
+      throw new NullPointerException(
+              MessageManager
+                      .getString("exception.null_string_like_given_to_regex_reverse_search"));
     }
     return _reverseSearch(sl, 0, sl.length());
   }
@@ -821,7 +832,9 @@ public class Regex extends RegRes implements FilenameFilter
   {
     if (s == null)
     {
-      throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search_from"));
+      throw new NullPointerException(
+              MessageManager
+                      .getString("exception.null_string_like_given_to_regex_search_from"));
     }
     return _search(s, start, s.length());
   }
@@ -830,7 +843,9 @@ public class Regex extends RegRes implements FilenameFilter
   {
     if (s == null)
     {
-        throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search_from"));
+      throw new NullPointerException(
+              MessageManager
+                      .getString("exception.null_string_like_given_to_regex_search_from"));
     }
     return _search(s, start, s.length());
   }
@@ -842,7 +857,9 @@ public class Regex extends RegRes implements FilenameFilter
   {
     if (s == null)
     {
-      throw new NullPointerException(MessageManager.getString("exception.null_string_like_given_to_regex_search_region"));
+      throw new NullPointerException(
+              MessageManager
+                      .getString("exception.null_string_like_given_to_regex_search_region"));
     }
     return _search(s, start, end);
   }
@@ -963,13 +980,13 @@ public class Regex extends RegRes implements FilenameFilter
    * 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; }
+   * 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)
@@ -1097,8 +1114,8 @@ public class Regex extends RegRes implements FilenameFilter
    * the Pattern.
    * 
    * @exception com.stevesoft.pat.RegSyntax
-   *                    is thrown when a nonsensensical pattern is supplied. For
-   *                    example, a pattern beginning with *.
+   *              is thrown when a nonsensensical pattern is supplied. For
+   *              example, a pattern beginning with *.
    */
   protected void compile1(StrPos sp, Rthings mk) throws RegSyntax
   {
@@ -1903,9 +1920,9 @@ public class Regex extends RegRes implements FilenameFilter
    * optimized() method.
    * 

    * 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.
+   * 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.
    * 

    * 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
diff --git a/src/com/stevesoft/pat/RegexReader.java b/src/com/stevesoft/pat/RegexReader.java
index 2e10f16..837821e 100755
--- a/src/com/stevesoft/pat/RegexReader.java
+++ b/src/com/stevesoft/pat/RegexReader.java
@@ -7,9 +7,10 @@
 //
 package com.stevesoft.pat;
 
-import java.io.*;
+import java.io.IOException;
+import java.io.Reader;
 
-import com.stevesoft.pat.wrap.*;
+import com.stevesoft.pat.wrap.StringBufferWrap;
 
 /**
  * This class allows you to replace the text in strings as you read them in. Be
diff --git a/src/com/stevesoft/pat/RegexTokenizer.java b/src/com/stevesoft/pat/RegexTokenizer.java
index 0378f3a..31fa2ba 100755
--- a/src/com/stevesoft/pat/RegexTokenizer.java
+++ b/src/com/stevesoft/pat/RegexTokenizer.java
@@ -7,7 +7,8 @@
 //
 package com.stevesoft.pat;
 
-import java.util.*;
+import java.util.Enumeration;
+import java.util.Vector;
 
 /**
  Shareware: package pat
diff --git a/src/com/stevesoft/pat/ReplaceRule.java b/src/com/stevesoft/pat/ReplaceRule.java
index bf56143..74a7a25 100755
--- a/src/com/stevesoft/pat/ReplaceRule.java
+++ b/src/com/stevesoft/pat/ReplaceRule.java
@@ -7,7 +7,7 @@
 //
 package com.stevesoft.pat;
 
-import java.util.*;
+import java.util.Hashtable;
 
 /**
  * ReplaceRule is a singly linked list of Objects which describe how to replace
diff --git a/src/com/stevesoft/pat/Replacer.java b/src/com/stevesoft/pat/Replacer.java
index b886f6a..6eaf5f6 100755
--- a/src/com/stevesoft/pat/Replacer.java
+++ b/src/com/stevesoft/pat/Replacer.java
@@ -9,7 +9,7 @@ package com.stevesoft.pat;
 
 import jalview.util.MessageManager;
 
-import com.stevesoft.pat.wrap.*;
+import com.stevesoft.pat.wrap.StringWrap;
 
 /** Internally used class. */
 class RegHolder
@@ -180,7 +180,9 @@ public class Replacer
     lastMatchedTo = 0;
     if (rh.me == null)
     {
-      throw new NullPointerException(MessageManager.getString("exception.replace_null_regex_pointer"));
+      throw new NullPointerException(
+              MessageManager
+                      .getString("exception.replace_null_regex_pointer"));
     }
     if (rh.me._search(s, start, end))
     {
diff --git a/src/com/stevesoft/pat/Skip.java b/src/com/stevesoft/pat/Skip.java
index d3f3822..f04653e 100755
--- a/src/com/stevesoft/pat/Skip.java
+++ b/src/com/stevesoft/pat/Skip.java
@@ -175,8 +175,8 @@ public class Skip
       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)))
+              && null != (subsk = findSkip(
+                      (Pattern) ((Or) p).v.elementAt(0), ignoreCase, trnc)))
       {
         subsk.offset += offset;
         return subsk;
diff --git a/src/com/stevesoft/pat/SkipBMH.java b/src/com/stevesoft/pat/SkipBMH.java
index 1397b90..8257548 100755
--- a/src/com/stevesoft/pat/SkipBMH.java
+++ b/src/com/stevesoft/pat/SkipBMH.java
@@ -7,15 +7,15 @@
 //
 package com.stevesoft.pat;
 
-import com.stevesoft.pat.wrap.*;
+import com.stevesoft.pat.wrap.StringWrap;
 
 /**
  * Like Skip, but implements a 
- * Boyer-Moore-Horspool type search method that has been modified to be
- * more like a "T-search" (see the Michael Tamm''s article in C'T, magazin
- * fuer computer und technic, August 97 p 292). Yet another important
- * source of information for me was the  type search method that has been modified to be more
+ * like a "T-search" (see the Michael Tamm''s article in C'T, magazin fuer
+ * computer und technic, August 97 p 292). Yet another important source of
+ * information for me was the  Deep Magic
  * article on string searching. As of this writing, I can beat String's indexOf
  * method in many cases.
diff --git a/src/com/stevesoft/pat/Skipped.java b/src/com/stevesoft/pat/Skipped.java
index 551166b..2d20845 100755
--- a/src/com/stevesoft/pat/Skipped.java
+++ b/src/com/stevesoft/pat/Skipped.java
@@ -7,7 +7,7 @@
 //
 package com.stevesoft.pat;
 
-import java.util.*;
+import java.util.Hashtable;
 
 /**
  * Implements the (?<number) Pattern, where number is an integer telling us
@@ -31,8 +31,8 @@ class Skipped extends Pattern
   {
     // 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()))
+            || CaseMgr.regionMatches(s, pt.ignoreCase, 0, pt.src, pos,
+                    s.length()))
     {
       return nextMatch(pos + s.length(), pt);
     }
diff --git a/src/com/stevesoft/pat/Start.java b/src/com/stevesoft/pat/Start.java
index 650e7a7..6cc0ce4 100755
--- a/src/com/stevesoft/pat/Start.java
+++ b/src/com/stevesoft/pat/Start.java
@@ -7,7 +7,7 @@
 //
 package com.stevesoft.pat;
 
-import java.util.*;
+import java.util.Hashtable;
 
 /** The '^' or the '\A' Pattern, matches the start of a string. */
 class Start extends Pattern
diff --git a/src/com/stevesoft/pat/StringLike.java b/src/com/stevesoft/pat/StringLike.java
index be98ff3..fa01fe6 100755
--- a/src/com/stevesoft/pat/StringLike.java
+++ b/src/com/stevesoft/pat/StringLike.java
@@ -11,10 +11,10 @@ com.stevesoft.pat;
  * Package pat can search anything that implements this interface. Package pat
  * assumes the following:
  * 
    
- * 
  • The StringLike object will not change. Calls to charAt(int) will not
- * vary with time.
- * 
  • The length of the object being searched is known before the search
- * begins and does not vary with time.
+ * 
  • The StringLike object will not change. Calls to charAt(int) will not vary
+ * with time.
+ * 
  • The length of the object being searched is known before the search begins
+ * and does not vary with time.
  * 

  * Note that searching String is probably faster than searching other objects,
  * so searching String is still preferred if possible.
diff --git a/src/com/stevesoft/pat/Transformer.java b/src/com/stevesoft/pat/Transformer.java
index 84a3a46..901a92d 100755
--- a/src/com/stevesoft/pat/Transformer.java
+++ b/src/com/stevesoft/pat/Transformer.java
@@ -9,7 +9,7 @@ package com.stevesoft.pat;
 
 import jalview.util.MessageManager;
 
-import com.stevesoft.pat.wrap.*;
+import com.stevesoft.pat.wrap.StringWrap;
 
 /**
  * Replacement rule used by the Transformer.
@@ -151,7 +151,9 @@ public class Transformer
     Regex r = Regex.perlCode(rs);
     if (r == null)
     {
-      throw new NullPointerException(MessageManager.formatMessage("exception.bad_pattern_to_regex_perl_code", new String[]{rs}));
+      throw new NullPointerException(MessageManager.formatMessage(
+              "exception.bad_pattern_to_regex_perl_code",
+              new String[] { rs }));
     }
     add(r);
   }
diff --git a/src/com/stevesoft/pat/lookAhead.java b/src/com/stevesoft/pat/lookAhead.java
index d7d71c3..5f2a1d0 100755
--- a/src/com/stevesoft/pat/lookAhead.java
+++ b/src/com/stevesoft/pat/lookAhead.java
@@ -7,7 +7,7 @@
 //
 package com.stevesoft.pat;
 
-import java.util.*;
+import java.util.Hashtable;
 
 /** Implements "(?= )" and "(?! )" */
 class lookAhead extends Or
diff --git a/src/com/stevesoft/pat/oneChar.java b/src/com/stevesoft/pat/oneChar.java
index ebbe991..b13c64d 100755
--- a/src/com/stevesoft/pat/oneChar.java
+++ b/src/com/stevesoft/pat/oneChar.java
@@ -7,7 +7,7 @@
 //
 package com.stevesoft.pat;
 
-import java.util.*;
+import java.util.Hashtable;
 
 /** This class matches a single character. */
 class oneChar extends Pattern
diff --git a/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java b/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
index c014a57..2735f12 100755
--- a/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
+++ b/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
@@ -7,7 +7,8 @@ package //
 //
 com.stevesoft.pat.wrap;
 
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
 
 /**
  * Allows the outcome of a replaceAll() or replaceFirst() to be an array of
diff --git a/src/com/stevesoft/pat/wrap/CharArrayWrap.java b/src/com/stevesoft/pat/wrap/CharArrayWrap.java
index bde9bd1..5fa0fb0 100755
--- a/src/com/stevesoft/pat/wrap/CharArrayWrap.java
+++ b/src/com/stevesoft/pat/wrap/CharArrayWrap.java
@@ -7,7 +7,8 @@
 //
 package com.stevesoft.pat.wrap;
 
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
 
 /**
  * This provides a wrapper for a char array so that it can be searched by Regex.
diff --git a/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java b/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
index f5b61ab..66a1014 100755
--- a/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
+++ b/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
@@ -9,9 +9,12 @@ package com.stevesoft.pat.wrap;
 
 import jalview.util.MessageManager;
 
-import java.io.*;
+import java.io.IOException;
+import java.io.RandomAccessFile;
 
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.Regex;
+import com.stevesoft.pat.StringLike;
 
 /**
  * Provides a wrapper for a RandomAccessFile so that it can be searched by
@@ -86,11 +89,11 @@ public class RandomAccessFileWrap implements StringLike
     {
     }
 
-    throw new ArrayIndexOutOfBoundsException(MessageManager.formatMessage("exception.out_of_bounds_for_file", new String[]{
-    		Integer.valueOf(i).toString(),
-    		Integer.valueOf(i0).toString(),
-    		Integer.valueOf(iend).toString()
-    }));
+    throw new ArrayIndexOutOfBoundsException(MessageManager.formatMessage(
+            "exception.out_of_bounds_for_file", new String[] {
+                Integer.valueOf(i).toString(),
+                Integer.valueOf(i0).toString(),
+                Integer.valueOf(iend).toString() }));
   }
 
   public String toString()
diff --git a/src/com/stevesoft/pat/wrap/StringBufferWrap.java b/src/com/stevesoft/pat/wrap/StringBufferWrap.java
index d522461..29ec042 100755
--- a/src/com/stevesoft/pat/wrap/StringBufferWrap.java
+++ b/src/com/stevesoft/pat/wrap/StringBufferWrap.java
@@ -7,7 +7,8 @@
 //
 package com.stevesoft.pat.wrap;
 
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
 
 /**
  * This provides a wrapper for StringBuffer to capture the output of a
diff --git a/src/com/stevesoft/pat/wrap/StringWrap.java b/src/com/stevesoft/pat/wrap/StringWrap.java
index 3ddf7c5..8396dd9 100755
--- a/src/com/stevesoft/pat/wrap/StringWrap.java
+++ b/src/com/stevesoft/pat/wrap/StringWrap.java
@@ -7,7 +7,8 @@
 //
 package com.stevesoft.pat.wrap;
 
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
 
 /**
  * A basic wrapper for the String object. Regex does not search String directly
diff --git a/src/com/stevesoft/pat/wrap/WriterWrap.java b/src/com/stevesoft/pat/wrap/WriterWrap.java
index e72b5fa..189b0f2 100755
--- a/src/com/stevesoft/pat/wrap/WriterWrap.java
+++ b/src/com/stevesoft/pat/wrap/WriterWrap.java
@@ -7,9 +7,11 @@
 //
 package com.stevesoft.pat.wrap;
 
-import java.io.*;
+import java.io.IOException;
+import java.io.Writer;
 
-import com.stevesoft.pat.*;
+import com.stevesoft.pat.BasicStringBufferLike;
+import com.stevesoft.pat.StringLike;
 
 /**
  * Allows the outcome of a replaceAll() or replaceFirst() to be directed to a
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
index aedf657..03f51f7 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
@@ -11,745 +11,941 @@ import org.slf4j.LoggerFactory;
 
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
 
-
-public abstract class ChimUtils {
-
-	private static Logger logger = LoggerFactory
-			.getLogger(ChimUtils.class);
-
-	static int MAX_SUB_MODELS = 1000;
-
-	public static final HashMap aaNames;
-
-	public static String RESIDUE_ATTR = "ChimeraResidue";
-	public static String RINALYZER_ATTR = "RINalyzerResidue";
-	public static String DEFAULT_STRUCTURE_KEY = "pdbFileName";
-
-	/**
-	 * Parse the model number returned by Chimera and return the int value
-	 */
-	// invoked by the ChimeraModel constructor
-	// line = model id #0 type Molecule name 1ert
-	public static int[] parseModelNumber(String inputLine) {
-		int hash = inputLine.indexOf('#');
-		int space = inputLine.indexOf(' ', hash);
-		int decimal = inputLine.substring(hash + 1, space).indexOf('.');
-		// model number is between hash+1 and space
-		int modelNumber = -1;
-		int subModelNumber = 0;
-		try {
-			if (decimal > 0) {
-				subModelNumber = Integer.parseInt(inputLine.substring(decimal + hash + 2, space));
-				space = decimal + hash + 1;
-			}
-			modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
-		} catch (Exception e) {
-			logger.warn("Unexpected return from Chimera: " + inputLine, e);
-		}
-		return new int[] { modelNumber, subModelNumber };
-	}
-
-	/**
-	 * Parse the model number returned by Chimera and return the int value
-	 */
-	// invoked by openModel in ChimeraManager
-	// line: #1, chain A: hiv-1 protease
-	public static int[] parseOpenedModelNumber(String inputLine) {
-		int hash = inputLine.indexOf('#');
-		int space = inputLine.indexOf(',', hash);
-		int decimal = inputLine.substring(hash + 1, space).indexOf('.');
-		// model number is between hash+1 and space
-		int modelNumber = -1;
-		int subModelNumber = 0;
-		try {
-			if (decimal > 0) {
-				subModelNumber = Integer.parseInt(inputLine.substring(decimal + hash + 2, space));
-				space = decimal + hash + 1;
-			}
-			modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
-		} catch (Exception e) {
-			logger.warn("Unexpected return from Chimera: " + inputLine, e);
-		}
-		return new int[] { modelNumber, subModelNumber };
-	}
-
-	/**
-	 * Parse the model identifier returned by Chimera and return the String value
-	 */
-	// invoked by the ChimeraModel constructor
-	// line = model id #0 type Molecule name 1ert
-	public static String parseModelName(String inputLine) {
-		int start = inputLine.indexOf("name ");
-		if (start < 0)
-			return null;
-		// Might get a quoted string (don't understand why, but there you have it)
-		if (inputLine.startsWith("\"", start + 5)) {
-			start += 6; // Skip over the first quote
-			int end = inputLine.lastIndexOf('"');
-			if (end >= 1) {
-				return inputLine.substring(start, end);
-			} else
-				return inputLine.substring(start);
-		} else {
-			return inputLine.substring(start + 5);
-		}
-	}
-
-	public static Color parseModelColor(String inputLine) {
-		try {
-			int colorStart = inputLine.indexOf("color ");
-			String colorString = inputLine.substring(colorStart + 6);
-			String[] rgbStrings = colorString.split(",");
-			float[] rgbValues = new float[4];
-			for (int i = 0; i < rgbStrings.length; i++) {
-				Float f = new Float(rgbStrings[i]);
-				rgbValues[i] = f.floatValue();
-			}
-			if (rgbStrings.length == 4) {
-				return new Color(rgbValues[0], rgbValues[1], rgbValues[2], rgbValues[3]);
-			} else {
-				return new Color(rgbValues[0], rgbValues[1], rgbValues[2]);
-			}
-		} catch (Exception ex) {
-			logger.warn("Unexpected return from Chimera: " + inputLine, ex);
-		}
-		return Color.white;
-	}
-
-	/**
-	 * Create the key to use for forming the model/submodel key into the modelHash
-	 * 
-	 * @param model
-	 *            the model number
-	 * @param subModel
-	 *            the submodel number
-	 * @return the model key as an Integer
-	 */
-	public static Integer makeModelKey(int model, int subModel) {
-		return new Integer(model * MAX_SUB_MODELS + subModel);
-	}
-
-	// invoked by the getResdiue (parseConnectivityReplies in CreateStructureNetworkTask)
-	// atomSpec = #0:1.A or #1:96.B@N
-	public static ChimeraModel getModel(String atomSpec, ChimeraManager chimeraManager) {
-		// System.out.println("getting model for "+atomSpec);
-		String[] split = atomSpec.split(":");
-		// No model specified....
-		if (split[0].length() == 0) {
-			logger.info("Unexpected return from Chimera: " + atomSpec);
-			return null;
-		}
-		// System.out.println("model = "+split[0].substring(1));
-		int model = 0;
-		int submodel = 0;
-		try {
-			String[] subSplit = split[0].substring(1).split("\\.");
-			if (subSplit.length > 0)
-				model = Integer.parseInt(subSplit[0]);
-			else
-				model = Integer.parseInt(split[0].substring(1));
-
-			if (subSplit.length > 1)
-				submodel = Integer.parseInt(subSplit[1]);
-		} catch (Exception e) {
-			// ignore
-			logger.warn("Unexpected return from Chimera: " + atomSpec, e);
-		}
-		return chimeraManager.getChimeraModel(model, submodel);
-	}
-
-	// invoked by the parseConnectivityReplies in CreateStructureNetworkTask
-	// atomSpec = #0:1.A or #1:96.B@N
-	public static ChimeraResidue getResidue(String atomSpec, ChimeraManager chimeraManager) {
-		// System.out.println("Getting residue from: "+atomSpec);
-		ChimeraModel model = getModel(atomSpec, chimeraManager); // Get the model
-		if (model == null) {
-			model = chimeraManager.getChimeraModel();
-		}
-		return getResidue(atomSpec, model);
-	}
-
-	// invoked by the getResdiue (parseConnectivityReplies in CreateStructureNetworkTask)
-	// atomSpec = #0:1.A or #1:96.B@N
-	public static ChimeraResidue getResidue(String atomSpec, ChimeraModel model) {
-		// System.out.println("Getting residue from: "+atomSpec);
-		String[] split = atomSpec.split(":|@");
-
-		// Split into residue and chain
-		String[] residueChain = split[1].split("\\.");
-
-		if (residueChain[0].length() == 0) {
-			logger.info("Unexpected return from Chimera: " + atomSpec);
-			return null;
-		}
-
-		if (residueChain.length == 2 && residueChain[1].length() > 0) {
-			ChimeraChain chain = model.getChain(residueChain[1]);
-			return chain.getResidue(residueChain[0]);
-		}
-		return model.getResidue("_", residueChain[0]);
-	}
-
-	public static ChimeraChain getChain(String atomSpec, ChimeraModel model) {
-		String[] split = atomSpec.split(":|@");
-
-		// Split into residue and chain
-		String[] residueChain = split[1].split("\\.");
-		if (residueChain.length == 1) {
-			logger.info("Unexpected return from Chimera: " + atomSpec);
-			return null;
-		}
-		return model.getChain(residueChain[1]);
-	}
-
-	public static String getAtomName(String atomSpec) {
-		String[] split = atomSpec.split("@");
-		if (split.length > 1) {
-			return split[1];
-		}
-		return atomSpec;
-	}
-
-	public static boolean isBackbone(String atom) {
-		if (atom.equals("C") || atom.equals("CA") || atom.equals("N") || atom.equals("O")
-				|| atom.equals("H"))
-			return true;
-		return false;
-	}
-
-	public static String getIntSubtype(String node, String atom) {
-		String[] split = node.split("#| ");
-		String resType = "";
-		if (split.length == 2) {
-			resType = split[0].trim().toUpperCase();
-		} else if (split.length == 3) {
-			resType = split[1].trim().toUpperCase();
-		}
-		if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT")) {
-			return "water";
-		} else if (aaNames.containsKey(resType)) {
-			if (atom.equals("C") || atom.equals("CA") || atom.equals("N") || atom.equals("O")
-					|| atom.equals("H")) {
-				return "mc";
-			} else {
-				return "sc";
-			}
-		} else {
-			return "other";
-		}
-	}
-
-
-	public static String[] getResKeyParts(String resKey) {
-		// [pdbID[.modelNo]#][residueID][.chainID]
-		// pdbID := 4-character code | "URL" | "path"
-		String[] resKeyParts = new String[4];
-		String[] split = resKey.split("#");
-		String resChain = null;
-		// if no "#" then it is either only a pdb id or a residue or a chain
-		if (split.length == 1) {
-			// pdb id without model
-			if (resKey.length() == 4 && resKey.indexOf("\\.") < 0) {
-				parseModelID(resKey, resKeyParts);
-			}
-			// pdb link or file
-			else if (resKey.startsWith("\"")) {
-				parseModelID(resKey, resKeyParts);
-			}
-			// chain and residue or model and number
-			else {
-				String[] splitSplit = resKey.split("\\.");
-				if (splitSplit.length == 1) {
-					// only a chain or a residue
-					resChain = resKey;
-				} else {
-					try {
-						// pdb with a model
-						Integer.parseInt(splitSplit[1]);
-						parseModelID(resKey, resKeyParts);
-					} catch (NumberFormatException ex) {
-						// residue and chain
-						resChain = resKey;
-					}
-				}
-			}
-		} else if (split.length == 2) {
-			// model and residue+chain
-			parseModelID(split[0], resKeyParts);
-			resChain = split[1];
-		} else {
-			// model string with "#"
-			// TODO: [Optional] Are there more possibilities?
-			parseModelID(resKey.substring(0, resKey.lastIndexOf("#")), resKeyParts);
-			resChain = resKey.substring(resKey.lastIndexOf("#") + 1, resKey.length());
-		}
-		if (resChain != null) {
-			//System.out.println(resChain);
-			String[] resChainSplit = resChain.split("\\.");
-			if (resChainSplit.length == 1) {
-				// TODO: [Optional] Find a better way to distinguish between chain and residue
-				// if only one character and not an int, probably a chain
-				if (resChainSplit[0].length() == 1) {
-					try {
-						Integer.parseInt(resChainSplit[0]);
-						resKeyParts[3] = resChainSplit[0];
-					} catch (NumberFormatException ex) {
-						resKeyParts[2] = resChainSplit[0];
-					}
-				} else {
-					resKeyParts[3] = resChainSplit[0];
-				}
-			} else if (resChainSplit.length == 2) {
-				resKeyParts[2] = resChainSplit[0];
-				resKeyParts[3] = resChainSplit[1];
-			} else {
-				// too many dots?
-				logger.info("Could not parse residue identifier: " + resKey);
-			}
-		}
-		// String print = "";
-		// for (int i = 0; i < resKeyParts.length; i++) {
-		// if (resKeyParts[i] == null) {
-		// print += i + ": null\t";
-		// } else {
-		// print += i + ": " + resKeyParts[i] + ";";
-		// }
-		// }
-		// System.out.println(print);
-		return resKeyParts;
-	}
-
-	public static void parseModelID(String modelID, String[] resKeyParts) {
-		if (modelID.startsWith("\"")) {
-			if (modelID.endsWith("\"")) {
-				resKeyParts[0] = modelID.substring(1, modelID.length() - 1);
-				return;
-			} else {
-				try {
-					Integer.parseInt(modelID.substring(modelID.lastIndexOf("\"") + 2,
-							modelID.length()));
-					resKeyParts[0] = modelID.substring(0, modelID.lastIndexOf("\"") - 1);
-					resKeyParts[1] = modelID.substring(modelID.lastIndexOf("\"") + 2,
-							modelID.length());
-				} catch (NumberFormatException ex) {
-					resKeyParts[0] = modelID.substring(1);
-				}
-			}
-		} else {
-			String[] modelIDNo = modelID.split("\\.");
-			if (modelIDNo.length == 1) {
-				resKeyParts[0] = modelIDNo[0];
-			} else if (modelIDNo.length == 2) {
-				try {
-					Integer.parseInt(modelIDNo[1]);
-					resKeyParts[0] = modelIDNo[0];
-					resKeyParts[1] = modelIDNo[1];
-				} catch (NumberFormatException ex) {
-					resKeyParts[0] = modelID;
-				}
-			} else {
-				logger.info("Could not parse model identifier: " + modelID);
-			}
-		}
-	}
-
-	/**
-	 * This method takes a Cytoscape attribute specification ([structure#][residue][.chainID]) and
-	 * returns the lowest-level object referenced by the spec. For example, if the spec is "1tkk",
-	 * this method will return a ChimeraModel. If the spec is ".A", it will return a ChimeraChain,
-	 * etc.
-	 * 
-	 * @param attrSpec
-	 *            the specification string
-	 * @param chimeraManager
-	 *            the Chimera object we're currently using
-	 * @return a ChimeraStructuralObject of the lowest type
-	 */
-	public static ChimeraStructuralObject fromAttributeOld(String attrSpec,
-			ChimeraManager chimeraManager) {
-		if (attrSpec == null || attrSpec.indexOf(',') > 0 || attrSpec.indexOf('-') > 0) {
-			// No support for either lists or ranges
-			logger.warn("No support for identifier: " + attrSpec);
-			return null;
-		}
-
-		String residue = null;
-		String model = null;
-		String chain = null;
-
-		ChimeraModel chimeraModel = null;
-		ChimeraChain chimeraChain = null;
-		ChimeraResidue chimeraResidue = null;
-
-		// System.out.println("Getting object from attribute: "+attrSpec);
-		try {
-			String[] split = attrSpec.split("#");
-			String resChain = null;
-			if (split.length == 1) {
-				// no model
-				resChain = split[0];
-			} else if (split.length == 2) {
-				// model and rest
-				model = split[0];
-				resChain = split[1];
-			} else {
-				// model string with "#"
-				model = attrSpec.substring(0, attrSpec.lastIndexOf("#"));
-				resChain = attrSpec.substring(attrSpec.lastIndexOf("#") + 1, attrSpec.length());
-			}
-			if (resChain != null) {
-				String[] resChainSplit = resChain.split("\\.");
-				if (resChainSplit.length == 1) {
-					residue = resChainSplit[0];
-				} else if (resChainSplit.length == 2) {
-					residue = resChainSplit[0];
-					chain = resChainSplit[1];
-				} else {
-					// too many dots?
-					logger.warn("No support for identifier: " + attrSpec);
-				}
-			}
-
-			// if (split.length == 1) {
-			// // No model
-			// residue = split[0];
-			// } else if (split.length == 3) {
-			// // We have all three
-			// model = split[0];
-			// residue = split[1];
-			// chain = split[2];
-			// } else if (split.length == 2 && attrSpec.indexOf('#') > 0) {
-			// // Model and Residue
-			// model = split[0];
-			// residue = split[1];
-			// } else {
-			// // Residue and Chain
-			// residue = split[0];
-			// chain = split[1];
-			// }
-
-			// System.out.println("model = " + model + " chain = " + chain + " residue = " +
-			// residue);
-			if (model != null) {
-				List models = chimeraManager.getChimeraModels(model,
-						ModelType.PDB_MODEL);
-				if (models.size() == 1) {
-					chimeraModel = models.get(0);
-				} else {
-					try {
-						chimeraModel = chimeraManager.getChimeraModel(Integer.valueOf(model), 0);
-					} catch (NumberFormatException ex) {
-						// ignore
-					}
-				}
-			}
-			if (chimeraModel == null) {
-				chimeraModel = chimeraManager.getChimeraModel();
-			}
-			// System.out.println("ChimeraModel = " + chimeraModel);
-
-			if (chain != null) {
-				chimeraChain = chimeraModel.getChain(chain);
-				// System.out.println("ChimeraChain = " + chimeraChain);
-			}
-			if (residue != null) {
-				if (chimeraChain != null) {
-					chimeraResidue = chimeraChain.getResidue(residue);
-				} else {
-					chimeraResidue = chimeraModel.getResidue("_", residue);
-				}
-				// System.out.println("ChimeraResidue = " + chimeraResidue);
-			}
-
-			if (chimeraResidue != null)
-				return chimeraResidue;
-
-			if (chimeraChain != null)
-				return chimeraChain;
-
-			if (chimeraModel != null)
-				return chimeraModel;
-
-		} catch (Exception ex) {
-			logger.warn("Could not parse residue identifier: " + attrSpec, ex);
-		}
-		return null;
-	}
-
-	public static ChimeraStructuralObject fromAttribute(String attrSpec,
-			ChimeraManager chimeraManager) {
-		// TODO: Make sure it is OK to remove this: || attrSpec.indexOf('-') > 0
-		if (attrSpec == null || attrSpec.indexOf(',') > 0) {
-			// No support for either lists or ranges
-			// System.out.println("No support for identifier: " + attrSpec);
-			logger.warn("No support for identifier: " + attrSpec);
-			return null;
-		}
-		String[] modelIDNoResChain = getResKeyParts(attrSpec);
-
-		ChimeraModel chimeraModel = null;
-		ChimeraChain chimeraChain = null;
-		ChimeraResidue chimeraResidue = null;
-
-		// System.out.println("Getting object from attribute: "+attrSpec);
-		try {
-			if (modelIDNoResChain[0] != null) {
-				String modelID = modelIDNoResChain[0];
-				List models = chimeraManager.getChimeraModels(modelID,
-						ModelType.PDB_MODEL);
-				if (models.size() == 1) { // usual case with only one model
-					chimeraModel = models.get(0);
-				} else if (models.size() > 1 && modelIDNoResChain[1] != null) {
-					// there are several submodels
-					try {
-						int modelNo = Integer.valueOf(modelIDNoResChain[1]);
-						for (ChimeraModel model : models) {
-							if (model.getSubModelNumber() == modelNo) {
-								chimeraModel = model;
-								break;
-							}
-						}
-					} catch (NumberFormatException ex) {
-						// ignore
-					}
-				} else {
-					// TODO: [Optional] What is this doing?
-					try {
-						chimeraModel = chimeraManager.getChimeraModel(Integer.valueOf(modelID), 0);
-					} catch (NumberFormatException ex) {
-						// ignore
-					}
-				}
-			}
-			if (chimeraModel == null) {
-				// TODO: [Optional] Find a better way to handle this case
-				// If no model can be matched, continue
-				// System.out.println("No matching model could be find for " + attrSpec);
-				return null;
-				// chimeraModel = chimeraManager.getChimeraModel();
-				// logger.warn("No matching model could be find for " + attrSpec + ". Trying with "
-				// + chimeraModel.toSpec());
-			}
-			// System.out.println("ChimeraModel = " + chimeraModel);
-
-			if (modelIDNoResChain[3] != null) {
-				chimeraChain = chimeraModel.getChain(modelIDNoResChain[3]);
-				// System.out.println("ChimeraChain = " + chimeraChain);
-			}
-			if (modelIDNoResChain[2] != null) {
-				String residue = modelIDNoResChain[2];
-				if (chimeraChain != null) {
-					chimeraResidue = chimeraChain.getResidue(residue);
-				} else if (chimeraModel.getChain("_") != null) {
-					chimeraResidue = chimeraModel.getResidue("_", residue);
-				} else if (chimeraModel.getChainCount() == 1) {
-					chimeraResidue = chimeraModel.getResidue(chimeraModel.getChainNames()
-							.iterator().next(), residue);
-				}
-				// System.out.println("ChimeraResidue = " + chimeraResidue);
-			}
-
-			if (chimeraResidue != null)
-				return chimeraResidue;
-
-			if (chimeraChain != null)
-				return chimeraChain;
-
-			if (chimeraModel != null)
-				return chimeraModel;
-
-		} catch (Exception ex) {
-			// System.out.println("Could not parse chimera identifier: " +
-			// attrSpec+"("+ex.getMessage()+")");
-			logger.warn("Could not parse chimera identifier: " + attrSpec, ex);
-		}
-		return null;
-	}
-
-	/**
-	 * Search for structure references in the residue list
-	 * 
-	 * @param residueList
-	 *            the list of residues
-	 * @return a concatenated list of structures encoded in the list
-	 */
-	public static String findStructures(String residueList) {
-		if (residueList == null)
-			return null;
-		String[] residues = residueList.split(",");
-		Map structureNameMap = new HashMap();
-		for (int i = 0; i < residues.length; i++) {
-			String[] components = residues[i].split("#");
-			if (components.length > 1) {
-				structureNameMap.put(components[0], components[1]);
-			}
-		}
-		if (structureNameMap.isEmpty())
-			return null;
-
-		String structure = null;
-		for (String struct : structureNameMap.keySet()) {
-			if (structure == null)
-				structure = new String();
-			else
-				structure = structure.concat(",");
-			structure = structure.concat(struct);
-		}
-		return structure;
-	}
-
-	// invoked by openStructures in StructureManager
-	public static List parseFuncRes(List residueNames, String modelName) {
-		List resRanges = new ArrayList();
-		for (int i = 0; i < residueNames.size(); i++) {
-			String residue = residueNames.get(i);
-			// Parse out the structure, if there is one
-			String[] components = residue.split("#");
-			if (components.length > 1 && !modelName.equals(components[0])) {
-				continue;
-			} else if (components.length > 1) {
-				residue = components[1];
-			} else if (components.length == 1) {
-				residue = components[0];
-			}
-			// Check to see if we have a range-spec
-			String resRange = "";
-			if (residue == null || residue.equals("") || residue.length() == 0) {
-				continue;
-			}
-			String[] range = residue.split("-", 2);
-			String chain = null;
-			for (int res = 0; res < range.length; res++) {
-				if (res == 1) {
-					resRange = resRange.concat("-");
-					if (chain != null && range[res].indexOf('.') == -1)
-						range[res] = range[res].concat("." + chain);
-				}
-
-				if (res == 0 && range.length >= 2 && range[res].indexOf('.') > 0) {
-					// This is a range spec with the leading residue containing a chain spec
-					String[] resChain = range[res].split("\\.");
-					chain = resChain[1];
-					range[res] = resChain[0];
-				}
-				// Fix weird SFLD syntax...
-				if (range[res].indexOf('|') > 0 && Character.isDigit(range[res].charAt(0))) {
-					int offset = range[res].indexOf('|');
-					String str = range[res].substring(offset + 1) + range[res].substring(0, offset);
-					range[res] = str;
-				}
-
-				// Convert to legal atom-spec
-				if (Character.isDigit(range[res].charAt(0))) {
-					resRange = resRange.concat(range[res]);
-				} else if (Character.isDigit(range[res].charAt(1))) {
-					resRange = resRange.concat(range[res].substring(1));
-				} else if (range[res].charAt(0) == '.') {
-					// Do we have a chain spec?
-					resRange = resRange.concat(range[res]);
-				} else {
-					resRange = resRange.concat(range[res].substring(3));
-				}
-			}
-			if (!resRanges.contains(resRange)) {
-				resRanges.add(resRange);
-			}
-		}
-		return resRanges;
-	}
-
-	static {
-		aaNames = new HashMap();
-		aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
-		aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
-		aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
-		aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
-		aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
-		aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
-		aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
-		aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
-		aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
-		aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
-		aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
-		aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
-		aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
-		aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
-		aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
-		aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
-		aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
-		aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
-		aaNames.put("TRP", "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
-		aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
-		aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
-		aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
-		aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
-		aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
-		aaNames.put("HOH", "HOH HOH Water [H]O[H]");
-	}
-
-	/**
-	 * Convert the amino acid type to a full name
-	 * 
-	 * @param aaType
-	 *            the residue type to convert
-	 * @return the full name of the residue
-	 */
-	public static String toFullName(String aaType) {
-		if (!aaNames.containsKey(aaType))
-			return aaType;
-		String[] ids = ((String) aaNames.get(aaType)).split(" ");
-		return ids[2].replace('_', ' ');
-	}
-
-	/**
-	 * Convert the amino acid type to a single letter
-	 * 
-	 * @param aaType
-	 *            the residue type to convert
-	 * @return the single letter representation of the residue
-	 */
-	public static String toSingleLetter(String aaType) {
-		if (!aaNames.containsKey(aaType))
-			return aaType;
-		String[] ids = ((String) aaNames.get(aaType)).split(" ");
-		return ids[0];
-	}
-
-	/**
-	 * Convert the amino acid type to three letters
-	 * 
-	 * @param aaType
-	 *            the residue type to convert
-	 * @return the three letter representation of the residue
-	 */
-	public static String toThreeLetter(String aaType) {
-		if (!aaNames.containsKey(aaType))
-			return aaType;
-		String[] ids = ((String) aaNames.get(aaType)).split(" ");
-		return ids[1];
-	}
-
-	/**
-	 * Convert the amino acid type to its SMILES string
-	 * 
-	 * @param aaType
-	 *            the residue type to convert
-	 * @return the SMILES representation of the residue
-	 */
-	public static String toSMILES(String aaType) {
-		if (!aaNames.containsKey(aaType))
-			return null;
-		String[] ids = ((String) aaNames.get(aaType)).split(" ");
-		if (ids.length < 4)
-			return null;
-		return ids[3];
-	}
-
-	public static String getAlignName(ChimeraStructuralObject chimObj) {
-		String name = chimObj.getChimeraModel().toString();
-		if (chimObj instanceof ChimeraChain) {
-			name = ((ChimeraChain) chimObj).toString() + " [" + name + "]";
-		}
-		return name;
-	}
+public abstract class ChimUtils
+{
+
+  private static Logger logger = LoggerFactory.getLogger(ChimUtils.class);
+
+  static int MAX_SUB_MODELS = 1000;
+
+  public static final HashMap aaNames;
+
+  public static String RESIDUE_ATTR = "ChimeraResidue";
+
+  public static String RINALYZER_ATTR = "RINalyzerResidue";
+
+  public static String DEFAULT_STRUCTURE_KEY = "pdbFileName";
+
+  /**
+   * Parse the model number returned by Chimera and return the int value
+   */
+  // invoked by the ChimeraModel constructor
+  // line = model id #0 type Molecule name 1ert
+  public static int[] parseModelNumber(String inputLine)
+  {
+    int hash = inputLine.indexOf('#');
+    int space = inputLine.indexOf(' ', hash);
+    int decimal = inputLine.substring(hash + 1, space).indexOf('.');
+    // model number is between hash+1 and space
+    int modelNumber = -1;
+    int subModelNumber = 0;
+    try
+    {
+      if (decimal > 0)
+      {
+        subModelNumber = Integer.parseInt(inputLine.substring(decimal
+                + hash + 2, space));
+        space = decimal + hash + 1;
+      }
+      modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
+    } catch (Exception e)
+    {
+      logger.warn("Unexpected return from Chimera: " + inputLine, e);
+    }
+    return new int[] { modelNumber, subModelNumber };
+  }
+
+  /**
+   * Parse the model number returned by Chimera and return the int value
+   */
+  // invoked by openModel in ChimeraManager
+  // line: #1, chain A: hiv-1 protease
+  public static int[] parseOpenedModelNumber(String inputLine)
+  {
+    int hash = inputLine.indexOf('#');
+    int space = inputLine.indexOf(',', hash);
+    int decimal = inputLine.substring(hash + 1, space).indexOf('.');
+    // model number is between hash+1 and space
+    int modelNumber = -1;
+    int subModelNumber = 0;
+    try
+    {
+      if (decimal > 0)
+      {
+        subModelNumber = Integer.parseInt(inputLine.substring(decimal
+                + hash + 2, space));
+        space = decimal + hash + 1;
+      }
+      modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
+    } catch (Exception e)
+    {
+      logger.warn("Unexpected return from Chimera: " + inputLine, e);
+    }
+    return new int[] { modelNumber, subModelNumber };
+  }
+
+  /**
+   * Parse the model identifier returned by Chimera and return the String value
+   */
+  // invoked by the ChimeraModel constructor
+  // line = model id #0 type Molecule name 1ert
+  public static String parseModelName(String inputLine)
+  {
+    int start = inputLine.indexOf("name ");
+    if (start < 0)
+      return null;
+    // Might get a quoted string (don't understand why, but there you have it)
+    if (inputLine.startsWith("\"", start + 5))
+    {
+      start += 6; // Skip over the first quote
+      int end = inputLine.lastIndexOf('"');
+      if (end >= 1)
+      {
+        return inputLine.substring(start, end);
+      }
+      else
+        return inputLine.substring(start);
+    }
+    else
+    {
+      return inputLine.substring(start + 5);
+    }
+  }
+
+  public static Color parseModelColor(String inputLine)
+  {
+    try
+    {
+      int colorStart = inputLine.indexOf("color ");
+      String colorString = inputLine.substring(colorStart + 6);
+      String[] rgbStrings = colorString.split(",");
+      float[] rgbValues = new float[4];
+      for (int i = 0; i < rgbStrings.length; i++)
+      {
+        Float f = new Float(rgbStrings[i]);
+        rgbValues[i] = f.floatValue();
+      }
+      if (rgbStrings.length == 4)
+      {
+        return new Color(rgbValues[0], rgbValues[1], rgbValues[2],
+                rgbValues[3]);
+      }
+      else
+      {
+        return new Color(rgbValues[0], rgbValues[1], rgbValues[2]);
+      }
+    } catch (Exception ex)
+    {
+      logger.warn("Unexpected return from Chimera: " + inputLine, ex);
+    }
+    return Color.white;
+  }
+
+  /**
+   * Create the key to use for forming the model/submodel key into the modelHash
+   * 
+   * @param model
+   *          the model number
+   * @param subModel
+   *          the submodel number
+   * @return the model key as an Integer
+   */
+  public static Integer makeModelKey(int model, int subModel)
+  {
+    return new Integer(model * MAX_SUB_MODELS + subModel);
+  }
+
+  // invoked by the getResdiue (parseConnectivityReplies in
+  // CreateStructureNetworkTask)
+  // atomSpec = #0:1.A or #1:96.B@N
+  public static ChimeraModel getModel(String atomSpec,
+          ChimeraManager chimeraManager)
+  {
+    // System.out.println("getting model for "+atomSpec);
+    String[] split = atomSpec.split(":");
+    // No model specified....
+    if (split[0].length() == 0)
+    {
+      logger.info("Unexpected return from Chimera: " + atomSpec);
+      return null;
+    }
+    // System.out.println("model = "+split[0].substring(1));
+    int model = 0;
+    int submodel = 0;
+    try
+    {
+      String[] subSplit = split[0].substring(1).split("\\.");
+      if (subSplit.length > 0)
+        model = Integer.parseInt(subSplit[0]);
+      else
+        model = Integer.parseInt(split[0].substring(1));
+
+      if (subSplit.length > 1)
+        submodel = Integer.parseInt(subSplit[1]);
+    } catch (Exception e)
+    {
+      // ignore
+      logger.warn("Unexpected return from Chimera: " + atomSpec, e);
+    }
+    return chimeraManager.getChimeraModel(model, submodel);
+  }
+
+  // invoked by the parseConnectivityReplies in CreateStructureNetworkTask
+  // atomSpec = #0:1.A or #1:96.B@N
+  public static ChimeraResidue getResidue(String atomSpec,
+          ChimeraManager chimeraManager)
+  {
+    // System.out.println("Getting residue from: "+atomSpec);
+    ChimeraModel model = getModel(atomSpec, chimeraManager); // Get the model
+    if (model == null)
+    {
+      model = chimeraManager.getChimeraModel();
+    }
+    return getResidue(atomSpec, model);
+  }
+
+  // invoked by the getResdiue (parseConnectivityReplies in
+  // CreateStructureNetworkTask)
+  // atomSpec = #0:1.A or #1:96.B@N
+  public static ChimeraResidue getResidue(String atomSpec,
+          ChimeraModel model)
+  {
+    // System.out.println("Getting residue from: "+atomSpec);
+    String[] split = atomSpec.split(":|@");
+
+    // Split into residue and chain
+    String[] residueChain = split[1].split("\\.");
+
+    if (residueChain[0].length() == 0)
+    {
+      logger.info("Unexpected return from Chimera: " + atomSpec);
+      return null;
+    }
+
+    if (residueChain.length == 2 && residueChain[1].length() > 0)
+    {
+      ChimeraChain chain = model.getChain(residueChain[1]);
+      return chain.getResidue(residueChain[0]);
+    }
+    return model.getResidue("_", residueChain[0]);
+  }
+
+  public static ChimeraChain getChain(String atomSpec, ChimeraModel model)
+  {
+    String[] split = atomSpec.split(":|@");
+
+    // Split into residue and chain
+    String[] residueChain = split[1].split("\\.");
+    if (residueChain.length == 1)
+    {
+      logger.info("Unexpected return from Chimera: " + atomSpec);
+      return null;
+    }
+    return model.getChain(residueChain[1]);
+  }
+
+  public static String getAtomName(String atomSpec)
+  {
+    String[] split = atomSpec.split("@");
+    if (split.length > 1)
+    {
+      return split[1];
+    }
+    return atomSpec;
+  }
+
+  public static boolean isBackbone(String atom)
+  {
+    if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
+            || atom.equals("O") || atom.equals("H"))
+      return true;
+    return false;
+  }
+
+  public static String getIntSubtype(String node, String atom)
+  {
+    String[] split = node.split("#| ");
+    String resType = "";
+    if (split.length == 2)
+    {
+      resType = split[0].trim().toUpperCase();
+    }
+    else if (split.length == 3)
+    {
+      resType = split[1].trim().toUpperCase();
+    }
+    if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT"))
+    {
+      return "water";
+    }
+    else if (aaNames.containsKey(resType))
+    {
+      if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
+              || atom.equals("O") || atom.equals("H"))
+      {
+        return "mc";
+      }
+      else
+      {
+        return "sc";
+      }
+    }
+    else
+    {
+      return "other";
+    }
+  }
+
+  public static String[] getResKeyParts(String resKey)
+  {
+    // [pdbID[.modelNo]#][residueID][.chainID]
+    // pdbID := 4-character code | "URL" | "path"
+    String[] resKeyParts = new String[4];
+    String[] split = resKey.split("#");
+    String resChain = null;
+    // if no "#" then it is either only a pdb id or a residue or a chain
+    if (split.length == 1)
+    {
+      // pdb id without model
+      if (resKey.length() == 4 && resKey.indexOf("\\.") < 0)
+      {
+        parseModelID(resKey, resKeyParts);
+      }
+      // pdb link or file
+      else if (resKey.startsWith("\""))
+      {
+        parseModelID(resKey, resKeyParts);
+      }
+      // chain and residue or model and number
+      else
+      {
+        String[] splitSplit = resKey.split("\\.");
+        if (splitSplit.length == 1)
+        {
+          // only a chain or a residue
+          resChain = resKey;
+        }
+        else
+        {
+          try
+          {
+            // pdb with a model
+            Integer.parseInt(splitSplit[1]);
+            parseModelID(resKey, resKeyParts);
+          } catch (NumberFormatException ex)
+          {
+            // residue and chain
+            resChain = resKey;
+          }
+        }
+      }
+    }
+    else if (split.length == 2)
+    {
+      // model and residue+chain
+      parseModelID(split[0], resKeyParts);
+      resChain = split[1];
+    }
+    else
+    {
+      // model string with "#"
+      // TODO: [Optional] Are there more possibilities?
+      parseModelID(resKey.substring(0, resKey.lastIndexOf("#")),
+              resKeyParts);
+      resChain = resKey.substring(resKey.lastIndexOf("#") + 1,
+              resKey.length());
+    }
+    if (resChain != null)
+    {
+      // System.out.println(resChain);
+      String[] resChainSplit = resChain.split("\\.");
+      if (resChainSplit.length == 1)
+      {
+        // TODO: [Optional] Find a better way to distinguish between chain and
+        // residue
+        // if only one character and not an int, probably a chain
+        if (resChainSplit[0].length() == 1)
+        {
+          try
+          {
+            Integer.parseInt(resChainSplit[0]);
+            resKeyParts[3] = resChainSplit[0];
+          } catch (NumberFormatException ex)
+          {
+            resKeyParts[2] = resChainSplit[0];
+          }
+        }
+        else
+        {
+          resKeyParts[3] = resChainSplit[0];
+        }
+      }
+      else if (resChainSplit.length == 2)
+      {
+        resKeyParts[2] = resChainSplit[0];
+        resKeyParts[3] = resChainSplit[1];
+      }
+      else
+      {
+        // too many dots?
+        logger.info("Could not parse residue identifier: " + resKey);
+      }
+    }
+    // String print = "";
+    // for (int i = 0; i < resKeyParts.length; i++) {
+    // if (resKeyParts[i] == null) {
+    // print += i + ": null\t";
+    // } else {
+    // print += i + ": " + resKeyParts[i] + ";";
+    // }
+    // }
+    // System.out.println(print);
+    return resKeyParts;
+  }
+
+  public static void parseModelID(String modelID, String[] resKeyParts)
+  {
+    if (modelID.startsWith("\""))
+    {
+      if (modelID.endsWith("\""))
+      {
+        resKeyParts[0] = modelID.substring(1, modelID.length() - 1);
+        return;
+      }
+      else
+      {
+        try
+        {
+          Integer.parseInt(modelID.substring(modelID.lastIndexOf("\"") + 2,
+                  modelID.length()));
+          resKeyParts[0] = modelID.substring(0,
+                  modelID.lastIndexOf("\"") - 1);
+          resKeyParts[1] = modelID.substring(modelID.lastIndexOf("\"") + 2,
+                  modelID.length());
+        } catch (NumberFormatException ex)
+        {
+          resKeyParts[0] = modelID.substring(1);
+        }
+      }
+    }
+    else
+    {
+      String[] modelIDNo = modelID.split("\\.");
+      if (modelIDNo.length == 1)
+      {
+        resKeyParts[0] = modelIDNo[0];
+      }
+      else if (modelIDNo.length == 2)
+      {
+        try
+        {
+          Integer.parseInt(modelIDNo[1]);
+          resKeyParts[0] = modelIDNo[0];
+          resKeyParts[1] = modelIDNo[1];
+        } catch (NumberFormatException ex)
+        {
+          resKeyParts[0] = modelID;
+        }
+      }
+      else
+      {
+        logger.info("Could not parse model identifier: " + modelID);
+      }
+    }
+  }
+
+  /**
+   * This method takes a Cytoscape attribute specification
+   * ([structure#][residue][.chainID]) and returns the lowest-level object
+   * referenced by the spec. For example, if the spec is "1tkk", this method
+   * will return a ChimeraModel. If the spec is ".A", it will return a
+   * ChimeraChain, etc.
+   * 
+   * @param attrSpec
+   *          the specification string
+   * @param chimeraManager
+   *          the Chimera object we're currently using
+   * @return a ChimeraStructuralObject of the lowest type
+   */
+  public static ChimeraStructuralObject fromAttributeOld(String attrSpec,
+          ChimeraManager chimeraManager)
+  {
+    if (attrSpec == null || attrSpec.indexOf(',') > 0
+            || attrSpec.indexOf('-') > 0)
+    {
+      // No support for either lists or ranges
+      logger.warn("No support for identifier: " + attrSpec);
+      return null;
+    }
+
+    String residue = null;
+    String model = null;
+    String chain = null;
+
+    ChimeraModel chimeraModel = null;
+    ChimeraChain chimeraChain = null;
+    ChimeraResidue chimeraResidue = null;
+
+    // System.out.println("Getting object from attribute: "+attrSpec);
+    try
+    {
+      String[] split = attrSpec.split("#");
+      String resChain = null;
+      if (split.length == 1)
+      {
+        // no model
+        resChain = split[0];
+      }
+      else if (split.length == 2)
+      {
+        // model and rest
+        model = split[0];
+        resChain = split[1];
+      }
+      else
+      {
+        // model string with "#"
+        model = attrSpec.substring(0, attrSpec.lastIndexOf("#"));
+        resChain = attrSpec.substring(attrSpec.lastIndexOf("#") + 1,
+                attrSpec.length());
+      }
+      if (resChain != null)
+      {
+        String[] resChainSplit = resChain.split("\\.");
+        if (resChainSplit.length == 1)
+        {
+          residue = resChainSplit[0];
+        }
+        else if (resChainSplit.length == 2)
+        {
+          residue = resChainSplit[0];
+          chain = resChainSplit[1];
+        }
+        else
+        {
+          // too many dots?
+          logger.warn("No support for identifier: " + attrSpec);
+        }
+      }
+
+      // if (split.length == 1) {
+      // // No model
+      // residue = split[0];
+      // } else if (split.length == 3) {
+      // // We have all three
+      // model = split[0];
+      // residue = split[1];
+      // chain = split[2];
+      // } else if (split.length == 2 && attrSpec.indexOf('#') > 0) {
+      // // Model and Residue
+      // model = split[0];
+      // residue = split[1];
+      // } else {
+      // // Residue and Chain
+      // residue = split[0];
+      // chain = split[1];
+      // }
+
+      // System.out.println("model = " + model + " chain = " + chain +
+      // " residue = " +
+      // residue);
+      if (model != null)
+      {
+        List models = chimeraManager.getChimeraModels(model,
+                ModelType.PDB_MODEL);
+        if (models.size() == 1)
+        {
+          chimeraModel = models.get(0);
+        }
+        else
+        {
+          try
+          {
+            chimeraModel = chimeraManager.getChimeraModel(
+                    Integer.valueOf(model), 0);
+          } catch (NumberFormatException ex)
+          {
+            // ignore
+          }
+        }
+      }
+      if (chimeraModel == null)
+      {
+        chimeraModel = chimeraManager.getChimeraModel();
+      }
+      // System.out.println("ChimeraModel = " + chimeraModel);
+
+      if (chain != null)
+      {
+        chimeraChain = chimeraModel.getChain(chain);
+        // System.out.println("ChimeraChain = " + chimeraChain);
+      }
+      if (residue != null)
+      {
+        if (chimeraChain != null)
+        {
+          chimeraResidue = chimeraChain.getResidue(residue);
+        }
+        else
+        {
+          chimeraResidue = chimeraModel.getResidue("_", residue);
+        }
+        // System.out.println("ChimeraResidue = " + chimeraResidue);
+      }
+
+      if (chimeraResidue != null)
+        return chimeraResidue;
+
+      if (chimeraChain != null)
+        return chimeraChain;
+
+      if (chimeraModel != null)
+        return chimeraModel;
+
+    } catch (Exception ex)
+    {
+      logger.warn("Could not parse residue identifier: " + attrSpec, ex);
+    }
+    return null;
+  }
+
+  public static ChimeraStructuralObject fromAttribute(String attrSpec,
+          ChimeraManager chimeraManager)
+  {
+    // TODO: Make sure it is OK to remove this: || attrSpec.indexOf('-') > 0
+    if (attrSpec == null || attrSpec.indexOf(',') > 0)
+    {
+      // No support for either lists or ranges
+      // System.out.println("No support for identifier: " + attrSpec);
+      logger.warn("No support for identifier: " + attrSpec);
+      return null;
+    }
+    String[] modelIDNoResChain = getResKeyParts(attrSpec);
+
+    ChimeraModel chimeraModel = null;
+    ChimeraChain chimeraChain = null;
+    ChimeraResidue chimeraResidue = null;
+
+    // System.out.println("Getting object from attribute: "+attrSpec);
+    try
+    {
+      if (modelIDNoResChain[0] != null)
+      {
+        String modelID = modelIDNoResChain[0];
+        List models = chimeraManager.getChimeraModels(
+                modelID, ModelType.PDB_MODEL);
+        if (models.size() == 1)
+        { // usual case with only one model
+          chimeraModel = models.get(0);
+        }
+        else if (models.size() > 1 && modelIDNoResChain[1] != null)
+        {
+          // there are several submodels
+          try
+          {
+            int modelNo = Integer.valueOf(modelIDNoResChain[1]);
+            for (ChimeraModel model : models)
+            {
+              if (model.getSubModelNumber() == modelNo)
+              {
+                chimeraModel = model;
+                break;
+              }
+            }
+          } catch (NumberFormatException ex)
+          {
+            // ignore
+          }
+        }
+        else
+        {
+          // TODO: [Optional] What is this doing?
+          try
+          {
+            chimeraModel = chimeraManager.getChimeraModel(
+                    Integer.valueOf(modelID), 0);
+          } catch (NumberFormatException ex)
+          {
+            // ignore
+          }
+        }
+      }
+      if (chimeraModel == null)
+      {
+        // TODO: [Optional] Find a better way to handle this case
+        // If no model can be matched, continue
+        // System.out.println("No matching model could be find for " +
+        // attrSpec);
+        return null;
+        // chimeraModel = chimeraManager.getChimeraModel();
+        // logger.warn("No matching model could be find for " + attrSpec +
+        // ". Trying with "
+        // + chimeraModel.toSpec());
+      }
+      // System.out.println("ChimeraModel = " + chimeraModel);
+
+      if (modelIDNoResChain[3] != null)
+      {
+        chimeraChain = chimeraModel.getChain(modelIDNoResChain[3]);
+        // System.out.println("ChimeraChain = " + chimeraChain);
+      }
+      if (modelIDNoResChain[2] != null)
+      {
+        String residue = modelIDNoResChain[2];
+        if (chimeraChain != null)
+        {
+          chimeraResidue = chimeraChain.getResidue(residue);
+        }
+        else if (chimeraModel.getChain("_") != null)
+        {
+          chimeraResidue = chimeraModel.getResidue("_", residue);
+        }
+        else if (chimeraModel.getChainCount() == 1)
+        {
+          chimeraResidue = chimeraModel.getResidue(chimeraModel
+                  .getChainNames().iterator().next(), residue);
+        }
+        // System.out.println("ChimeraResidue = " + chimeraResidue);
+      }
+
+      if (chimeraResidue != null)
+        return chimeraResidue;
+
+      if (chimeraChain != null)
+        return chimeraChain;
+
+      if (chimeraModel != null)
+        return chimeraModel;
+
+    } catch (Exception ex)
+    {
+      // System.out.println("Could not parse chimera identifier: " +
+      // attrSpec+"("+ex.getMessage()+")");
+      logger.warn("Could not parse chimera identifier: " + attrSpec, ex);
+    }
+    return null;
+  }
+
+  /**
+   * Search for structure references in the residue list
+   * 
+   * @param residueList
+   *          the list of residues
+   * @return a concatenated list of structures encoded in the list
+   */
+  public static String findStructures(String residueList)
+  {
+    if (residueList == null)
+      return null;
+    String[] residues = residueList.split(",");
+    Map structureNameMap = new HashMap();
+    for (int i = 0; i < residues.length; i++)
+    {
+      String[] components = residues[i].split("#");
+      if (components.length > 1)
+      {
+        structureNameMap.put(components[0], components[1]);
+      }
+    }
+    if (structureNameMap.isEmpty())
+      return null;
+
+    String structure = null;
+    for (String struct : structureNameMap.keySet())
+    {
+      if (structure == null)
+        structure = new String();
+      else
+        structure = structure.concat(",");
+      structure = structure.concat(struct);
+    }
+    return structure;
+  }
+
+  // invoked by openStructures in StructureManager
+  public static List parseFuncRes(List residueNames,
+          String modelName)
+  {
+    List resRanges = new ArrayList();
+    for (int i = 0; i < residueNames.size(); i++)
+    {
+      String residue = residueNames.get(i);
+      // Parse out the structure, if there is one
+      String[] components = residue.split("#");
+      if (components.length > 1 && !modelName.equals(components[0]))
+      {
+        continue;
+      }
+      else if (components.length > 1)
+      {
+        residue = components[1];
+      }
+      else if (components.length == 1)
+      {
+        residue = components[0];
+      }
+      // Check to see if we have a range-spec
+      String resRange = "";
+      if (residue == null || residue.equals("") || residue.length() == 0)
+      {
+        continue;
+      }
+      String[] range = residue.split("-", 2);
+      String chain = null;
+      for (int res = 0; res < range.length; res++)
+      {
+        if (res == 1)
+        {
+          resRange = resRange.concat("-");
+          if (chain != null && range[res].indexOf('.') == -1)
+            range[res] = range[res].concat("." + chain);
+        }
+
+        if (res == 0 && range.length >= 2 && range[res].indexOf('.') > 0)
+        {
+          // This is a range spec with the leading residue containing a chain
+          // spec
+          String[] resChain = range[res].split("\\.");
+          chain = resChain[1];
+          range[res] = resChain[0];
+        }
+        // Fix weird SFLD syntax...
+        if (range[res].indexOf('|') > 0
+                && Character.isDigit(range[res].charAt(0)))
+        {
+          int offset = range[res].indexOf('|');
+          String str = range[res].substring(offset + 1)
+                  + range[res].substring(0, offset);
+          range[res] = str;
+        }
+
+        // Convert to legal atom-spec
+        if (Character.isDigit(range[res].charAt(0)))
+        {
+          resRange = resRange.concat(range[res]);
+        }
+        else if (Character.isDigit(range[res].charAt(1)))
+        {
+          resRange = resRange.concat(range[res].substring(1));
+        }
+        else if (range[res].charAt(0) == '.')
+        {
+          // Do we have a chain spec?
+          resRange = resRange.concat(range[res]);
+        }
+        else
+        {
+          resRange = resRange.concat(range[res].substring(3));
+        }
+      }
+      if (!resRanges.contains(resRange))
+      {
+        resRanges.add(resRange);
+      }
+    }
+    return resRanges;
+  }
+
+  static
+  {
+    aaNames = new HashMap();
+    aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
+    aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
+    aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
+    aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
+    aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
+    aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
+    aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
+    aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
+    aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
+    aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
+    aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
+    aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
+    aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
+    aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
+    aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+    aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
+    aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
+    aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
+    aaNames.put("TRP",
+            "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
+    aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
+    aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
+    aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
+    aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
+    aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
+    aaNames.put("HOH", "HOH HOH Water [H]O[H]");
+  }
+
+  /**
+   * Convert the amino acid type to a full name
+   * 
+   * @param aaType
+   *          the residue type to convert
+   * @return the full name of the residue
+   */
+  public static String toFullName(String aaType)
+  {
+    if (!aaNames.containsKey(aaType))
+      return aaType;
+    String[] ids = ((String) aaNames.get(aaType)).split(" ");
+    return ids[2].replace('_', ' ');
+  }
+
+  /**
+   * Convert the amino acid type to a single letter
+   * 
+   * @param aaType
+   *          the residue type to convert
+   * @return the single letter representation of the residue
+   */
+  public static String toSingleLetter(String aaType)
+  {
+    if (!aaNames.containsKey(aaType))
+      return aaType;
+    String[] ids = ((String) aaNames.get(aaType)).split(" ");
+    return ids[0];
+  }
+
+  /**
+   * Convert the amino acid type to three letters
+   * 
+   * @param aaType
+   *          the residue type to convert
+   * @return the three letter representation of the residue
+   */
+  public static String toThreeLetter(String aaType)
+  {
+    if (!aaNames.containsKey(aaType))
+      return aaType;
+    String[] ids = ((String) aaNames.get(aaType)).split(" ");
+    return ids[1];
+  }
+
+  /**
+   * Convert the amino acid type to its SMILES string
+   * 
+   * @param aaType
+   *          the residue type to convert
+   * @return the SMILES representation of the residue
+   */
+  public static String toSMILES(String aaType)
+  {
+    if (!aaNames.containsKey(aaType))
+      return null;
+    String[] ids = ((String) aaNames.get(aaType)).split(" ");
+    if (ids.length < 4)
+      return null;
+    return ids[3];
+  }
+
+  public static String getAlignName(ChimeraStructuralObject chimObj)
+  {
+    String name = chimObj.getChimeraModel().toString();
+    if (chimObj instanceof ChimeraChain)
+    {
+      name = ((ChimeraChain) chimObj).toString() + " [" + name + "]";
+    }
+    return name;
+  }
 }
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
index 92193f2..9a29a99 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
@@ -44,287 +44,329 @@ import java.util.TreeMap;
  * 
  */
 // TODO: [Optional] Implement toAttr() method
-public class ChimeraChain implements ChimeraStructuralObject {
+public class ChimeraChain implements ChimeraStructuralObject
+{
 
-	/**
-	 * The model/subModel number this chain is a part of
-	 */
-	private int modelNumber;
-	private int subModelNumber;
+  /**
+   * The model/subModel number this chain is a part of
+   */
+  private int modelNumber;
 
-	/**
-	 * A pointer to the model this chain is a part of
-	 */
-	private ChimeraModel chimeraModel;
+  private int subModelNumber;
 
-	/**
-	 * The chainID (from the PDB record)
-	 */
-	private String chainId;
+  /**
+   * A pointer to the model this chain is a part of
+   */
+  private ChimeraModel chimeraModel;
 
-	/**
-	 * The residues that are part of this chain
-	 */
-	private TreeMap residueMap;
+  /**
+   * The chainID (from the PDB record)
+   */
+  private String chainId;
 
-	/**
-	 * userData to associate with this chain
-	 */
-	private Object userData;
+  /**
+   * The residues that are part of this chain
+   */
+  private TreeMap residueMap;
 
-	/**
-	 * Flag to indicate the selection state
-	 */
-	private boolean selected = false;
+  /**
+   * userData to associate with this chain
+   */
+  private Object userData;
 
-	/**
-	 * Constructor to create a new ChimeraChain
-	 * 
-	 * @param model
-	 *          the model number this chain is part of
-	 * @param subModel
-	 *          the subModel number this chain is part of
-	 * @param chainId
-	 *          the chain ID for this chain
-	 */
-	public ChimeraChain(int model, int subModel, String chainId) {
-		this.modelNumber = model;
-		this.subModelNumber = subModel;
-		this.chainId = chainId;
-		residueMap = new TreeMap();
-	}
+  /**
+   * Flag to indicate the selection state
+   */
+  private boolean selected = false;
 
-	/**
-	 * set the selected state of this chain
-	 * 
-	 * @param selected
-	 *          a boolean to set the selected state to
-	 */
-	public void setSelected(boolean selected) {
-		this.selected = selected;
-	}
+  /**
+   * Constructor to create a new ChimeraChain
+   * 
+   * @param model
+   *          the model number this chain is part of
+   * @param subModel
+   *          the subModel number this chain is part of
+   * @param chainId
+   *          the chain ID for this chain
+   */
+  public ChimeraChain(int model, int subModel, String chainId)
+  {
+    this.modelNumber = model;
+    this.subModelNumber = subModel;
+    this.chainId = chainId;
+    residueMap = new TreeMap();
+  }
 
-	/**
-	 * return the selected state of this chain
-	 * 
-	 * @return the selected state
-	 */
-	public boolean isSelected() {
-		return selected;
-	}
+  /**
+   * set the selected state of this chain
+   * 
+   * @param selected
+   *          a boolean to set the selected state to
+   */
+  public void setSelected(boolean selected)
+  {
+    this.selected = selected;
+  }
 
-	public boolean hasSelectedChildren() {
-		if (selected) {
-			return true;
-		} else {
-			for (ChimeraResidue residue : getResidues()) {
-				if (residue.isSelected())
-					return true;
-			}
-		}
-		return false;
-	}
+  /**
+   * return the selected state of this chain
+   * 
+   * @return the selected state
+   */
+  public boolean isSelected()
+  {
+    return selected;
+  }
 
-	/**
-	 * Return the list of selected residues
-	 * 
-	 * @return all selected residues
-	 */
-	public List getSelectedResidues() {
-		List residueList = new ArrayList();
-		if (selected) {
-			residueList.addAll(getResidues());
-		} else {
-			for (ChimeraResidue residue : getResidues()) {
-				if (residue.isSelected())
-					residueList.add(residue);
-			}
-		}
-		return residueList;
-	}
+  public boolean hasSelectedChildren()
+  {
+    if (selected)
+    {
+      return true;
+    }
+    else
+    {
+      for (ChimeraResidue residue : getResidues())
+      {
+        if (residue.isSelected())
+          return true;
+      }
+    }
+    return false;
+  }
 
-	/**
-	 * Add a residue to the chain.
-	 * 
-	 * @param residue
-	 *          the ChimeraResidue to add to the chain.
-	 */
-	public void addResidue(ChimeraResidue residue) {
-		String index = residue.getIndex();
-		// Put it in our map so that we can return it in order
-		residueMap.put(index, residue);
-	}
+  /**
+   * Return the list of selected residues
+   * 
+   * @return all selected residues
+   */
+  public List getSelectedResidues()
+  {
+    List residueList = new ArrayList();
+    if (selected)
+    {
+      residueList.addAll(getResidues());
+    }
+    else
+    {
+      for (ChimeraResidue residue : getResidues())
+      {
+        if (residue.isSelected())
+          residueList.add(residue);
+      }
+    }
+    return residueList;
+  }
 
-	/**
-	 * Return the list of residues in this chain in pdb residue order
-	 * 
-	 * @return a Collection of residues in residue order
-	 */
-	public Collection getResidues() {
-		return residueMap.values();
-	}
+  /**
+   * Add a residue to the chain.
+   * 
+   * @param residue
+   *          the ChimeraResidue to add to the chain.
+   */
+  public void addResidue(ChimeraResidue residue)
+  {
+    String index = residue.getIndex();
+    // Put it in our map so that we can return it in order
+    residueMap.put(index, residue);
+  }
 
-	/**
-	 * Return the list of residues in this chain as a list
-	 * 
-	 * @return List of residues
-	 */
-	public List getChildren() {
-		return new ArrayList(residueMap.values());
-	}
+  /**
+   * Return the list of residues in this chain in pdb residue order
+   * 
+   * @return a Collection of residues in residue order
+   */
+  public Collection getResidues()
+  {
+    return residueMap.values();
+  }
 
-	/**
-	 * Get a specific residue
-	 * 
-	 * @param residueIndex
-	 *          String representation of the residue index
-	 * @return the ChimeraResidue represented by the residueIndex
-	 */
-	public ChimeraResidue getResidue(String index) {
-		// Integer index = new Integer(residueIndex);
-		if (residueMap.containsKey(index))
-			return residueMap.get(index);
-		return null;
-	}
+  /**
+   * Return the list of residues in this chain as a list
+   * 
+   * @return List of residues
+   */
+  public List getChildren()
+  {
+    return new ArrayList(residueMap.values());
+  }
 
-	/**
-	 * Get a list of residues as a residue range
-	 * 
-	 * @param residueRange
-	 *          String representation of the residue range
-	 * @return the List of ChimeraResidues represented by the range
-	 */
-	public List getResidueRange(String residueRange) {
-		String[] range = residueRange.split("-", 2);
-		if (range[1] == null || range[1].length() == 0) {
-			range[1] = range[0];
-		}
-		List resultRange = new ArrayList();
-		int start = Integer.parseInt(range[0]);
-		int end = Integer.parseInt(range[1]);
-		for (int i = start; i <= end; i++) {
-			String index = String.valueOf(i);
-			if (residueMap.containsKey(index))
-				resultRange.add(residueMap.get(index));
-		}
-		return resultRange;
-	}
+  /**
+   * Get a specific residue
+   * 
+   * @param residueIndex
+   *          String representation of the residue index
+   * @return the ChimeraResidue represented by the residueIndex
+   */
+  public ChimeraResidue getResidue(String index)
+  {
+    // Integer index = new Integer(residueIndex);
+    if (residueMap.containsKey(index))
+      return residueMap.get(index);
+    return null;
+  }
 
-	/**
-	 * Get the ID for this chain
-	 * 
-	 * @return String value of the chainId
-	 */
-	public String getChainId() {
-		return chainId;
-	}
+  /**
+   * Get a list of residues as a residue range
+   * 
+   * @param residueRange
+   *          String representation of the residue range
+   * @return the List of ChimeraResidues represented by the range
+   */
+  public List getResidueRange(String residueRange)
+  {
+    String[] range = residueRange.split("-", 2);
+    if (range[1] == null || range[1].length() == 0)
+    {
+      range[1] = range[0];
+    }
+    List resultRange = new ArrayList();
+    int start = Integer.parseInt(range[0]);
+    int end = Integer.parseInt(range[1]);
+    for (int i = start; i <= end; i++)
+    {
+      String index = String.valueOf(i);
+      if (residueMap.containsKey(index))
+        resultRange.add(residueMap.get(index));
+    }
+    return resultRange;
+  }
 
-	/**
-	 * Get the model number for this chain
-	 * 
-	 * @return the model number
-	 */
-	public int getModelNumber() {
-		return modelNumber;
-	}
+  /**
+   * Get the ID for this chain
+   * 
+   * @return String value of the chainId
+   */
+  public String getChainId()
+  {
+    return chainId;
+  }
 
-	/**
-	 * Get the sub-model number for this chain
-	 * 
-	 * @return the sub-model number
-	 */
-	public int getSubModelNumber() {
-		return subModelNumber;
-	}
+  /**
+   * Get the model number for this chain
+   * 
+   * @return the model number
+   */
+  public int getModelNumber()
+  {
+    return modelNumber;
+  }
 
-	/**
-	 * Return a string representation of this chain as follows: Chain chainId
-	 * (residue_count residues)
-	 * 
-	 * @return String representation of chain
-	 */
-	public String displayName() {
-		if (chainId.equals("_")) {
-			return ("Chain (no ID) (" + getResidueCount() + " residues)");
-		} else {
-			return ("Chain " + chainId + " (" + getResidueCount() + " residues)");
-		}
-	}
+  /**
+   * Get the sub-model number for this chain
+   * 
+   * @return the sub-model number
+   */
+  public int getSubModelNumber()
+  {
+    return subModelNumber;
+  }
 
-	/**
-	 * Return a string representation of this chain as follows: Node xxx [Model yyyy Chain
-	 * chainId]
-	 * 
-	 * @return String representation of chain
-	 */
-	public String toString() {
-		String displayName = chimeraModel.getModelName();
-		if (displayName.length() > 14)
-			displayName = displayName.substring(0, 13) + "...";
-		if (chainId.equals("_")) {
-			return (displayName + " Chain (no ID) (" + getResidueCount() + " residues)");
-		} else {
-			return (displayName + " Chain " + chainId + " (" + getResidueCount() + " residues)");
-		}
-	}
+  /**
+   * Return a string representation of this chain as follows: Chain
+   * chainId (residue_count residues)
+   * 
+   * @return String representation of chain
+   */
+  public String displayName()
+  {
+    if (chainId.equals("_"))
+    {
+      return ("Chain (no ID) (" + getResidueCount() + " residues)");
+    }
+    else
+    {
+      return ("Chain " + chainId + " (" + getResidueCount() + " residues)");
+    }
+  }
 
-	/**
-	 * Return the Chimera specification for this chain
-	 * 
-	 * @return Chimera specification
-	 */
-	public String toSpec() {
-		if (chainId.equals("_")) {
-			return ("#" + modelNumber + "." + subModelNumber + ":.");
-		} else {
-			return ("#" + modelNumber + "." + subModelNumber + ":." + chainId);
-		}
-	}
+  /**
+   * Return a string representation of this chain as follows: Node xxx [Model
+   * yyyy Chain chainId]
+   * 
+   * @return String representation of chain
+   */
+  public String toString()
+  {
+    String displayName = chimeraModel.getModelName();
+    if (displayName.length() > 14)
+      displayName = displayName.substring(0, 13) + "...";
+    if (chainId.equals("_"))
+    {
+      return (displayName + " Chain (no ID) (" + getResidueCount() + " residues)");
+    }
+    else
+    {
+      return (displayName + " Chain " + chainId + " (" + getResidueCount() + " residues)");
+    }
+  }
 
-	/**
-	 * Return the number of residues in this chain
-	 * 
-	 * @return integer number of residues
-	 */
-	public int getResidueCount() {
-		return residueMap.size();
-	}
+  /**
+   * Return the Chimera specification for this chain
+   * 
+   * @return Chimera specification
+   */
+  public String toSpec()
+  {
+    if (chainId.equals("_"))
+    {
+      return ("#" + modelNumber + "." + subModelNumber + ":.");
+    }
+    else
+    {
+      return ("#" + modelNumber + "." + subModelNumber + ":." + chainId);
+    }
+  }
 
-	/**
-	 * Set the ChimeraModel for this chain
-	 * 
-	 * @param model
-	 *          ChimeraModel to associate with this chain
-	 */
-	public void setChimeraModel(ChimeraModel model) {
-		this.chimeraModel = model;
-	}
+  /**
+   * Return the number of residues in this chain
+   * 
+   * @return integer number of residues
+   */
+  public int getResidueCount()
+  {
+    return residueMap.size();
+  }
 
-	/**
-	 * Get the ChimeraModel for this chain
-	 * 
-	 * @return ChimeraModel associated with this chain
-	 */
-	public ChimeraModel getChimeraModel() {
-		return chimeraModel;
-	}
+  /**
+   * Set the ChimeraModel for this chain
+   * 
+   * @param model
+   *          ChimeraModel to associate with this chain
+   */
+  public void setChimeraModel(ChimeraModel model)
+  {
+    this.chimeraModel = model;
+  }
 
-	/**
-	 * Get the user data for this Chain
-	 * 
-	 * @return user data
-	 */
-	public Object getUserData() {
-		return userData;
-	}
+  /**
+   * Get the ChimeraModel for this chain
+   * 
+   * @return ChimeraModel associated with this chain
+   */
+  public ChimeraModel getChimeraModel()
+  {
+    return chimeraModel;
+  }
 
-	/**
-	 * Set the user data for this Chain
-	 * 
-	 * @param data
-	 *          the user data to associate with this chain
-	 */
-	public void setUserData(Object data) {
-		this.userData = data;
-	}
+  /**
+   * Get the user data for this Chain
+   * 
+   * @return user data
+   */
+  public Object getUserData()
+  {
+    return userData;
+  }
+
+  /**
+   * Set the user data for this Chain
+   * 
+   * @param data
+   *          the user data to associate with this chain
+   */
+  public void setUserData(Object data)
+  {
+    this.userData = data;
+  }
 }
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index d53d498..2de2829 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -302,13 +302,12 @@ public class ChimeraManager
     // TODO: [Optional] Convert path to name in a better way
     if (modelPath.lastIndexOf(File.separator) > 0)
     {
-      modelName = modelPath.substring(modelPath
-              .lastIndexOf(File.separator) + 1);
+      modelName = modelPath
+              .substring(modelPath.lastIndexOf(File.separator) + 1);
     }
     else if (modelPath.lastIndexOf("/") > 0)
     {
-      modelName = modelPath
-              .substring(modelPath.lastIndexOf("/") + 1);
+      modelName = modelPath.substring(modelPath.lastIndexOf("/") + 1);
     }
     return modelName;
   }
@@ -355,7 +354,8 @@ public class ChimeraManager
   public void startListening(String uri)
   {
     sendChimeraCommand("listen start models url " + uri
-    + ";listen start select prefix SelectionChanged url " + uri, false);
+            + ";listen start select prefix SelectionChanged url " + uri,
+            false);
   }
 
   /**
@@ -379,7 +379,7 @@ public class ChimeraManager
   {
     chimera = null;
     currentModelsMap.clear();
-      this.chimeraRestPort = 0;
+    this.chimeraRestPort = 0;
     structureManager.clearOnChimeraExit();
   }
 
@@ -630,8 +630,7 @@ public class ChimeraManager
     } catch (Exception e)
     {
       logger.error("Failed to get REST port number from " + responses
-              + ": "
-              + e.getMessage());
+              + ": " + e.getMessage());
     } finally
     {
       try
@@ -776,7 +775,7 @@ public class ChimeraManager
    */
   public List sendChimeraCommand(String command, boolean reply)
   {
-//    System.out.println("chimeradebug>> " + command);
+    // System.out.println("chimeradebug>> " + command);
     if (!isChimeraLaunched() || command == null
             || "".equals(command.trim()))
     {
@@ -827,11 +826,13 @@ public class ChimeraManager
 
     List reply = new ArrayList();
     BufferedReader response = null;
-    try {
+    try
+    {
       response = HttpClientUtils
               .doHttpUrlPost(restUrl, commands, 100, 5000);
       String line = "";
-      while ((line = response.readLine()) != null) {
+      while ((line = response.readLine()) != null)
+      {
         reply.add(line);
       }
     } catch (Exception e)
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java
index 432c6fb..0700565 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java
@@ -3,464 +3,555 @@ package ext.edu.ucsf.rbvi.strucviz2;
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 import java.util.TreeMap;
 
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
 
 /**
- * This class provides the implementation for the ChimeraModel, ChimeraChain, and ChimeraResidue
- * objects
+ * This class provides the implementation for the ChimeraModel, ChimeraChain,
+ * and ChimeraResidue objects
  * 
  * @author scooter
  * 
  */
-public class ChimeraModel implements ChimeraStructuralObject {
-
-	private String name; // The name of this model
-	private ModelType type; // The type of the model
-	private int modelNumber; // The model number
-	private int subModelNumber; // The sub-model number
-
-	private Color modelColor = null; // The color of this model (from Chimera)
-	private Object userData = null; // User data associated with this model
-	private boolean selected = false; // The selected state of this model
-
-	private TreeMap chainMap; // The list of chains
-	// private TreeMap residueMap; // The list of residues
-	private HashSet funcResidues; // List of functional residues
-
-	/**
-	 * Constructor to create a model
-	 * 
-	 * @param name
-	 *            the name of this model
-	 * @param color
-	 *            the model Color
-	 * @param modelNumber
-	 *            the model number
-	 * @param subModelNumber
-	 *            the sub-model number
-	 */
-	public ChimeraModel(String name, ModelType type, int modelNumber, int subModelNumber) {
-		this.name = name;
-		this.type = type;
-		this.modelNumber = modelNumber;
-		this.subModelNumber = subModelNumber;
-
-		this.chainMap = new TreeMap();
-		this.funcResidues = new HashSet();
-	}
-
-	/**
-	 * Constructor to create a model from the Chimera input line
-	 * 
-	 * @param inputLine
-	 *            Chimera input line from which to construct this model
-	 */
-	// TODO: [Optional] How to distinguish between PDB and MODBASE?
-	// invoked when listing models: listm type molecule; lists level molecule
-	// line = model id #0 type Molecule name 1ert
-	public ChimeraModel(String inputLine) {
-		this.name = ChimUtils.parseModelName(inputLine);
-		// TODO: [Optional] Write a separate method to get model type
-		if (name.startsWith("smiles")) {
-			this.type = ModelType.SMILES;
-		} else {
-			this.type = ModelType.PDB_MODEL;
-		}
-		this.modelNumber = ChimUtils.parseModelNumber(inputLine)[0];
-		this.subModelNumber = ChimUtils.parseModelNumber(inputLine)[1];
-
-		this.chainMap = new TreeMap();
-		this.funcResidues = new HashSet();
-	}
-
-	/**
-	 * Add a residue to this model
-	 * 
-	 * @param residue
-	 *            to add to the model
-	 */
-	public void addResidue(ChimeraResidue residue) {
-		residue.setChimeraModel(this);
-		// residueMap.put(residue.getIndex(), residue);
-		String chainId = residue.getChainId();
-		if (chainId != null) {
-			addResidue(chainId, residue);
-		} else {
-			addResidue("_", residue);
-		}
-		// Put it in our map so that we can return it in order
-		// residueMap.put(residue.getIndex(), residue);
-	}
-
-	/**
-	 * Add a residue to a chain in this model. If the chain associated with chainId doesn't exist,
-	 * it will be created.
-	 * 
-	 * @param chainId
-	 *            to add the residue to
-	 * @param residue
-	 *            to add to the chain
-	 */
-	public void addResidue(String chainId, ChimeraResidue residue) {
-		ChimeraChain chain = null;
-		if (!chainMap.containsKey(chainId)) {
-			chain = new ChimeraChain(this.modelNumber, this.subModelNumber, chainId);
-			chain.setChimeraModel(this);
-			chainMap.put(chainId, chain);
-		} else {
-			chain = chainMap.get(chainId);
-		}
-		chain.addResidue(residue);
-	}
-
-	/**
-	 * Get the ChimeraModel (required for ChimeraStructuralObject interface)
-	 * 
-	 * @return ChimeraModel
-	 */
-	public ChimeraModel getChimeraModel() {
-		return this;
-	}
-
-	/**
-	 * Get the model color of this model
-	 * 
-	 * @return model color of this model
-	 */
-	public Color getModelColor() {
-		return this.modelColor;
-	}
-
-	/**
-	 * Set the color of this model
-	 * 
-	 * @param color
-	 *            Color of this model
-	 */
-	public void setModelColor(Color color) {
-		this.modelColor = color;
-	}
-
-	/**
-	 * Return the name of this model
-	 * 
-	 * @return model name
-	 */
-	public String getModelName() {
-		return name;
-	}
-
-	/**
-	 * Set the name of this model
-	 * 
-	 * @param name
-	 *            model name
-	 */
-	public void setModelName(String name) {
-		this.name = name;
-	}
-
-	/**
-	 * Get the model number of this model
-	 * 
-	 * @return integer model number
-	 */
-	public int getModelNumber() {
-		return modelNumber;
-	}
-
-	/**
-	 * Set the model number of this model
-	 * 
-	 * @param modelNumber
-	 *            integer model number
-	 */
-	public void setModelNumber(int modelNumber) {
-		this.modelNumber = modelNumber;
-	}
-
-	/**
-	 * Get the sub-model number of this model
-	 * 
-	 * @return integer sub-model number
-	 */
-	public int getSubModelNumber() {
-		return subModelNumber;
-	}
-
-	/**
-	 * Set the sub-model number of this model
-	 * 
-	 * @param subModelNumber
-	 *            integer model number
-	 */
-	public void setSubModelNumber(int subModelNumber) {
-		this.subModelNumber = subModelNumber;
-	}
-
-	public ModelType getModelType() {
-		return type;
-	}
-
-	public void setModelType(ModelType type) {
-		this.type = type;
-	}
-
-	public HashSet getFuncResidues() {
-		return funcResidues;
-	}
-
-	public void setFuncResidues(List residues) {
-		for (String residue : residues) {
-			for (ChimeraChain chain : getChains()) {
-				if (residue.indexOf("-") > 0) {
-					funcResidues.addAll(chain.getResidueRange(residue));
-				} else {
-					funcResidues.add(chain.getResidue(residue));
-				}
-			}
-		}
-	}
-
-	/**
-	 * Get the user data for this model
-	 * 
-	 * @return user data
-	 */
-	public Object getUserData() {
-		return userData;
-	}
-
-	/**
-	 * Set the user data for this model
-	 * 
-	 * @param data
-	 *            user data to associate with this model
-	 */
-	public void setUserData(Object data) {
-		this.userData = data;
-	}
-
-	/**
-	 * Return the selected state of this model
-	 * 
-	 * @return the selected state
-	 */
-	public boolean isSelected() {
-		return selected;
-	}
-
-	/**
-	 * Set the selected state of this model
-	 * 
-	 * @param selected
-	 *            a boolean to set the selected state to
-	 */
-	public void setSelected(boolean selected) {
-		this.selected = selected;
-	}
-
-	/**
-	 * Return the chains in this model as a List
-	 * 
-	 * @return the chains in this model as a list
-	 */
-	public List getChildren() {
-		return new ArrayList(chainMap.values());
-	}
-
-	/**
-	 * Return the chains in this model as a colleciton
-	 * 
-	 * @return the chains in this model
-	 */
-	public Collection getChains() {
-		return chainMap.values();
-	}
-
-	/**
-	 * Get the number of chains in this model
-	 * 
-	 * @return integer chain count
-	 */
-	public int getChainCount() {
-		return chainMap.size();
-	}
-
-	/**
-	 * Get the list of chain names associated with this model
-	 * 
-	 * @return return the list of chain names for this model
-	 */
-	public Collection getChainNames() {
-		return chainMap.keySet();
-	}
-
-	/**
-	 * Get the residues associated with this model
-	 * 
-	 * @return the list of residues in this model
-	 */
-	public Collection getResidues() {
-		Collection residues = new ArrayList();
-		for (ChimeraChain chain : getChains()) {
-			residues.addAll(chain.getResidues());
-		}
-		return residues;
-	}
-
-	/**
-	 * Get the number of residues in this model
-	 * 
-	 * @return integer residues count
-	 */
-	public int getResidueCount() {
-		int count = 0;
-		for (ChimeraChain chain : getChains()) {
-			count += chain.getResidueCount();
-		}
-		return count;
-	}
-
-	/**
-	 * Get a specific chain from the model
-	 * 
-	 * @param chain
-	 *            the ID of the chain to return
-	 * @return ChimeraChain associated with the chain
-	 */
-	public ChimeraChain getChain(String chain) {
-		if (chainMap.containsKey(chain)) {
-			return chainMap.get(chain);
-		}
-		return null;
-	}
-
-	/**
-	 * Return a specific residue based on its index
-	 * 
-	 * @param index
-	 *            of the residue to return
-	 * @return the residue associated with that index
-	 */
-	public ChimeraResidue getResidue(String chainId, String index) {
-		if (chainMap.containsKey(chainId)) {
-			return chainMap.get(chainId).getResidue(index);
-		}
-		return null;
-	}
-
-	/**
-	 * Checks if this model has selected children.
-	 */
-	public boolean hasSelectedChildren() {
-		if (selected) {
-			return true;
-		} else {
-			for (ChimeraChain chain : getChains()) {
-				if (chain.hasSelectedChildren()) {
-					return true;
-				}
-			}
-		}
-		return false;
-	}
-
-	/**
-	 * Return the list of selected residues
-	 * 
-	 * @return all selected residues
-	 */
-	public List getSelectedResidues() {
-		List residueList = new ArrayList();
-		for (ChimeraChain chain : getChains()) {
-			if (selected) {
-				residueList.addAll(chain.getSelectedResidues());
-			} else {
-				residueList.addAll(getResidues());
-			}
-		}
-		return residueList;
-	}
-
-
-	/**
-	 * Return the Chimera specification for this model.
-	 */
-	public String toSpec() {
-		if (subModelNumber == 0)
-			return ("#" + modelNumber);
-		return ("#" + modelNumber + "." + subModelNumber);
-	}
-
-	/**
-	 * Return a string representation for the model. Shorten if longer than 100 characters.
-	 */
-	public String toString() {
-		String modelName = "";
-		// TODO: [Optional] Change cutoff for shortening model names in the structure naviagator dialog
-		if (getChainCount() > 0) {
-			modelName = "Model " + toSpec() + " " + name + " (" + getChainCount() + " chains, "
-					+ getResidueCount() + " residues)";
-		} else if (getResidueCount() > 0) {
-			modelName = "Model " + toSpec() + " " + name + " (" + getResidueCount() + " residues)";
-		} else {
-			modelName = "Model " + toSpec() + " " + name + "";
-		}
-
-		Set networkNames = new HashSet();
-		Set nodeNames = new HashSet();
-		Set edgeNames = new HashSet();
-
-		String cytoName = " [";
-		if (networkNames.size() > 0) {
-			if (networkNames.size() == 1) {
-				cytoName += "Network {";
-			} else if (networkNames.size() > 1) {
-				cytoName += "Networks {";
-			}
-			for (String cName : networkNames) {
-				cytoName += cName + ",";
-			}
-			cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
-		}
-		if (nodeNames.size() > 0) {
-			if (nodeNames.size() == 1) {
-				cytoName += "Node {";
-			} else if (nodeNames.size() > 1) {
-				cytoName += "Nodes {";
-			}
-			for (String cName : nodeNames) {
-				cytoName += cName + ",";
-			}
-			cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
-		}
-		if (edgeNames.size() > 0) {
-			if (edgeNames.size() == 1) {
-				cytoName += "Edge {";
-			} else if (edgeNames.size() > 1) {
-				cytoName += "Edges {";
-			}
-			for (String cName : edgeNames) {
-				cytoName += cName + ",";
-			}
-			cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
-		}
-		if (cytoName.endsWith(", ")) {
-			cytoName = cytoName.substring(0, cytoName.length() - 2);
-		}
-		cytoName += "]";
-		String nodeName = modelName + cytoName;
-		if (nodeName.length() > 100) {
-			nodeName = nodeName.substring(0, 100) + "...";
-		}
-		return nodeName;
-	}
+public class ChimeraModel implements ChimeraStructuralObject
+{
+
+  private String name; // The name of this model
+
+  private ModelType type; // The type of the model
+
+  private int modelNumber; // The model number
+
+  private int subModelNumber; // The sub-model number
+
+  private Color modelColor = null; // The color of this model (from Chimera)
+
+  private Object userData = null; // User data associated with this model
+
+  private boolean selected = false; // The selected state of this model
+
+  private TreeMap chainMap; // The list of chains
+
+  // private TreeMap residueMap; // The list of residues
+  private HashSet funcResidues; // List of functional residues
+
+  /**
+   * Constructor to create a model
+   * 
+   * @param name
+   *          the name of this model
+   * @param color
+   *          the model Color
+   * @param modelNumber
+   *          the model number
+   * @param subModelNumber
+   *          the sub-model number
+   */
+  public ChimeraModel(String name, ModelType type, int modelNumber,
+          int subModelNumber)
+  {
+    this.name = name;
+    this.type = type;
+    this.modelNumber = modelNumber;
+    this.subModelNumber = subModelNumber;
+
+    this.chainMap = new TreeMap();
+    this.funcResidues = new HashSet();
+  }
+
+  /**
+   * Constructor to create a model from the Chimera input line
+   * 
+   * @param inputLine
+   *          Chimera input line from which to construct this model
+   */
+  // TODO: [Optional] How to distinguish between PDB and MODBASE?
+  // invoked when listing models: listm type molecule; lists level molecule
+  // line = model id #0 type Molecule name 1ert
+  public ChimeraModel(String inputLine)
+  {
+    this.name = ChimUtils.parseModelName(inputLine);
+    // TODO: [Optional] Write a separate method to get model type
+    if (name.startsWith("smiles"))
+    {
+      this.type = ModelType.SMILES;
+    }
+    else
+    {
+      this.type = ModelType.PDB_MODEL;
+    }
+    this.modelNumber = ChimUtils.parseModelNumber(inputLine)[0];
+    this.subModelNumber = ChimUtils.parseModelNumber(inputLine)[1];
+
+    this.chainMap = new TreeMap();
+    this.funcResidues = new HashSet();
+  }
+
+  /**
+   * Add a residue to this model
+   * 
+   * @param residue
+   *          to add to the model
+   */
+  public void addResidue(ChimeraResidue residue)
+  {
+    residue.setChimeraModel(this);
+    // residueMap.put(residue.getIndex(), residue);
+    String chainId = residue.getChainId();
+    if (chainId != null)
+    {
+      addResidue(chainId, residue);
+    }
+    else
+    {
+      addResidue("_", residue);
+    }
+    // Put it in our map so that we can return it in order
+    // residueMap.put(residue.getIndex(), residue);
+  }
+
+  /**
+   * Add a residue to a chain in this model. If the chain associated with
+   * chainId doesn't exist, it will be created.
+   * 
+   * @param chainId
+   *          to add the residue to
+   * @param residue
+   *          to add to the chain
+   */
+  public void addResidue(String chainId, ChimeraResidue residue)
+  {
+    ChimeraChain chain = null;
+    if (!chainMap.containsKey(chainId))
+    {
+      chain = new ChimeraChain(this.modelNumber, this.subModelNumber,
+              chainId);
+      chain.setChimeraModel(this);
+      chainMap.put(chainId, chain);
+    }
+    else
+    {
+      chain = chainMap.get(chainId);
+    }
+    chain.addResidue(residue);
+  }
+
+  /**
+   * Get the ChimeraModel (required for ChimeraStructuralObject interface)
+   * 
+   * @return ChimeraModel
+   */
+  public ChimeraModel getChimeraModel()
+  {
+    return this;
+  }
+
+  /**
+   * Get the model color of this model
+   * 
+   * @return model color of this model
+   */
+  public Color getModelColor()
+  {
+    return this.modelColor;
+  }
+
+  /**
+   * Set the color of this model
+   * 
+   * @param color
+   *          Color of this model
+   */
+  public void setModelColor(Color color)
+  {
+    this.modelColor = color;
+  }
+
+  /**
+   * Return the name of this model
+   * 
+   * @return model name
+   */
+  public String getModelName()
+  {
+    return name;
+  }
+
+  /**
+   * Set the name of this model
+   * 
+   * @param name
+   *          model name
+   */
+  public void setModelName(String name)
+  {
+    this.name = name;
+  }
+
+  /**
+   * Get the model number of this model
+   * 
+   * @return integer model number
+   */
+  public int getModelNumber()
+  {
+    return modelNumber;
+  }
+
+  /**
+   * Set the model number of this model
+   * 
+   * @param modelNumber
+   *          integer model number
+   */
+  public void setModelNumber(int modelNumber)
+  {
+    this.modelNumber = modelNumber;
+  }
+
+  /**
+   * Get the sub-model number of this model
+   * 
+   * @return integer sub-model number
+   */
+  public int getSubModelNumber()
+  {
+    return subModelNumber;
+  }
+
+  /**
+   * Set the sub-model number of this model
+   * 
+   * @param subModelNumber
+   *          integer model number
+   */
+  public void setSubModelNumber(int subModelNumber)
+  {
+    this.subModelNumber = subModelNumber;
+  }
+
+  public ModelType getModelType()
+  {
+    return type;
+  }
+
+  public void setModelType(ModelType type)
+  {
+    this.type = type;
+  }
+
+  public HashSet getFuncResidues()
+  {
+    return funcResidues;
+  }
+
+  public void setFuncResidues(List residues)
+  {
+    for (String residue : residues)
+    {
+      for (ChimeraChain chain : getChains())
+      {
+        if (residue.indexOf("-") > 0)
+        {
+          funcResidues.addAll(chain.getResidueRange(residue));
+        }
+        else
+        {
+          funcResidues.add(chain.getResidue(residue));
+        }
+      }
+    }
+  }
+
+  /**
+   * Get the user data for this model
+   * 
+   * @return user data
+   */
+  public Object getUserData()
+  {
+    return userData;
+  }
+
+  /**
+   * Set the user data for this model
+   * 
+   * @param data
+   *          user data to associate with this model
+   */
+  public void setUserData(Object data)
+  {
+    this.userData = data;
+  }
+
+  /**
+   * Return the selected state of this model
+   * 
+   * @return the selected state
+   */
+  public boolean isSelected()
+  {
+    return selected;
+  }
+
+  /**
+   * Set the selected state of this model
+   * 
+   * @param selected
+   *          a boolean to set the selected state to
+   */
+  public void setSelected(boolean selected)
+  {
+    this.selected = selected;
+  }
+
+  /**
+   * Return the chains in this model as a List
+   * 
+   * @return the chains in this model as a list
+   */
+  public List getChildren()
+  {
+    return new ArrayList(chainMap.values());
+  }
+
+  /**
+   * Return the chains in this model as a colleciton
+   * 
+   * @return the chains in this model
+   */
+  public Collection getChains()
+  {
+    return chainMap.values();
+  }
+
+  /**
+   * Get the number of chains in this model
+   * 
+   * @return integer chain count
+   */
+  public int getChainCount()
+  {
+    return chainMap.size();
+  }
+
+  /**
+   * Get the list of chain names associated with this model
+   * 
+   * @return return the list of chain names for this model
+   */
+  public Collection getChainNames()
+  {
+    return chainMap.keySet();
+  }
+
+  /**
+   * Get the residues associated with this model
+   * 
+   * @return the list of residues in this model
+   */
+  public Collection getResidues()
+  {
+    Collection residues = new ArrayList();
+    for (ChimeraChain chain : getChains())
+    {
+      residues.addAll(chain.getResidues());
+    }
+    return residues;
+  }
+
+  /**
+   * Get the number of residues in this model
+   * 
+   * @return integer residues count
+   */
+  public int getResidueCount()
+  {
+    int count = 0;
+    for (ChimeraChain chain : getChains())
+    {
+      count += chain.getResidueCount();
+    }
+    return count;
+  }
+
+  /**
+   * Get a specific chain from the model
+   * 
+   * @param chain
+   *          the ID of the chain to return
+   * @return ChimeraChain associated with the chain
+   */
+  public ChimeraChain getChain(String chain)
+  {
+    if (chainMap.containsKey(chain))
+    {
+      return chainMap.get(chain);
+    }
+    return null;
+  }
+
+  /**
+   * Return a specific residue based on its index
+   * 
+   * @param index
+   *          of the residue to return
+   * @return the residue associated with that index
+   */
+  public ChimeraResidue getResidue(String chainId, String index)
+  {
+    if (chainMap.containsKey(chainId))
+    {
+      return chainMap.get(chainId).getResidue(index);
+    }
+    return null;
+  }
+
+  /**
+   * Checks if this model has selected children.
+   */
+  public boolean hasSelectedChildren()
+  {
+    if (selected)
+    {
+      return true;
+    }
+    else
+    {
+      for (ChimeraChain chain : getChains())
+      {
+        if (chain.hasSelectedChildren())
+        {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
+  /**
+   * Return the list of selected residues
+   * 
+   * @return all selected residues
+   */
+  public List getSelectedResidues()
+  {
+    List residueList = new ArrayList();
+    for (ChimeraChain chain : getChains())
+    {
+      if (selected)
+      {
+        residueList.addAll(chain.getSelectedResidues());
+      }
+      else
+      {
+        residueList.addAll(getResidues());
+      }
+    }
+    return residueList;
+  }
+
+  /**
+   * Return the Chimera specification for this model.
+   */
+  public String toSpec()
+  {
+    if (subModelNumber == 0)
+      return ("#" + modelNumber);
+    return ("#" + modelNumber + "." + subModelNumber);
+  }
+
+  /**
+   * Return a string representation for the model. Shorten if longer than 100
+   * characters.
+   */
+  public String toString()
+  {
+    String modelName = "";
+    // TODO: [Optional] Change cutoff for shortening model names in the
+    // structure naviagator dialog
+    if (getChainCount() > 0)
+    {
+      modelName = "Model " + toSpec() + " " + name + " (" + getChainCount()
+              + " chains, " + getResidueCount() + " residues)";
+    }
+    else if (getResidueCount() > 0)
+    {
+      modelName = "Model " + toSpec() + " " + name + " ("
+              + getResidueCount() + " residues)";
+    }
+    else
+    {
+      modelName = "Model " + toSpec() + " " + name + "";
+    }
+
+    Set networkNames = new HashSet();
+    Set nodeNames = new HashSet();
+    Set edgeNames = new HashSet();
+
+    String cytoName = " [";
+    if (networkNames.size() > 0)
+    {
+      if (networkNames.size() == 1)
+      {
+        cytoName += "Network {";
+      }
+      else if (networkNames.size() > 1)
+      {
+        cytoName += "Networks {";
+      }
+      for (String cName : networkNames)
+      {
+        cytoName += cName + ",";
+      }
+      cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
+    }
+    if (nodeNames.size() > 0)
+    {
+      if (nodeNames.size() == 1)
+      {
+        cytoName += "Node {";
+      }
+      else if (nodeNames.size() > 1)
+      {
+        cytoName += "Nodes {";
+      }
+      for (String cName : nodeNames)
+      {
+        cytoName += cName + ",";
+      }
+      cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
+    }
+    if (edgeNames.size() > 0)
+    {
+      if (edgeNames.size() == 1)
+      {
+        cytoName += "Edge {";
+      }
+      else if (edgeNames.size() > 1)
+      {
+        cytoName += "Edges {";
+      }
+      for (String cName : edgeNames)
+      {
+        cytoName += cName + ",";
+      }
+      cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
+    }
+    if (cytoName.endsWith(", "))
+    {
+      cytoName = cytoName.substring(0, cytoName.length() - 2);
+    }
+    cytoName += "]";
+    String nodeName = modelName + cytoName;
+    if (nodeName.length() > 100)
+    {
+      nodeName = nodeName.substring(0, 100) + "...";
+    }
+    return nodeName;
+  }
 }
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.java
index 10825ae..0045e97 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.java
@@ -46,349 +46,411 @@ import org.slf4j.LoggerFactory;
  * 
  */
 
-public class ChimeraResidue implements ChimeraStructuralObject, Comparable {
-
-	/* Constants */
-	public static final int SINGLE_LETTER = 0; // Display residues as a single
-																							// letter
-	public static final int THREE_LETTER = 1; // Display residues as three letters
-	public static final int FULL_NAME = 2; // Display full residue names
-
-	private String type; // Residue type
-	private String index; // Residue index
-	private String chainId; // ChainID for this residue
-	private int modelNumber; // model number for this residue
-	private int subModelNumber; // sub-model number for this residue
-	protected int residueNumber;
-	protected String insertionCode;
-	private ChimeraModel chimeraModel; // ChimeraModel the residue is part of
-	private Object userData; // user data to associate with this residue
-	// public static HashMap aaNames = null; // a map of amino acid
-	// names
-	private static int displayType = THREE_LETTER; // the current display type
-	private boolean selected = false; // the selection state
-
-	/**
-	 * Constructor to create a new ChimeraResidue
-	 * 
-	 * @param type
-	 *          the residue type
-	 * @param index
-	 *          the index of the residue
-	 * @param modelNumber
-	 *          the model number this residue is part of
-	 */
-	public ChimeraResidue(String type, String index, int modelNumber) {
-		this(type, index, modelNumber, 0);
-	}
-
-	/**
-	 * Constructor to create a new ChimeraResidue
-	 * 
-	 * @param type
-	 *          the residue type
-	 * @param index
-	 *          the index of the residue
-	 * @param modelNumber
-	 *          the model number this residue is part of
-	 * @param subModelNumber
-	 *          the sub-model number this residue is part of
-	 */
-	public ChimeraResidue(String type, String index, int modelNumber, int subModelNumber) {
-		this.type = type;
-		this.index = index;
-		this.modelNumber = modelNumber;
-		this.subModelNumber = subModelNumber;
-		splitInsertionCode(this.index);
-		// if (aaNames == null) {
-		// initNames();
-		// }
-	}
-
-	/**
-	 * Constructor to create a new ChimeraResidue from an input line
-	 * 
-	 * @param chimeraInputLine
-	 *          a Chimera residue description
-	 */
-	// invoked when listing (selected) residues: listr spec #0; lists level residue
-	// Line: residue id #0:37.A type MET
-	public ChimeraResidue(String chimeraInputLine) {
-		// initNames();
-		String[] split1 = chimeraInputLine.split(":");
-
-		// First half has model number -- get the number
-		int numberOffset = split1[0].indexOf('#');
-		String model = split1[0].substring(numberOffset + 1);
-		int decimalOffset = model.indexOf('.'); // Do we have a sub-model?
-		try {
-			this.subModelNumber = 0;
-			if (decimalOffset > 0) {
-				this.subModelNumber = Integer.parseInt(model.substring(decimalOffset + 1));
-				this.modelNumber = Integer.parseInt(model.substring(0, decimalOffset));
-			} else {
-				this.modelNumber = Integer.parseInt(model);
-			}
-		} catch (Exception e) {
-			LoggerFactory.getLogger(ChimeraResidue.class)
-					.error("Unexpected return from Chimera: " + model);
-			this.modelNumber = -1;
-		}
-
-		// Second half has residue info: index & type
-		String[] rTokens = split1[1].split(" ");
-		this.type = rTokens[2];
-
-		String[] iTokens = rTokens[0].split("\\.");
-		if (iTokens.length > 0) {
-			this.index = iTokens[0];
-
-			// Careful, might or might not have a chainID
-			if (iTokens.length > 1)
-				this.chainId = iTokens[1];
-			else
-				this.chainId = "_";
-		} else
-			this.index = rTokens[0];
-
-		splitInsertionCode(this.index);
-	}
-
-	/**
-	 * Set the selected state for this residue
-	 * 
-	 * @param selected
-	 *          the selection state to set
-	 */
-	public void setSelected(boolean selected) {
-		this.selected = selected;
-	}
-
-	/**
-	 * Return the selected state of this residue
-	 * 
-	 * @return the selected state
-	 */
-	public boolean isSelected() {
-		return selected;
-	}
-
-	/**
-	 * Return an array made up of this residue (required for ChimeraStructuralObject interface
-	 * 
-	 * @return a List with this residue as its sole member
-	 */
-	public List getChildren() {
-		List v = new ArrayList();
-		v.add(this);
-		return v;
-	}
-
-	/**
-	 * Return the string representation of this residue as follows: "residue_name index"
-	 * where residue_name could be either the single letter, three letter, or full name
-	 * representation of the amino acid.
-	 * 
-	 * @return the string representation
-	 */
-	public String displayName() {
-		return toString();
-	}
-
-	/**
-	 * Return the string representation of this residue as follows: "residue_name index"
-	 * where residue_name could be either the single letter, three letter, or full name
-	 * representation of the amino acid.
-	 * 
-	 * @return the string representation
-	 */
-	public String toString() {
-		if (displayType == FULL_NAME) {
-			return (ChimUtils.toFullName(type) + " " + index);
-		} else if (displayType == SINGLE_LETTER) {
-			return (ChimUtils.toSingleLetter(type) + " " + index);
-		} else if (displayType == THREE_LETTER) {
-			return (ChimUtils.toThreeLetter(type) + " " + index);
-		} else {
-			return (type + " " + index);
-		}
-	}
-
-	/**
-	 * Return the Chimera specification for this Residue
-	 * 
-	 * @return Chimera specification
-	 */
-	public String toSpec() {
-		if (!chainId.equals("_"))
-			return ("#" + modelNumber + ":" + index + "." + chainId);
-		else
-			return ("#" + modelNumber + ":" + index + ".");
-	}
-
-	/**
-	 * Get the index of this residue
-	 * 
-	 * @return residue index
-	 */
-	public String getIndex() {
-		return this.index;
-	}
-
-	/**
-	 * Get the chainID for this residue
-	 * 
-	 * @return String value of the chainId
-	 */
-	public String getChainId() {
-		return this.chainId;
-	}
-
-	/**
-	 * Get the type for this residue
-	 * 
-	 * @return residue type
-	 */
-	public String getType() {
-		return this.type;
-	}
-
-	/**
-	 * Get the model number for this residue
-	 * 
-	 * @return the model number
-	 */
-	public int getModelNumber() {
-		return this.modelNumber;
-	}
-
-	/**
-	 * Get the sub-model number for this residue
-	 * 
-	 * @return the sub-model number
-	 */
-	public int getSubModelNumber() {
-		return this.subModelNumber;
-	}
-
-	/**
-	 * Get the model this residue is part of
-	 * 
-	 * @return the ChimeraModel
-	 */
-	public ChimeraModel getChimeraModel() {
-		return this.chimeraModel;
-	}
-
-	/**
-	 * Set the model this residue is part of
-	 * 
-	 * @param chimeraModel
-	 *          the ChimeraModel this model is part of
-	 */
-	public void setChimeraModel(ChimeraModel chimeraModel) {
-		this.chimeraModel = chimeraModel;
-	}
-
-	/**
-	 * Get the user data for this residue
-	 * 
-	 * @return user data
-	 */
-	public Object getUserData() {
-		return userData;
-	}
-
-	/**
-	 * Set the user data for this Residue
-	 * 
-	 * @param data
-	 *          the user data to associate with this residue
-	 */
-	public void setUserData(Object data) {
-		this.userData = data;
-	}
-
-	public int compareTo(ChimeraResidue c2) {
-		if (residueNumber < c2.residueNumber)
-			return -1;
-		else if (residueNumber == c2.residueNumber) {
-			if (insertionCode == null && c2.insertionCode == null)
-				return 0;
-			else if (insertionCode == null)
-				return -1;
-			else if (c2.insertionCode == null)
-				return 1;
-			return (insertionCode.compareTo(c2.insertionCode));
-		}
-		return 1;
-	}
-
-	public void splitInsertionCode(String residue) {
-		// OK, split the index into number and insertion code
-		Pattern p = Pattern.compile("(\\d*)([A-Z]?)");
-		Matcher m = p.matcher(residue);
-		if (m.matches()) {
-			this.residueNumber = Integer.parseInt(m.group(1));
-			if (m.groupCount() > 1)
-				this.insertionCode = m.group(2);
-			else
-				this.insertionCode = null;
-		}
-	}
-
-	/**********************************************
-	 * Static routines
-	 *********************************************/
-
-	/**
-	 * Initialize the residue names
-	 */
-	// private static void initNames() {
-	// // Create our residue name table
-	// aaNames = new HashMap();
-	// aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
-	// aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
-	// aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
-	// aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
-	// aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
-	// aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
-	// aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
-	// aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
-	// aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
-	// aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
-	// aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
-	// aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
-	// aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
-	// aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
-	// aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
-	// aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
-	// aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
-	// aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
-	// aaNames.put("TRP", "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
-	// aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
-	// aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
-	// aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
-	// aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
-	// aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
-	// aaNames.put("HOH", "HOH HOH Water [H]O[H]");
-	// }
-
-	/**
-	 * Set the display type.
-	 * 
-	 * @param type
-	 *          the display type
-	 */
-	public static void setDisplayType(int type) {
-		displayType = type;
-	}
-
-	public static int getDisplayType() {
-		return displayType;
-	}
-
-	public boolean hasSelectedChildren() {
-		return false;
-	}
+public class ChimeraResidue implements ChimeraStructuralObject,
+        Comparable
+{
+
+  /* Constants */
+  public static final int SINGLE_LETTER = 0; // Display residues as a single
+                                             // letter
+
+  public static final int THREE_LETTER = 1; // Display residues as three letters
+
+  public static final int FULL_NAME = 2; // Display full residue names
+
+  private String type; // Residue type
+
+  private String index; // Residue index
+
+  private String chainId; // ChainID for this residue
+
+  private int modelNumber; // model number for this residue
+
+  private int subModelNumber; // sub-model number for this residue
+
+  protected int residueNumber;
+
+  protected String insertionCode;
+
+  private ChimeraModel chimeraModel; // ChimeraModel the residue is part of
+
+  private Object userData; // user data to associate with this residue
+
+  // public static HashMap aaNames = null; // a map of amino
+  // acid
+  // names
+  private static int displayType = THREE_LETTER; // the current display type
+
+  private boolean selected = false; // the selection state
+
+  /**
+   * Constructor to create a new ChimeraResidue
+   * 
+   * @param type
+   *          the residue type
+   * @param index
+   *          the index of the residue
+   * @param modelNumber
+   *          the model number this residue is part of
+   */
+  public ChimeraResidue(String type, String index, int modelNumber)
+  {
+    this(type, index, modelNumber, 0);
+  }
+
+  /**
+   * Constructor to create a new ChimeraResidue
+   * 
+   * @param type
+   *          the residue type
+   * @param index
+   *          the index of the residue
+   * @param modelNumber
+   *          the model number this residue is part of
+   * @param subModelNumber
+   *          the sub-model number this residue is part of
+   */
+  public ChimeraResidue(String type, String index, int modelNumber,
+          int subModelNumber)
+  {
+    this.type = type;
+    this.index = index;
+    this.modelNumber = modelNumber;
+    this.subModelNumber = subModelNumber;
+    splitInsertionCode(this.index);
+    // if (aaNames == null) {
+    // initNames();
+    // }
+  }
+
+  /**
+   * Constructor to create a new ChimeraResidue from an input line
+   * 
+   * @param chimeraInputLine
+   *          a Chimera residue description
+   */
+  // invoked when listing (selected) residues: listr spec #0; lists level
+  // residue
+  // Line: residue id #0:37.A type MET
+  public ChimeraResidue(String chimeraInputLine)
+  {
+    // initNames();
+    String[] split1 = chimeraInputLine.split(":");
+
+    // First half has model number -- get the number
+    int numberOffset = split1[0].indexOf('#');
+    String model = split1[0].substring(numberOffset + 1);
+    int decimalOffset = model.indexOf('.'); // Do we have a sub-model?
+    try
+    {
+      this.subModelNumber = 0;
+      if (decimalOffset > 0)
+      {
+        this.subModelNumber = Integer.parseInt(model
+                .substring(decimalOffset + 1));
+        this.modelNumber = Integer.parseInt(model.substring(0,
+                decimalOffset));
+      }
+      else
+      {
+        this.modelNumber = Integer.parseInt(model);
+      }
+    } catch (Exception e)
+    {
+      LoggerFactory.getLogger(ChimeraResidue.class).error(
+              "Unexpected return from Chimera: " + model);
+      this.modelNumber = -1;
+    }
+
+    // Second half has residue info: index & type
+    String[] rTokens = split1[1].split(" ");
+    this.type = rTokens[2];
+
+    String[] iTokens = rTokens[0].split("\\.");
+    if (iTokens.length > 0)
+    {
+      this.index = iTokens[0];
+
+      // Careful, might or might not have a chainID
+      if (iTokens.length > 1)
+        this.chainId = iTokens[1];
+      else
+        this.chainId = "_";
+    }
+    else
+      this.index = rTokens[0];
+
+    splitInsertionCode(this.index);
+  }
+
+  /**
+   * Set the selected state for this residue
+   * 
+   * @param selected
+   *          the selection state to set
+   */
+  public void setSelected(boolean selected)
+  {
+    this.selected = selected;
+  }
+
+  /**
+   * Return the selected state of this residue
+   * 
+   * @return the selected state
+   */
+  public boolean isSelected()
+  {
+    return selected;
+  }
+
+  /**
+   * Return an array made up of this residue (required for
+   * ChimeraStructuralObject interface
+   * 
+   * @return a List with this residue as its sole member
+   */
+  public List getChildren()
+  {
+    List v = new ArrayList();
+    v.add(this);
+    return v;
+  }
+
+  /**
+   * Return the string representation of this residue as follows:
+   * "residue_name index" where residue_name could be
+   * either the single letter, three letter, or full name representation of the
+   * amino acid.
+   * 
+   * @return the string representation
+   */
+  public String displayName()
+  {
+    return toString();
+  }
+
+  /**
+   * Return the string representation of this residue as follows:
+   * "residue_name index" where residue_name could be
+   * either the single letter, three letter, or full name representation of the
+   * amino acid.
+   * 
+   * @return the string representation
+   */
+  public String toString()
+  {
+    if (displayType == FULL_NAME)
+    {
+      return (ChimUtils.toFullName(type) + " " + index);
+    }
+    else if (displayType == SINGLE_LETTER)
+    {
+      return (ChimUtils.toSingleLetter(type) + " " + index);
+    }
+    else if (displayType == THREE_LETTER)
+    {
+      return (ChimUtils.toThreeLetter(type) + " " + index);
+    }
+    else
+    {
+      return (type + " " + index);
+    }
+  }
+
+  /**
+   * Return the Chimera specification for this Residue
+   * 
+   * @return Chimera specification
+   */
+  public String toSpec()
+  {
+    if (!chainId.equals("_"))
+      return ("#" + modelNumber + ":" + index + "." + chainId);
+    else
+      return ("#" + modelNumber + ":" + index + ".");
+  }
+
+  /**
+   * Get the index of this residue
+   * 
+   * @return residue index
+   */
+  public String getIndex()
+  {
+    return this.index;
+  }
+
+  /**
+   * Get the chainID for this residue
+   * 
+   * @return String value of the chainId
+   */
+  public String getChainId()
+  {
+    return this.chainId;
+  }
+
+  /**
+   * Get the type for this residue
+   * 
+   * @return residue type
+   */
+  public String getType()
+  {
+    return this.type;
+  }
+
+  /**
+   * Get the model number for this residue
+   * 
+   * @return the model number
+   */
+  public int getModelNumber()
+  {
+    return this.modelNumber;
+  }
+
+  /**
+   * Get the sub-model number for this residue
+   * 
+   * @return the sub-model number
+   */
+  public int getSubModelNumber()
+  {
+    return this.subModelNumber;
+  }
+
+  /**
+   * Get the model this residue is part of
+   * 
+   * @return the ChimeraModel
+   */
+  public ChimeraModel getChimeraModel()
+  {
+    return this.chimeraModel;
+  }
+
+  /**
+   * Set the model this residue is part of
+   * 
+   * @param chimeraModel
+   *          the ChimeraModel this model is part of
+   */
+  public void setChimeraModel(ChimeraModel chimeraModel)
+  {
+    this.chimeraModel = chimeraModel;
+  }
+
+  /**
+   * Get the user data for this residue
+   * 
+   * @return user data
+   */
+  public Object getUserData()
+  {
+    return userData;
+  }
+
+  /**
+   * Set the user data for this Residue
+   * 
+   * @param data
+   *          the user data to associate with this residue
+   */
+  public void setUserData(Object data)
+  {
+    this.userData = data;
+  }
+
+  public int compareTo(ChimeraResidue c2)
+  {
+    if (residueNumber < c2.residueNumber)
+      return -1;
+    else if (residueNumber == c2.residueNumber)
+    {
+      if (insertionCode == null && c2.insertionCode == null)
+        return 0;
+      else if (insertionCode == null)
+        return -1;
+      else if (c2.insertionCode == null)
+        return 1;
+      return (insertionCode.compareTo(c2.insertionCode));
+    }
+    return 1;
+  }
+
+  public void splitInsertionCode(String residue)
+  {
+    // OK, split the index into number and insertion code
+    Pattern p = Pattern.compile("(\\d*)([A-Z]?)");
+    Matcher m = p.matcher(residue);
+    if (m.matches())
+    {
+      this.residueNumber = Integer.parseInt(m.group(1));
+      if (m.groupCount() > 1)
+        this.insertionCode = m.group(2);
+      else
+        this.insertionCode = null;
+    }
+  }
+
+  /**********************************************
+   * Static routines
+   *********************************************/
+
+  /**
+   * Initialize the residue names
+   */
+  // private static void initNames() {
+  // // Create our residue name table
+  // aaNames = new HashMap();
+  // aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
+  // aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
+  // aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
+  // aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
+  // aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
+  // aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
+  // aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
+  // aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
+  // aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
+  // aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
+  // aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
+  // aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
+  // aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
+  // aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
+  // aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+  // aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
+  // aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
+  // aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
+  // aaNames.put("TRP",
+  // "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
+  // aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
+  // aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
+  // aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
+  // aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
+  // aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
+  // aaNames.put("HOH", "HOH HOH Water [H]O[H]");
+  // }
+
+  /**
+   * Set the display type.
+   * 
+   * @param type
+   *          the display type
+   */
+  public static void setDisplayType(int type)
+  {
+    displayType = type;
+  }
+
+  public static int getDisplayType()
+  {
+    return displayType;
+  }
+
+  public boolean hasSelectedChildren()
+  {
+    return false;
+  }
 }
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.java
index 1678317..64568a7 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.java
@@ -32,81 +32,81 @@
  */
 package ext.edu.ucsf.rbvi.strucviz2;
 
-import java.lang.String;
 import java.util.List;
 
 /**
- * This interface provides a common set of methods that are implemented by the ChimeraModel,
- * ChimeraChain, and ChimeraResidue classes.
+ * This interface provides a common set of methods that are implemented by the
+ * ChimeraModel, ChimeraChain, and ChimeraResidue classes.
  * 
  * @author scooter
  * 
  */
 
-public interface ChimeraStructuralObject {
+public interface ChimeraStructuralObject
+{
 
-	/**
-	 * Return the Chimera selection specification for this object
-	 * 
-	 * @return a String representing a Chimera atom-spec
-	 */
-	public String toSpec();
+  /**
+   * Return the Chimera selection specification for this object
+   * 
+   * @return a String representing a Chimera atom-spec
+   */
+  public String toSpec();
 
-	/**
-	 * Return a String representation for this object
-	 * 
-	 * @return a String representing the object name
-	 */
-	public String toString();
+  /**
+   * Return a String representation for this object
+   * 
+   * @return a String representing the object name
+   */
+  public String toString();
 
-	/**
-	 * Return the userData for this object
-	 * 
-	 * @return an Object representing the userData (usually TreePath)
-	 */
-	public Object getUserData();
+  /**
+   * Return the userData for this object
+   * 
+   * @return an Object representing the userData (usually TreePath)
+   */
+  public Object getUserData();
 
-	/**
-	 * Set the userData for this object
-	 * 
-	 * @param userData
-	 *          the Object representing the userData (usually TreePath)
-	 */
-	public void setUserData(Object userData);
+  /**
+   * Set the userData for this object
+   * 
+   * @param userData
+   *          the Object representing the userData (usually TreePath)
+   */
+  public void setUserData(Object userData);
 
-	/**
-	 * Return the ChimeraModel for this object
-	 * 
-	 * @return the ChimeraModel this object is part of
-	 */
-	public ChimeraModel getChimeraModel();
+  /**
+   * Return the ChimeraModel for this object
+   * 
+   * @return the ChimeraModel this object is part of
+   */
+  public ChimeraModel getChimeraModel();
 
-	/**
-	 * Set the "selected" state of this object
-	 * 
-	 * @param selected
-	 *          boolean value as to whether this object is selected
-	 */
-	public void setSelected(boolean selected);
+  /**
+   * Set the "selected" state of this object
+   * 
+   * @param selected
+   *          boolean value as to whether this object is selected
+   */
+  public void setSelected(boolean selected);
 
-	/**
-	 * Get the "selected" state of this object
-	 * 
-	 * @return the selected state of this object
-	 */
-	public boolean isSelected();
+  /**
+   * Get the "selected" state of this object
+   * 
+   * @return the selected state of this object
+   */
+  public boolean isSelected();
 
-	/**
-	 * Get the selected state of this object and its children.
-	 * 
-	 * @return true if any child is selected.
-	 */
-	public boolean hasSelectedChildren();
+  /**
+   * Get the selected state of this object and its children.
+   * 
+   * @return true if any child is selected.
+   */
+  public boolean hasSelectedChildren();
 
-	/**
-	 * Get the children of this object (if any)
-	 * 
-	 * @return the children of the object
-	 */
-	public List getChildren();
+  /**
+   * Get the children of this object (if any)
+   * 
+   * @return the children of the object
+   */
+  public List getChildren();
 }
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
index f3447ce..9ecc6a7 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
@@ -46,149 +46,171 @@ import javax.swing.tree.TreePath;
 // StructureViz imports
 
 /**
- * The ChimeraTreeModel class provides the underlying model
- * for the navigation tree in the ModelNavigatorDialog.
+ * The ChimeraTreeModel class provides the underlying model for the navigation
+ * tree in the ModelNavigatorDialog.
  *
  * @author scooter
  * @see ModelNavigatorDialog
-	 */
-public class ChimeraTreeModel extends DefaultTreeModel {
-	private ChimeraManager chimeraManager;
-	private JTree navigationTree;
-	private int residueDisplay = ChimeraResidue.THREE_LETTER;
-
-	/**
-	 * Constructor for the ChimeraTreeModel.
-	 *
-	 * @param chimeraObject the Chimera object that this tree represents
-	 * @param tree the JTree used to display the object
-	 * @see Chimera
-	 */
-	public ChimeraTreeModel (ChimeraManager chimeraManager, JTree tree) {
-		super(new DefaultMutableTreeNode());
-		this.chimeraManager = chimeraManager;
-		this.navigationTree = tree;
-		DefaultMutableTreeNode rootNode = buildTree();
-		this.setRoot(rootNode);
-	}
-
-	/**
-	 * Set the display type for the residues.  The display type
-	 * must be one of:
-	 *
-	 *	ChimeraResidue.THREE_LETTER
-	 *	ChimeraResidue.SINGLE_LETTER
-	 *	ChimeraResidue.FULL_NAME
-	 *
-	 * @param newDisplay the display type
-	 * @see ChimeraResidue
-	 */
-	public void setResidueDisplay(int newDisplay) {
-		this.residueDisplay = newDisplay;
-	}
-		
-	/**
-	 * This method is called to rebuild the tree model "from scratch"
-	 */
-	public void reload() {
-		// First, rebuild the tree with the new data
-		DefaultMutableTreeNode rootNode = buildTree();
-		this.setRoot(rootNode);
-
-		// Now let the superclass do all of the work
-		super.reload();
-	}
-
-	/**
-	 * Rebuild an existing tree
-	 */
-	public void rebuildTree() {
-		DefaultMutableTreeNode rootNode = buildTree();
-		DefaultTreeModel model = (DefaultTreeModel)navigationTree.getModel();
-		model.setRoot(rootNode);
-		model.reload();
-	}
-
-	/**
-	 * Build the tree from the current Chimera data
-	 *
-	 * @return DefaultMutableTreeNode that represents the currently loaded Chimera models
-	 */
-	private DefaultMutableTreeNode buildTree() {
-		int modelCount = chimeraManager.getChimeraModelsCount(true);
-		DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(modelCount+" Open Chimera Models");
-		TreePath rootPath = new TreePath(rootNode);
-
-		TreePath path = null;
-		DefaultMutableTreeNode model = null;
-
-		// Add all of the Chimera models
-		for (ChimeraModel chimeraModel: chimeraManager.getChimeraModels()) {
-			model = new DefaultMutableTreeNode(chimeraModel);
-			path = rootPath.pathByAddingChild(model);
-			chimeraModel.setUserData(path);
-			addChainNodes(chimeraModel, model, path);
-			rootNode.add(model);
-		}
-		return rootNode;
-	}
-
-	/**
-	 * add chains to a tree model
-	 *
-	 * @param chimeraModel the ChimeraModel to get the chains from
-	 * @param treeModel the tree model to add the chains to
-	 * @param treePath the tree path where the chains should be added
-	 */
-	private void addChainNodes(ChimeraModel chimeraModel, 
-														 DefaultMutableTreeNode treeModel,
-														 TreePath treePath) {
-		DefaultMutableTreeNode chain = null;
-		TreePath chainPath = null;
-
-		// Get the list of chains
-		Collection chainList = chimeraModel.getChains();
-
-		if (chainList.size() == 0) {
-			// No chains!  Just add the residues
-			addResidues(chimeraModel.getResidues(), treeModel, treePath);	
-			return;
-		}
-
-		// Iterate over the chains and add the chain and all of
-		// the chain's residues
-		for (ChimeraChain chimeraChain: chainList) {
-			chain = new DefaultMutableTreeNode(chimeraChain);
-			chainPath = treePath.pathByAddingChild(chain);
-			chimeraChain.setUserData(chainPath);
-			addResidues(chimeraChain.getResidues(), chain, chainPath);
-			treeModel.add(chain);	
-		}
-	}
-
-	/**
-	 * add residues to a tree model
-	 *
-	 * @param residues the residues to add
-	 * @param treeModel the tree model to add the residues to
-	 * @param treePath the tree path where the residues should be added
-	 */
-	private void addResidues(Collection residues, 
-													 DefaultMutableTreeNode treeModel,
-													 TreePath treePath) {
-		DefaultMutableTreeNode residue = null;
-		TreePath residuePath = null;
-
-		List sortedResidues = new ArrayList(residues);
-		Collections.sort(sortedResidues);
-
-		// Iterate over all residues & add them to the tree
-		for (ChimeraResidue res: sortedResidues) {
-			res.setDisplayType(this.residueDisplay);
-			residue = new DefaultMutableTreeNode(res);
-			residuePath = treePath.pathByAddingChild(residue);
-			res.setUserData(residuePath);
-			treeModel.add(residue);
-		}
-	}	
+ */
+public class ChimeraTreeModel extends DefaultTreeModel
+{
+  private ChimeraManager chimeraManager;
+
+  private JTree navigationTree;
+
+  private int residueDisplay = ChimeraResidue.THREE_LETTER;
+
+  /**
+   * Constructor for the ChimeraTreeModel.
+   *
+   * @param chimeraObject
+   *          the Chimera object that this tree represents
+   * @param tree
+   *          the JTree used to display the object
+   * @see Chimera
+   */
+  public ChimeraTreeModel(ChimeraManager chimeraManager, JTree tree)
+  {
+    super(new DefaultMutableTreeNode());
+    this.chimeraManager = chimeraManager;
+    this.navigationTree = tree;
+    DefaultMutableTreeNode rootNode = buildTree();
+    this.setRoot(rootNode);
+  }
+
+  /**
+   * Set the display type for the residues. The display type must be one of:
+   *
+   * ChimeraResidue.THREE_LETTER ChimeraResidue.SINGLE_LETTER
+   * ChimeraResidue.FULL_NAME
+   *
+   * @param newDisplay
+   *          the display type
+   * @see ChimeraResidue
+   */
+  public void setResidueDisplay(int newDisplay)
+  {
+    this.residueDisplay = newDisplay;
+  }
+
+  /**
+   * This method is called to rebuild the tree model "from scratch"
+   */
+  public void reload()
+  {
+    // First, rebuild the tree with the new data
+    DefaultMutableTreeNode rootNode = buildTree();
+    this.setRoot(rootNode);
+
+    // Now let the superclass do all of the work
+    super.reload();
+  }
+
+  /**
+   * Rebuild an existing tree
+   */
+  public void rebuildTree()
+  {
+    DefaultMutableTreeNode rootNode = buildTree();
+    DefaultTreeModel model = (DefaultTreeModel) navigationTree.getModel();
+    model.setRoot(rootNode);
+    model.reload();
+  }
+
+  /**
+   * Build the tree from the current Chimera data
+   *
+   * @return DefaultMutableTreeNode that represents the currently loaded Chimera
+   *         models
+   */
+  private DefaultMutableTreeNode buildTree()
+  {
+    int modelCount = chimeraManager.getChimeraModelsCount(true);
+    DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(modelCount
+            + " Open Chimera Models");
+    TreePath rootPath = new TreePath(rootNode);
+
+    TreePath path = null;
+    DefaultMutableTreeNode model = null;
+
+    // Add all of the Chimera models
+    for (ChimeraModel chimeraModel : chimeraManager.getChimeraModels())
+    {
+      model = new DefaultMutableTreeNode(chimeraModel);
+      path = rootPath.pathByAddingChild(model);
+      chimeraModel.setUserData(path);
+      addChainNodes(chimeraModel, model, path);
+      rootNode.add(model);
+    }
+    return rootNode;
+  }
+
+  /**
+   * add chains to a tree model
+   *
+   * @param chimeraModel
+   *          the ChimeraModel to get the chains from
+   * @param treeModel
+   *          the tree model to add the chains to
+   * @param treePath
+   *          the tree path where the chains should be added
+   */
+  private void addChainNodes(ChimeraModel chimeraModel,
+          DefaultMutableTreeNode treeModel, TreePath treePath)
+  {
+    DefaultMutableTreeNode chain = null;
+    TreePath chainPath = null;
+
+    // Get the list of chains
+    Collection chainList = chimeraModel.getChains();
+
+    if (chainList.size() == 0)
+    {
+      // No chains! Just add the residues
+      addResidues(chimeraModel.getResidues(), treeModel, treePath);
+      return;
+    }
+
+    // Iterate over the chains and add the chain and all of
+    // the chain's residues
+    for (ChimeraChain chimeraChain : chainList)
+    {
+      chain = new DefaultMutableTreeNode(chimeraChain);
+      chainPath = treePath.pathByAddingChild(chain);
+      chimeraChain.setUserData(chainPath);
+      addResidues(chimeraChain.getResidues(), chain, chainPath);
+      treeModel.add(chain);
+    }
+  }
+
+  /**
+   * add residues to a tree model
+   *
+   * @param residues
+   *          the residues to add
+   * @param treeModel
+   *          the tree model to add the residues to
+   * @param treePath
+   *          the tree path where the residues should be added
+   */
+  private void addResidues(Collection residues,
+          DefaultMutableTreeNode treeModel, TreePath treePath)
+  {
+    DefaultMutableTreeNode residue = null;
+    TreePath residuePath = null;
+
+    List sortedResidues = new ArrayList(
+            residues);
+    Collections.sort(sortedResidues);
+
+    // Iterate over all residues & add them to the tree
+    for (ChimeraResidue res : sortedResidues)
+    {
+      res.setDisplayType(this.residueDisplay);
+      residue = new DefaultMutableTreeNode(res);
+      residuePath = treePath.pathByAddingChild(residue);
+      res.setUserData(residuePath);
+      treeModel.add(residue);
+    }
+  }
 }
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index 4797b37..6fd6340 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
@@ -24,15 +24,15 @@ import org.slf4j.LoggerFactory;
 
 public class StructureManager
 {
-  static final String[] defaultStructureKeys =
-  { "Structure", "pdb", "pdbFileName", "PDB ID", "structure",
-      "biopax.xref.PDB", "pdb_ids", "ModelName", "ModelNumber" };
+  static final String[] defaultStructureKeys = { "Structure", "pdb",
+      "pdbFileName", "PDB ID", "structure", "biopax.xref.PDB", "pdb_ids",
+      "ModelName", "ModelNumber" };
 
-  static final String[] defaultChemStructKeys =
-  { "Smiles", "smiles", "SMILES" };
+  static final String[] defaultChemStructKeys = { "Smiles", "smiles",
+      "SMILES" };
 
-  static final String[] defaultResidueKeys =
-  { "FunctionalResidues", "ResidueList", "Residues" };
+  static final String[] defaultResidueKeys = { "FunctionalResidues",
+      "ResidueList", "Residues" };
 
   public enum ModelType
   {
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java
index 161ab13..08a6cb7 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java
@@ -1,25 +1,30 @@
 package ext.edu.ucsf.rbvi.strucviz2;
 
 /**
- * This object maintains the relationship between Chimera objects and Cytoscape objects.
+ * This object maintains the relationship between Chimera objects and Cytoscape
+ * objects.
  */
-public class StructureSettings {
+public class StructureSettings
+{
 
-//	@Tunable(description = "Path to UCSF Chimera application", gravity = 4.0)
-	public String chimeraPath = null;
+  // @Tunable(description = "Path to UCSF Chimera application", gravity = 4.0)
+  public String chimeraPath = null;
 
-	public StructureSettings(StructureManager manager) {
-		
-		chimeraPath = manager.getCurrentChimeraPath(null);
+  public StructureSettings(StructureManager manager)
+  {
 
-		// This seems a little strange, but it has to do with the order of tunable interceptor
-		// handling. We need to set these selectors in our structure manager and dynamically
-		// pull the data out as needed....
-		manager.setStructureSettings( this);
-	}
+    chimeraPath = manager.getCurrentChimeraPath(null);
 
+    // This seems a little strange, but it has to do with the order of tunable
+    // interceptor
+    // handling. We need to set these selectors in our structure manager and
+    // dynamically
+    // pull the data out as needed....
+    manager.setStructureSettings(this);
+  }
 
-	public String getChimeraPath() {
-		return chimeraPath;
-	}
+  public String getChimeraPath()
+  {
+    return chimeraPath;
+  }
 }
diff --git a/src/ext/vamsas/IRegistryServiceLocator.java b/src/ext/vamsas/IRegistryServiceLocator.java
index f419e52..5da24db 100755
--- a/src/ext/vamsas/IRegistryServiceLocator.java
+++ b/src/ext/vamsas/IRegistryServiceLocator.java
@@ -111,7 +111,10 @@ public class IRegistryServiceLocator extends org.apache.axis.client.Service
     {
       throw new javax.xml.rpc.ServiceException(t);
     }
-    throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+    throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+            "exception.no_stub_implementation_for_interface",
+            new String[] { (serviceEndpointInterface == null ? "null"
+                    : serviceEndpointInterface.getName()) }));
   }
 
   /**
@@ -168,7 +171,10 @@ public class IRegistryServiceLocator extends org.apache.axis.client.Service
     }
     else
     { // Unknown Port Name
-      throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
+      throw new javax.xml.rpc.ServiceException(
+              MessageManager.formatMessage(
+                      "exception.cannot_set_endpoint_address_unknown_port",
+                      new String[] { portName }));
     }
   }
 
diff --git a/src/ext/vamsas/JpredServiceLocator.java b/src/ext/vamsas/JpredServiceLocator.java
index 802e3df..aa6d6ba 100755
--- a/src/ext/vamsas/JpredServiceLocator.java
+++ b/src/ext/vamsas/JpredServiceLocator.java
@@ -109,7 +109,10 @@ public class JpredServiceLocator extends org.apache.axis.client.Service
     {
       throw new javax.xml.rpc.ServiceException(t);
     }
-    throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+    throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+            "exception.no_stub_implementation_for_interface",
+            new String[] { (serviceEndpointInterface == null ? "null"
+                    : serviceEndpointInterface.getName()) }));
   }
 
   /**
@@ -166,7 +169,10 @@ public class JpredServiceLocator extends org.apache.axis.client.Service
     }
     else
     { // Unknown Port Name
-      throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
+      throw new javax.xml.rpc.ServiceException(
+              MessageManager.formatMessage(
+                      "exception.cannot_set_endpoint_address_unknown_port",
+                      new String[] { portName }));
     }
   }
 
diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java
index 2ec1562..cff8081 100755
--- a/src/ext/vamsas/JpredSoapBindingStub.java
+++ b/src/ext/vamsas/JpredSoapBindingStub.java
@@ -277,8 +277,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { seq });
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] { seq });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -316,8 +315,7 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { msf });
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] { msf });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -354,8 +352,8 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { job_id });
+    java.lang.Object _resp = _call
+            .invoke(new java.lang.Object[] { job_id });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -392,8 +390,8 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { job_id });
+    java.lang.Object _resp = _call
+            .invoke(new java.lang.Object[] { job_id });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
diff --git a/src/ext/vamsas/MuscleWSServiceLocator.java b/src/ext/vamsas/MuscleWSServiceLocator.java
index 0725555..2427405 100755
--- a/src/ext/vamsas/MuscleWSServiceLocator.java
+++ b/src/ext/vamsas/MuscleWSServiceLocator.java
@@ -117,7 +117,10 @@ public class MuscleWSServiceLocator extends org.apache.axis.client.Service
       throw new javax.xml.rpc.ServiceException(t);
     }
 
-    throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+    throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+            "exception.no_stub_implementation_for_interface",
+            new String[] { (serviceEndpointInterface == null ? "null"
+                    : serviceEndpointInterface.getName()) }));
   }
 
   /**
@@ -176,7 +179,10 @@ public class MuscleWSServiceLocator extends org.apache.axis.client.Service
     }
     else
     { // Unknown Port Name
-      throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
+      throw new javax.xml.rpc.ServiceException(
+              MessageManager.formatMessage(
+                      "exception.cannot_set_endpoint_address_unknown_port",
+                      new String[] { portName }));
     }
   }
 
diff --git a/src/ext/vamsas/MuscleWSSoapBindingStub.java b/src/ext/vamsas/MuscleWSSoapBindingStub.java
index f01c1fe..1f8d231 100755
--- a/src/ext/vamsas/MuscleWSSoapBindingStub.java
+++ b/src/ext/vamsas/MuscleWSSoapBindingStub.java
@@ -315,8 +315,8 @@ public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub
     setRequestHeaders(_call);
     setAttachments(_call);
 
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { seqSet });
+    java.lang.Object _resp = _call
+            .invoke(new java.lang.Object[] { seqSet });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -356,8 +356,8 @@ public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub
     setRequestHeaders(_call);
     setAttachments(_call);
 
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { job_id });
+    java.lang.Object _resp = _call
+            .invoke(new java.lang.Object[] { job_id });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -397,8 +397,8 @@ public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub
     setRequestHeaders(_call);
     setAttachments(_call);
 
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { job_id });
+    java.lang.Object _resp = _call
+            .invoke(new java.lang.Object[] { job_id });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -437,8 +437,7 @@ public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub
     setRequestHeaders(_call);
     setAttachments(_call);
 
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { jobId });
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobId });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
diff --git a/src/ext/vamsas/RegistryServiceSoapBindingStub.java b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
index 4798fa3..08b2a6b 100755
--- a/src/ext/vamsas/RegistryServiceSoapBindingStub.java
+++ b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
@@ -209,8 +209,7 @@ public class RegistryServiceSoapBindingStub extends
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    {});
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] {});
 
     if (_resp instanceof java.rmi.RemoteException)
     {
diff --git a/src/ext/vamsas/SeqSearchServiceLocator.java b/src/ext/vamsas/SeqSearchServiceLocator.java
index f7ef5aa..daf7dd3 100644
--- a/src/ext/vamsas/SeqSearchServiceLocator.java
+++ b/src/ext/vamsas/SeqSearchServiceLocator.java
@@ -111,7 +111,10 @@ public class SeqSearchServiceLocator extends org.apache.axis.client.Service
     {
       throw new javax.xml.rpc.ServiceException(t);
     }
-    throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.no_stub_implementation_for_interface", new String[]{(serviceEndpointInterface == null ? "null": serviceEndpointInterface.getName())}));
+    throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+            "exception.no_stub_implementation_for_interface",
+            new String[] { (serviceEndpointInterface == null ? "null"
+                    : serviceEndpointInterface.getName()) }));
   }
 
   /**
@@ -168,7 +171,10 @@ public class SeqSearchServiceLocator extends org.apache.axis.client.Service
     }
     else
     { // Unknown Port Name
-      throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage("exception.cannot_set_endpoint_address_unknown_port", new String[]{portName}));
+      throw new javax.xml.rpc.ServiceException(
+              MessageManager.formatMessage(
+                      "exception.cannot_set_endpoint_address_unknown_port",
+                      new String[] { portName }));
     }
   }
 
diff --git a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
index da7a7a8..390ceb6 100644
--- a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
+++ b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
@@ -315,8 +315,7 @@ public class SeqSearchServiceSoapBindingStub extends
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    {});
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] {});
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -353,8 +352,8 @@ public class SeqSearchServiceSoapBindingStub extends
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { job_id });
+    java.lang.Object _resp = _call
+            .invoke(new java.lang.Object[] { job_id });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -392,8 +391,8 @@ public class SeqSearchServiceSoapBindingStub extends
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { al, database });
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] { al,
+        database });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -430,8 +429,8 @@ public class SeqSearchServiceSoapBindingStub extends
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { s, database });
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] { s,
+        database });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -467,8 +466,7 @@ public class SeqSearchServiceSoapBindingStub extends
 
     setRequestHeaders(_call);
     setAttachments(_call);
-    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
-    { jobId });
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobId });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 50045dc..5227795 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -198,9 +198,8 @@ public class AAFrequency
       if (profile)
       {
         // TODO use a 1-dimensional array with jSize, nongap in [0] and [1]
-        residueHash.put(PROFILE, new int[][]
-        { values, new int[]
-        { jSize, nongap } });
+        residueHash.put(PROFILE, new int[][] { values,
+            new int[] { jSize, nongap } });
       }
       residueHash.put(MAXCOUNT, new Integer(maxCount));
       residueHash.put(MAXRESIDUE, maxResidue);
@@ -369,8 +368,7 @@ public class AAFrequency
                 .append("%");
       }
       consensus.annotations[i] = new Annotation(maxRes,
-              mouseOver.toString(), ' ',
-              value);
+              mouseOver.toString(), ' ', value);
     }
   }
 
@@ -462,7 +460,8 @@ public class AAFrequency
    * @param hashtable
    * @return
    */
-  public static int[] extractCdnaProfile(Hashtable hashtable, boolean ignoreGaps)
+  public static int[] extractCdnaProfile(Hashtable hashtable,
+          boolean ignoreGaps)
   {
     // this holds #seqs, #ungapped, and then codon count, indexed by encoded
     // codon triplet
@@ -507,7 +506,7 @@ public class AAFrequency
     result[1] = distinctValuesCount;
     return Arrays.copyOfRange(result, 0, j);
   }
-    
+
   /**
    * Compute a consensus for the cDNA coding for a protein alignment.
    * 
@@ -664,8 +663,7 @@ public class AAFrequency
         final int pct = codonCount * 100 / totalCount;
         String codon = String
                 .valueOf(CodingUtils.decodeCodon(codonEncoded));
-        percent = fmt == null ? Integer.toString(pct) : fmt
-                .form(pct);
+        percent = fmt == null ? Integer.toString(pct) : fmt.form(pct);
         if (showProfileLogo || codonCount == modalCodonCount)
         {
           if (percent.equals(lastPercent) && j > 0)
@@ -678,8 +676,7 @@ public class AAFrequency
             if (samePercent.length() > 0)
             {
               mouseOver.append(samePercent).append(": ")
-                      .append(lastPercent)
-                      .append("% ");
+                      .append(lastPercent).append("% ");
             }
             samePercent.setLength(0);
             samePercent.append(codon);
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 5612133..3ca3d90 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,13 +20,6 @@
  */
 package jalview.analysis;
 
-import java.awt.Color;
-import java.awt.Graphics;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.StringTokenizer;
-
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
@@ -39,6 +32,13 @@ import jalview.util.Format;
 import jalview.util.MapList;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
+
 /**
  * 
  * 
@@ -53,13 +53,11 @@ public class AlignSeq
 
   private static final String NEWLINE = System.lineSeparator();
 
-  static String[] dna =
-  { "A", "C", "G", "T", "-" };
+  static String[] dna = { "A", "C", "G", "T", "-" };
 
   // "C", "T", "A", "G", "-"};
-  static String[] pep =
-  { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
-      "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" };
+  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;
 
@@ -451,7 +449,8 @@ public class AlignSeq
     else
     {
       output.append("Wrong type = dna or pep only");
-      throw new Error(MessageManager.formatMessage("error.unknown_type_dna_or_pep", new String[]{type2}));
+      throw new Error(MessageManager.formatMessage(
+              "error.unknown_type_dna_or_pep", new String[] { type2 }));
     }
   }
 
@@ -1097,8 +1096,8 @@ public class AlignSeq
    */
   public static List> replaceMatchingSeqsWith(
           List seqs, List annotations,
-          List ochains,
-          AlignmentI al, String dnaOrProtein, boolean removeOldAnnots)
+          List ochains, AlignmentI al, String dnaOrProtein,
+          boolean removeOldAnnots)
   {
     List orig = new ArrayList(), repl = new ArrayList();
     List aligs = new ArrayList();
@@ -1106,7 +1105,7 @@ public class AlignSeq
     {
       ArrayList matches = new ArrayList();
       ArrayList aligns = new ArrayList();
-  
+
       for (SequenceI sq : ochains)
       {
         SequenceI bestm = null;
@@ -1114,8 +1113,7 @@ public class AlignSeq
         int bestscore = 0;
         for (SequenceI msq : al.getSequences())
         {
-          AlignSeq aseq = doGlobalNWAlignment(msq, sq,
-                  dnaOrProtein);
+          AlignSeq aseq = doGlobalNWAlignment(msq, sq, dnaOrProtein);
           if (bestm == null || aseq.getMaxScore() > bestscore)
           {
             bestscore = aseq.getMaxScore();
@@ -1141,7 +1139,8 @@ public class AlignSeq
           sq.setName(sp.getName());
           sq.setDescription(sp.getDescription());
           Mapping sp2sq;
-          sq.transferAnnotation(sp, sp2sq = aligns.get(q).getMappingFromS1(false));
+          sq.transferAnnotation(sp,
+                  sp2sq = aligns.get(q).getMappingFromS1(false));
           aligs.add(aligns.get(q));
           int inspos = -1;
           for (int ap = 0; ap < annotations.size();)
@@ -1152,9 +1151,12 @@ public class AlignSeq
               {
                 inspos = ap;
               }
-              if (removeOldAnnots) {
+              if (removeOldAnnots)
+              {
                 annotations.remove(ap);
-              } else {
+              }
+              else
+              {
                 AlignmentAnnotation alan = annotations.remove(ap);
                 alan.liftOver(sq, sp2sq);
                 alan.setSequenceRef(sq);
diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java
index e02aa9e..a8e61e9 100644
--- a/src/jalview/analysis/AlignmentAnnotationUtils.java
+++ b/src/jalview/analysis/AlignmentAnnotationUtils.java
@@ -1,5 +1,9 @@
 package jalview.analysis;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -8,10 +12,6 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-
 public class AlignmentAnnotationUtils
 {
 
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 0022af6..b810050 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -551,8 +551,7 @@ public class AlignmentSorter
    * @return DOCUMENT ME!
    */
   private static List _sortByTree(SequenceNode node,
-          List tmp,
-          List seqset)
+          List tmp, List seqset)
   {
     if (node == null)
     {
@@ -719,9 +718,9 @@ public class AlignmentSorter
   public static void sortByFeature(String featureLabel, String groupLabel,
           int start, int stop, AlignmentI alignment, String method)
   {
-    sortByFeature(featureLabel == null ? null : new String[]
-    { featureLabel }, groupLabel == null ? null : new String[]
-    { groupLabel }, start, stop, alignment, method);
+    sortByFeature(featureLabel == null ? null
+            : new String[] { featureLabel }, groupLabel == null ? null
+            : new String[] { groupLabel }, start, stop, alignment, method);
   }
 
   private static boolean containsIgnoreCase(final String lab,
@@ -752,7 +751,9 @@ public class AlignmentSorter
     if (method != FEATURE_SCORE && method != FEATURE_LABEL
             && method != FEATURE_DENSITY)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_sortbyfeature"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_sortbyfeature"));
     }
     boolean ignoreScore = method != FEATURE_SCORE;
     StringBuffer scoreLabel = new StringBuffer();
@@ -928,7 +929,8 @@ public class AlignmentSorter
     {
       if (method == FEATURE_LABEL)
       {
-        throw new Error(MessageManager.getString("error.not_yet_implemented"));
+        throw new Error(
+                MessageManager.getString("error.not_yet_implemented"));
       }
     }
     if (lastSortByFeatureScore == null
diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 3af4913..cbd9c96 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -228,8 +228,7 @@ public class AlignmentUtils
    * @param cdnaAlignment
    * @return
    */
-  public static boolean mapProteinToCdna(
-          final AlignmentI proteinAlignment,
+  public static boolean mapProteinToCdna(final AlignmentI proteinAlignment,
           final AlignmentI cdnaAlignment)
   {
     if (proteinAlignment == null || cdnaAlignment == null)
@@ -414,8 +413,7 @@ public class AlignmentUtils
     if (cdnaLength != mappedLength
             && cdnaLength > 2
             && String.valueOf(cdnaSeqChars, 0, 3).toUpperCase()
-                    .equals(
-                    ResidueProperties.START))
+                    .equals(ResidueProperties.START))
     {
       cdnaStart += 3;
       cdnaLength -= 3;
@@ -429,9 +427,8 @@ public class AlignmentUtils
     {
       return null;
     }
-    MapList map = new MapList(new int[]
-    { cdnaStart, cdnaEnd }, new int[]
-    { proteinStart, proteinEnd }, 3, 1);
+    MapList map = new MapList(new int[] { cdnaStart, cdnaEnd }, new int[] {
+        proteinStart, proteinEnd }, 3, 1);
     return map;
   }
 
@@ -458,8 +455,7 @@ public class AlignmentUtils
             && aaResidue < aaSeqChars.length; i += 3, aaResidue++)
     {
       String codon = String.valueOf(cdnaSeqChars, i, 3);
-      final String translated = ResidueProperties.codonTranslate(
-              codon);
+      final String translated = ResidueProperties.codonTranslate(codon);
       /*
        * allow * in protein to match untranslatable in dna
        */
@@ -468,8 +464,7 @@ public class AlignmentUtils
       {
         continue;
       }
-      if (translated == null
-              || !(aaRes == translated.charAt(0)))
+      if (translated == null || !(aaRes == translated.charAt(0)))
       {
         // debug
         // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
@@ -500,7 +495,8 @@ public class AlignmentUtils
           boolean preserveUnmappedGaps)
   {
     /*
-     * Get any mappings from the source alignment to the target (dataset) sequence.
+     * Get any mappings from the source alignment to the target (dataset)
+     * sequence.
      */
     // TODO there may be one AlignedCodonFrame per dataset sequence, or one with
     // all mappings. Would it help to constrain this?
@@ -509,7 +505,7 @@ public class AlignmentUtils
     {
       return false;
     }
-  
+
     /*
      * Locate the aligned source sequence whose dataset sequence is mapped. We
      * just take the first match here (as we can't align cDNA like more than one
@@ -526,7 +522,7 @@ public class AlignmentUtils
         break;
       }
     }
-  
+
     if (alignFrom == null)
     {
       return false;
@@ -551,15 +547,15 @@ public class AlignmentUtils
    * @param preserveMappedGaps
    */
   public static void alignSequenceAs(SequenceI alignTo,
-          SequenceI alignFrom,
-          AlignedCodonFrame mapping, String myGap, char sourceGap,
-          boolean preserveMappedGaps, boolean preserveUnmappedGaps)
+          SequenceI alignFrom, AlignedCodonFrame mapping, String myGap,
+          char sourceGap, boolean preserveMappedGaps,
+          boolean preserveUnmappedGaps)
   {
     // TODO generalise to work for Protein-Protein, dna-dna, dna-protein
     final char[] thisSeq = alignTo.getSequence();
     final char[] thatAligned = alignFrom.getSequence();
     StringBuilder thisAligned = new StringBuilder(2 * thisSeq.length);
-  
+
     // aligned and dataset sequence positions, all base zero
     int thisSeqPos = 0;
     int sourceDsPos = 0;
@@ -696,8 +692,8 @@ public class AlignmentUtils
    */
   protected static int calculateGapsToInsert(boolean preserveMappedGaps,
           boolean preserveUnmappedGaps, int sourceGapMappedLength,
-          boolean inExon, int trailingGapLength,
-          int intronLength, final boolean startOfCodon)
+          boolean inExon, int trailingGapLength, int intronLength,
+          final boolean startOfCodon)
   {
     int gapsToAdd = 0;
     if (startOfCodon)
@@ -821,8 +817,8 @@ public class AlignmentUtils
       // mapping is from protein to nucleotide
       toDna = true;
       // should ideally get gap count ratio from mapping
-      gap = String.valueOf(new char[]
-      { gapCharacter, gapCharacter, gapCharacter });
+      gap = String.valueOf(new char[] { gapCharacter, gapCharacter,
+          gapCharacter });
     }
     else
     {
@@ -965,9 +961,9 @@ public class AlignmentUtils
     int column = 0;
     for (AlignedCodon codon : alignedCodons.keySet())
     {
-      final Map columnResidues = alignedCodons.get(codon);
-      for (Entry entry : columnResidues
-              .entrySet())
+      final Map columnResidues = alignedCodons
+              .get(codon);
+      for (Entry entry : columnResidues.entrySet())
       {
         // place translated codon at its column position in sequence
         entry.getKey().getSequence()[column] = entry.getValue().charAt(0);
@@ -994,8 +990,7 @@ public class AlignmentUtils
    *          the map we are building up
    */
   static void addCodonPositions(SequenceI dna, SequenceI protein,
-          char gapChar,
-          Mapping seqMap,
+          char gapChar, Mapping seqMap,
           Map> alignedCodons)
   {
     Iterator codons = seqMap.getCodonIterator(dna, gapChar);
@@ -1068,23 +1063,25 @@ public class AlignmentUtils
    * @return
    */
   protected static boolean isMappable(SequenceI dnaSeq,
-          SequenceI proteinSeq,
-          Set mappings)
+          SequenceI proteinSeq, Set mappings)
   {
     if (dnaSeq == null || proteinSeq == null)
     {
       return false;
     }
 
-    SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq.getDatasetSequence();
+    SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq
+            .getDatasetSequence();
     SequenceI proteinDs = proteinSeq.getDatasetSequence() == null ? proteinSeq
             : proteinSeq.getDatasetSequence();
-    
+
     /*
      * Already mapped?
      */
-    for (AlignedCodonFrame mapping : mappings) {
-      if ( proteinDs == mapping.getAaForDnaSeq(dnaDs)) {
+    for (AlignedCodonFrame mapping : mappings)
+    {
+      if (proteinDs == mapping.getAaForDnaSeq(dnaDs))
+      {
         return true;
       }
     }
@@ -1112,7 +1109,8 @@ public class AlignmentUtils
    *          the alignment to check for presence of annotations
    */
   public static void findAddableReferenceAnnotations(
-          List sequenceScope, Map labelForCalcId,
+          List sequenceScope,
+          Map labelForCalcId,
           final Map> candidates,
           AlignmentI al)
   {
@@ -1120,7 +1118,7 @@ public class AlignmentUtils
     {
       return;
     }
-  
+
     /*
      * For each sequence in scope, make a list of any annotations on the
      * underlying dataset sequence which are not already on the alignment.
@@ -1148,8 +1146,7 @@ public class AlignmentUtils
          * sequence.
          */
         final Iterable matchedAlignmentAnnotations = al
-                .findAnnotations(seq, dsann.getCalcId(),
-                        dsann.label);
+                .findAnnotations(seq, dsann.getCalcId(), dsann.label);
         if (!matchedAlignmentAnnotations.iterator().hasNext())
         {
           result.add(dsann);
@@ -1197,7 +1194,7 @@ public class AlignmentUtils
           endRes = selectionGroup.getEndRes();
         }
         copyAnn.restrict(startRes, endRes);
-  
+
         /*
          * Add to the sequence (sets copyAnn.datasetSequence), unless the
          * original annotation is already on the sequence.
@@ -1235,8 +1232,7 @@ public class AlignmentUtils
           Collection types, List forSequences,
           boolean anyType, boolean doShow)
   {
-    for (AlignmentAnnotation aa : al
-            .getAlignmentAnnotation())
+    for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
     {
       if (anyType || types.contains(aa.label))
       {
@@ -1311,7 +1307,7 @@ public class AlignmentUtils
   {
     Set newMappings = new LinkedHashSet();
     List exonSequences = new ArrayList();
-    
+
     for (SequenceI dnaSeq : dna)
     {
       final SequenceI ds = dnaSeq.getDatasetSequence();
@@ -1414,11 +1410,9 @@ public class AlignmentUtils
        * contiguous exons
        */
       List exonRange = new ArrayList();
-      exonRange.add(new int[]
-      { 1, newSequence.length() });
+      exonRange.add(new int[] { 1, newSequence.length() });
       MapList map = new MapList(exonRange, seqMapping.getMap()
-              .getToRanges(),
-              3, 1);
+              .getToRanges(), 3, 1);
       newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
       MapList cdsToDnaMap = new MapList(dnaExonRanges, exonRange, 1, 1);
       newMapping.addMap(dnaSeq, exon.getDatasetSequence(), cdsToDnaMap);
diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index 0873f89..b0cfe20 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -46,7 +46,8 @@ public class AnnotationSorter
       return description;
     }
 
-    public static SequenceAnnotationOrder forDescription(String d) {
+    public static SequenceAnnotationOrder forDescription(String d)
+    {
       for (SequenceAnnotationOrder order : values())
       {
         if (order.toString().equals(d))
@@ -279,9 +280,11 @@ public class AnnotationSorter
           AlignmentAnnotation[] alignmentAnnotations)
   {
     sequenceIndices.clear();
-    for (AlignmentAnnotation ann : alignmentAnnotations) {
+    for (AlignmentAnnotation ann : alignmentAnnotations)
+    {
       SequenceI seq = ann.sequenceRef;
-      if (seq != null) {
+      if (seq != null)
+      {
         int index = AlignmentUtils.getSequenceIndex(alignment, seq);
         sequenceIndices.put(seq, index);
       }
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index b8f1d92..d4ae57d 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -280,8 +280,7 @@ public class Conservation
                 resultHash.put(type, ht.get("-"));
               }
             }
-            else if (((Integer) resultHash.get(type)).equals(ht
-                    .get(res)) == false)
+            else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
             {
               resultHash.put(type, new Integer(-1));
             }
@@ -374,14 +373,14 @@ public class Conservation
     {
       consString.append('-');
     }
-    consSymbs = new String[end-start+1];
+    consSymbs = new String[end - start + 1];
     for (int i = start; i <= end; i++)
     {
       gapcons = countConsNGaps(i);
       totGaps = gapcons[1];
       pgaps = ((float) totGaps * 100) / sequences.length;
-      consSymbs[i-start]=new String();
-      
+      consSymbs[i - start] = new String();
+
       if (percentageGaps > pgaps)
       {
         resultHash = total[i - start];
@@ -398,7 +397,7 @@ public class Conservation
           {
             if (result.intValue() == 1)
             {
-              consSymbs[i-start] = type+" "+consSymbs[i-start];
+              consSymbs[i - start] = type + " " + consSymbs[i - start];
               count++;
             }
           }
@@ -406,14 +405,17 @@ public class Conservation
           {
             if (result.intValue() != -1)
             {
-              { 
-                 if (result.intValue()==0) {
-                   consSymbs[i-start] = consSymbs[i-start]+ " !"+type;
-                 } else {
-                   consSymbs[i-start] = type+" "+consSymbs[i-start];
-                 }
+              {
+                if (result.intValue() == 0)
+                {
+                  consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+                }
+                else
+                {
+                  consSymbs[i - start] = type + " " + consSymbs[i - start];
+                }
               }
-              
+
               count++;
             }
           }
@@ -702,9 +704,8 @@ public class Conservation
       String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
               : "";
       conservation.annotations[i] = new Annotation(String.valueOf(c),
-              conssym, ' ', value, new Color(minR
-                      + (maxR * vprop), minG + (maxG * vprop), minB
-                      + (maxB * vprop)));
+              conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+                      + (maxG * vprop), minB + (maxB * vprop)));
 
       // Quality calc
       if (quality2 != null)
diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 7238239..2e6431c 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -20,10 +20,6 @@
  */
 package jalview.analysis;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -35,6 +31,10 @@ import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
 /**
  * Functions for cross-referencing sequence databases. user must first specify
  * if cross-referencing from protein or dna (set dna==true)
@@ -267,7 +267,7 @@ public class CrossRef
           {
             found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf); // ,false,!dna);
             if (found)
-             {
+            {
               xrfs[r] = null; // we've recovered seqs for this one.
             }
           }
@@ -408,8 +408,7 @@ public class CrossRef
    */
   private static boolean searchDatasetXrefs(SequenceI sequenceI,
           boolean dna, DBRefEntry[] lrfs, AlignmentI dataset,
-          List rseqs,
-          AlignedCodonFrame cf)
+          List rseqs, AlignedCodonFrame cf)
   {
     boolean found = false;
     if (lrfs == null)
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 5696838..9ce00cc 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -208,9 +208,8 @@ public class Dna
     for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
-      DBRefEntry[] dnarefs = DBRefUtils
-              .selectRefs(dna.getDBRef(),
-                      jalview.datamodel.DBRefSource.DNACODINGDBS);
+      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+              jalview.datamodel.DBRefSource.DNACODINGDBS);
       if (dnarefs != null)
       {
         // intersect with pep
@@ -300,8 +299,7 @@ public class Dna
         aa.graphHeight = annotation.graphHeight;
         if (annotation.getThreshold() != null)
         {
-          aa.setThreshold(new GraphLine(annotation
-                  .getThreshold()));
+          aa.setThreshold(new GraphLine(annotation.getThreshold()));
         }
         if (annotation.hasScore)
         {
@@ -446,8 +444,10 @@ public class Dna
           aa = gapString;
           if (skipint == null)
           {
-            skipint = new int[]
-            { alignedCodon.pos1, alignedCodon.pos3 /* cdp[0], cdp[2] */};
+            skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /*
+                                                                        * cdp[0],
+                                                                        * cdp[2]
+                                                                        */};
           }
           skipint[1] = alignedCodon.pos3; // cdp[2];
         }
@@ -683,8 +683,7 @@ public class Dna
          * range iv[0] = skipint[1]; } else { } } } else if (iv[0] proteinSeqs)
+  protected void insertAAGap(int pos, List proteinSeqs)
   {
     aaWidth++;
     for (SequenceI seq : proteinSeqs)
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 875322b..72097e0 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -206,7 +206,7 @@ public class Finder
           {
             continue;
           }
-// if invalid string used, then regex has no matched to/from
+          // if invalid string used, then regex has no matched to/from
           int sres = seq
                   .findPosition(resIndex
                           + Integer.parseInt(spaces.elementAt(resIndex)
diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 787e036..51a818f 100644
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -91,8 +91,8 @@ public class Grouping
     i = 0;
     for (String key : gps.keySet())
     {
-      SequenceGroup group = new SequenceGroup(gps.get(key),
-              "Subseq: " + key, null, true, true, false, 0, width - 1);
+      SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
+              + key, null, true, true, false, 0, width - 1);
 
       groups[i++] = group;
     }
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 3470dbc..4489783 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1099,8 +1099,7 @@ public class NJTree
               + ((SequenceI) node.element()).getName());
     }
 
-    System.out.println(" dist = " + node.dist + " "
-            + node.count + " "
+    System.out.println(" dist = " + node.dist + " " + node.count + " "
             + node.height);
   }
 
diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index caf7baf..06a139b 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -20,14 +20,14 @@
  */
 package jalview.analysis;
 
-import java.io.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.BinarySequence;
 import jalview.datamodel.BinarySequence.InvalidSequenceTypeException;
-import jalview.math.*;
+import jalview.math.Matrix;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.ScoreMatrix;
 
+import java.io.PrintStream;
+
 /**
  * Performs Principal Component Analysis on given sequences
  * 
diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 3347800..eb639b6 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -20,12 +20,12 @@
  */
 package jalview.analysis;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
+import com.stevesoft.pat.Regex;
+
 public class ParseProperties
 {
   /**
@@ -57,9 +57,8 @@ public class ParseProperties
   public int getScoresFromDescription(String ScoreName,
           String ScoreDescriptions, String regex, boolean repeat)
   {
-    return getScoresFromDescription(new String[]
-    { ScoreName }, new String[]
-    { ScoreDescriptions }, regex, repeat);
+    return getScoresFromDescription(new String[] { ScoreName },
+            new String[] { ScoreDescriptions }, regex, repeat);
   }
 
   public int getScoresFromDescription(String[] ScoreNames,
diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 1b89cd1..e752126 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -42,15 +42,13 @@ public class Rna
 
   static Hashtable pairHash = new Hashtable();
 
-  private static final Character[] openingPars =
-  { '(', '[', '{', '<', 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J',
-      'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
-      'Y', 'Z' };
+  private static final Character[] openingPars = { '(', '[', '{', '<', 'A',
+      'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O',
+      'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z' };
 
-  private static final Character[] closingPars =
-  { ')', ']', '}', '>', 'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j',
-      'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x',
-      'y', 'z' };
+  private static final Character[] closingPars = { ')', ']', '}', '>', 'a',
+      'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o',
+      'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z' };
 
   private static HashSet openingParsSet = new HashSet(
           Arrays.asList(openingPars));
@@ -86,7 +84,11 @@ public class Rna
   {
     if (!isClosingParenthesis(closingParenthesis))
     {
-      throw new WUSSParseException(MessageManager.formatMessage("exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis", new String[]{new StringBuffer(closingParenthesis).toString()}), -1);
+      throw new WUSSParseException(
+              MessageManager.formatMessage(
+                      "exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis",
+                      new String[] { new StringBuffer(closingParenthesis)
+                              .toString() }), -1);
     }
 
     return closingToOpening.get(closingParenthesis);
@@ -130,14 +132,18 @@ public class Rna
 
         if (!stacks.containsKey(opening))
         {
-          throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_unseen_closing_char", new String[]{new StringBuffer(base).toString()}), i);
+          throw new WUSSParseException(MessageManager.formatMessage(
+                  "exception.mismatched_unseen_closing_char",
+                  new String[] { new StringBuffer(base).toString() }), i);
         }
 
         Stack stack = stacks.get(opening);
         if (stack.isEmpty())
         {
           // error whilst parsing i'th position. pass back
-          throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_closing_char", new String[]{new StringBuffer(base).toString()}), i);
+          throw new WUSSParseException(MessageManager.formatMessage(
+                  "exception.mismatched_closing_char",
+                  new String[] { new StringBuffer(base).toString() }), i);
         }
         int temp = stack.pop();
 
@@ -150,7 +156,10 @@ public class Rna
       Stack stack = stacks.get(opening);
       if (!stack.empty())
       {
-        throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_opening_char", new String[]{new StringBuffer(opening).toString(),Integer.valueOf(stack.pop()).toString()}), i);
+        throw new WUSSParseException(MessageManager.formatMessage(
+                "exception.mismatched_opening_char",
+                new String[] { new StringBuffer(opening).toString(),
+                    Integer.valueOf(stack.pop()).toString() }), i);
       }
     }
     return pairs;
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index c23f03c..40bedad 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -20,15 +20,15 @@
  */
 package jalview.analysis;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
 public class SeqsetUtils
 {
 
@@ -60,8 +60,9 @@ public class SeqsetUtils
       }
     }
     sqinfo.put("SeqFeatures", sfeat);
-    sqinfo.put("PdbId", (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
-            : new Vector());
+    sqinfo.put("PdbId",
+            (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+                    : new Vector());
     sqinfo.put("datasetSequence",
             (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
                     : new Sequence("THISISAPLACEHOLDER", ""));
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 5b812dd..35a72e3 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -58,7 +58,7 @@ public class SequenceIdMatcher
       // associated with this key.
       names.put(new SeqIdName(seq.getDisplayId(true)), seq);
       SequenceI dbseq = seq;
-      while (dbseq.getDatasetSequence()!=null)
+      while (dbseq.getDatasetSequence() != null)
       {
         dbseq = dbseq.getDatasetSequence();
       }
@@ -191,7 +191,7 @@ public class SequenceIdMatcher
 
     SeqIdName nam = new SeqIdName(seqnam);
     List m = findAllIdMatches(nam);
-    if (m!=null)
+    if (m != null)
     {
       return m.toArray(new SequenceI[m.size()]);
     }
diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 3c8274e..88387dd 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -194,9 +194,8 @@ public class StructureFrequency
       if (profile)
       {
         // TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
-        residueHash.put(PROFILE, new int[][]
-        { values, new int[]
-        { jSize, (jSize - values['-']) } });
+        residueHash.put(PROFILE, new int[][] { values,
+            new int[] { jSize, (jSize - values['-']) } });
 
         residueHash.put(PAIRPROFILE, pairs);
       }
@@ -239,9 +238,8 @@ public class StructureFrequency
         }
         if (profile)
         {
-          residueHash.put(PROFILE, new int[][]
-          { values, new int[]
-          { jSize, (jSize - values['-']) } });
+          residueHash.put(PROFILE, new int[][] { values,
+              new int[] { jSize, (jSize - values['-']) } });
 
           residueHash.put(PAIRPROFILE, pairs);
         }
@@ -427,8 +425,7 @@ public class StructureFrequency
         {
           for (int d = 65; d < 90; d++)
           {
-            ca[x] = new int[]
-            { c, d };
+            ca[x] = new int[] { c, d };
             vl[x] = pairs[c][d];
             x++;
           }
@@ -447,8 +444,7 @@ public class StructureFrequency
           {
             tval = (vl[c] * 100f / divisor);
             mouseOver += ((p == 0) ? "" : "; ") + (char) ca[c][0]
-                    + (char) ca[c][1] + " " + fmt.form(tval)
-                    + "%";
+                    + (char) ca[c][1] + " " + fmt.form(tval) + "%";
             p++;
 
           }
@@ -493,8 +489,7 @@ public class StructureFrequency
     {
       for (int d = 65; d < 90; d++)
       {
-        ca[x] = new int[]
-        { c, d };
+        ca[x] = new int[] { c, d };
         vl[x] = pairs[c][d];
         x++;
       }
diff --git a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java b/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
index 52e8451..2ff2518 100644
--- a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
+++ b/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
@@ -22,7 +22,6 @@ package jalview.analysis.scoremodels;
 
 import jalview.api.analysis.ScoreModelI;
 import jalview.datamodel.AlignmentView;
-import jalview.schemes.ScoreMatrix;
 import jalview.util.Comparison;
 
 public abstract class PairwiseSeqScoreModel implements ScoreModelI
diff --git a/src/jalview/api/AlignViewControllerGuiI.java b/src/jalview/api/AlignViewControllerGuiI.java
index 4896b35..86e61e7 100644
--- a/src/jalview/api/AlignViewControllerGuiI.java
+++ b/src/jalview/api/AlignViewControllerGuiI.java
@@ -43,9 +43,9 @@ public interface AlignViewControllerGuiI
   void addHistoryItem(CommandI command);
 
   void setShowSeqFeatures(boolean show);
-  
+
   void setMenusForViewport();
-  
+
   void changeColour(ColourSchemeI cs);
 
   /**
diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index fef9f14..a2f2204 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -65,14 +65,20 @@ public interface AlignViewControllerI
           boolean extendCurrent, boolean clearColumns, String featureType);
 
   /**
-   * sort the alignment or current selection by average score over the given set of features
-   * @param typ list of feature names or null to use currently displayed features
+   * sort the alignment or current selection by average score over the given set
+   * of features
+   * 
+   * @param typ
+   *          list of feature names or null to use currently displayed features
    */
   void sortAlignmentByFeatureScore(String[] typ);
 
   /**
-   * sort the alignment or current selection by distribution of the given set of features
-   * @param typ list of feature names or null to use currently displayed features
+   * sort the alignment or current selection by distribution of the given set of
+   * features
+   * 
+   * @param typ
+   *          list of feature names or null to use currently displayed features
    */
   void sortAlignmentByFeatureDensity(String[] typ);
 
diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 93b2134..5df38d6 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -178,7 +178,7 @@ public interface AlignViewportI extends ViewStyleI
    */
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
-  
+
   void setSequenceColour(SequenceI seq, Color col);
 
   Color getSequenceColour(SequenceI seq);
@@ -251,8 +251,11 @@ public interface AlignViewportI extends ViewStyleI
 
   /**
    * get a copy of the currently visible alignment annotation
-   * @param selectedOnly if true - trim to selected regions on the alignment
-   * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
+   * 
+   * @param selectedOnly
+   *          if true - trim to selected regions on the alignment
+   * @return an empty list or new alignment annotation objects shown only
+   *         visible columns trimmed to selected region only
    */
   List getVisibleAlignmentAnnotation(
           boolean selectedOnly);
diff --git a/src/jalview/api/AlignmentViewPanel.java b/src/jalview/api/AlignmentViewPanel.java
index f0fd2e1..ef59996 100644
--- a/src/jalview/api/AlignmentViewPanel.java
+++ b/src/jalview/api/AlignmentViewPanel.java
@@ -56,7 +56,7 @@ public interface AlignmentViewPanel extends OOMHandlerI
   FeatureRenderer getFeatureRenderer();
 
   FeatureRenderer cloneFeatureRenderer();
-  
+
   /**
    * 
    * @return displayed name for the view
diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index cf98b2f..0d0adaa 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -85,7 +85,7 @@ public interface FeatureRenderer
    * 
    * @return
    */
-  Map getFeatureColours();
+  Map getFeatureColours();
 
   /**
    * query the alignment view to find all features
@@ -100,7 +100,7 @@ public interface FeatureRenderer
    * 
    * @return
    */
-  Map getDisplayedFeatureCols();
+  Map getDisplayedFeatureCols();
 
   /**
    * get all registered groups
diff --git a/src/jalview/api/FeatureSettingsControllerI.java b/src/jalview/api/FeatureSettingsControllerI.java
index 2bcd667..3f1b863 100644
--- a/src/jalview/api/FeatureSettingsControllerI.java
+++ b/src/jalview/api/FeatureSettingsControllerI.java
@@ -4,5 +4,5 @@ public interface FeatureSettingsControllerI
 {
 
   void discoverAllFeatureData();
-  
+
 }
diff --git a/src/jalview/api/ViewStyleI.java b/src/jalview/api/ViewStyleI.java
index 933c270..85fa2df 100644
--- a/src/jalview/api/ViewStyleI.java
+++ b/src/jalview/api/ViewStyleI.java
@@ -157,7 +157,7 @@ public interface ViewStyleI
   void setUpperCasebold(boolean upperCasebold);
 
   boolean isUpperCasebold();
-  
+
   boolean sameStyle(ViewStyleI them);
 
   void setFontName(String name);
diff --git a/src/jalview/api/analysis/ViewBasedAnalysisI.java b/src/jalview/api/analysis/ViewBasedAnalysisI.java
index 3404afc..55deaae 100644
--- a/src/jalview/api/analysis/ViewBasedAnalysisI.java
+++ b/src/jalview/api/analysis/ViewBasedAnalysisI.java
@@ -1,6 +1,5 @@
 package jalview.api.analysis;
 
-import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 
 public interface ViewBasedAnalysisI
@@ -8,6 +7,7 @@ public interface ViewBasedAnalysisI
 
   /**
    * Parameterise the analysis model using the current view
+   * 
    * @param view
    * @return true if model is applicable and calculation should proceed
    */
diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index edbbbbf..fd66388 100644
--- a/src/jalview/api/structures/JalviewStructureDisplayI.java
+++ b/src/jalview/api/structures/JalviewStructureDisplayI.java
@@ -54,8 +54,10 @@ public interface JalviewStructureDisplayI
    *          if true, force close any linked external viewer process
    */
   void closeViewer(boolean closeExternalViewer);
+
   /**
    * apply a colourscheme to the structures in the viewer
+   * 
    * @param colourScheme
    */
   void setJalviewColourScheme(ColourSchemeI colourScheme);
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 30f2e7f..1d2feb2 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -181,7 +181,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
           MessageManager.getString("label.sequence_details"));
 
   MenuItem makeReferenceSeq = new MenuItem();
-  
+
   SequenceI seq;
 
   MenuItem revealAll = new MenuItem();
@@ -231,8 +231,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (sg != null && sg.getSize() > 0)
     {
       editGroupName.setLabel(MessageManager.formatMessage(
-              "label.name_param", new Object[]
-              { sg.getName() }));
+              "label.name_param", new Object[] { sg.getName() }));
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
@@ -275,8 +274,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
           // collect matching db-refs
           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
-                  seq.getDBRef(), new String[]
-                  { target });
+                  seq.getDBRef(), new String[] { target });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
@@ -390,8 +388,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
                 .getString("action.set_as_reference")); // );
       }
       repGroup.setLabel(MessageManager.formatMessage(
-              "label.represent_group_with", new Object[]
-              { seq.getName() }));
+              "label.represent_group_with", new Object[] { seq.getName() }));
     }
     else
     {
@@ -720,7 +717,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
         if (dialog.accept)
         {
-          EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
+          EditCommand editCommand = new EditCommand(
+                  MessageManager.getString("label.edit_sequences"),
                   Action.REPLACE, dialog.getName().replace(' ',
                           ap.av.getGapCharacter()),
                   sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
@@ -807,7 +805,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
               features, true, ap))
       {
         ap.alignFrame.sequenceFeatures.setState(true);
-        ap.av.setShowSequenceFeatures(true);;
+        ap.av.setShowSequenceFeatures(true);
+        ;
         ap.highlightSearchResults(null);
       }
     }
@@ -825,8 +824,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-            "label.selection_output_command", new Object[]
-            { e.getActionCommand() }), 600, 500);
+            "label.selection_output_command",
+            new Object[] { e.getActionCommand() }), 600, 500);
     // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
     // now returns a full copy of sequence data
     // TODO consider using getSequenceSelection instead here
@@ -843,8 +842,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   protected void showSequenceDetails()
   {
-    createSequenceDetailsReport(new SequenceI[]
-    { seq });
+    createSequenceDetailsReport(new SequenceI[] { seq });
   }
 
   public void createSequenceDetailsReport(SequenceI[] sequences)
@@ -856,17 +854,16 @@ public class APopupMenu extends java.awt.PopupMenu implements
     for (SequenceI seq : sequences)
     {
       contents.append(MessageManager.formatMessage(
-              "label.annotation_for_displayid", new Object[]
-              { seq.getDisplayId(true) }));
-      new SequenceAnnotationReport(null)
-              .createSequenceAnnotationReport(
-                      contents,
-                      seq,
-                      true,
-                      true,
-                      false,
-                      (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()
-                              : null);
+              "label.annotation_for_displayid",
+              new Object[] { seq.getDisplayId(true) }));
+      new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+              contents,
+              seq,
+              true,
+              true,
+              false,
+              (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
+                      .getMinMax() : null);
       contents.append("
");
     }
     Frame frame = new Frame();
@@ -875,8 +872,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
                     : "Selection"), 600, 500);
     cap.setText(MessageManager.formatMessage("label.html_content",
-            new Object[]
-            { contents.toString() }));
+            new Object[] { contents.toString() }));
   }
 
   void editName()
@@ -902,13 +898,13 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
       if (ap.av.applet.jmolAvailable)
       {
-        new jalview.appletgui.AppletJmol(entry, new SequenceI[]
-        { seq }, null, ap, AppletFormatAdapter.URL);
+        new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
+                null, ap, AppletFormatAdapter.URL);
       }
       else
       {
-        new MCview.AppletPDBViewer(entry, new SequenceI[]
-        { seq }, null, ap, AppletFormatAdapter.URL);
+        new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+                ap, AppletFormatAdapter.URL);
       }
 
     }
@@ -920,8 +916,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-              "label.paste_pdb_file_for_sequence", new Object[]
-              { seq.getName() }), 400, 300);
+              "label.paste_pdb_file_for_sequence",
+              new Object[] { seq.getName() }), 400, 300);
     }
   }
 
@@ -964,8 +960,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
     hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
     repGroup.setLabel(MessageManager.formatMessage(
-            "label.represent_group_with", new Object[]
-            { "" }));
+            "label.represent_group_with", new Object[] { "" }));
     revealAll.setLabel(MessageManager.getString("action.reveal_all"));
     revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
     menu1.setLabel(MessageManager.getString("label.group") + ":");
@@ -1005,32 +1000,39 @@ public class APopupMenu extends java.awt.PopupMenu implements
     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
     noColourmenuItem.addActionListener(this);
 
-    clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
+    clustalColour.setLabel(MessageManager
+            .getString("label.clustalx_colours"));
     clustalColour.addActionListener(this);
     zappoColour.setLabel(MessageManager.getString("label.zappo"));
     zappoColour.addActionListener(this);
     taylorColour.setLabel(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(this);
-    hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
+    hydrophobicityColour.setLabel(MessageManager
+            .getString("label.hydrophobicity"));
     hydrophobicityColour.addActionListener(this);
-    helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
+    helixColour
+            .setLabel(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(this);
-    strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
+    strandColour.setLabel(MessageManager
+            .getString("label.strand_propensity"));
     strandColour.addActionListener(this);
     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(this);
     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(this);
-    abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
+    abovePIDColour.setLabel(MessageManager
+            .getString("label.above_identity_percentage"));
 
-    userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
+    userDefinedColour.setLabel(MessageManager
+            .getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel(MessageManager
             .getString("label.percentage_identity"));
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel("BLOSUM62");
     BLOSUM62Colour.addActionListener(this);
-    conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
+    conservationMenuItem.setLabel(MessageManager
+            .getString("label.conservation"));
 
     editMenu.add(copy);
     copy.addActionListener(this);
@@ -1259,6 +1261,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     getGroup().setDisplayText(showText.getState());
     refresh();
   }
+
   public void makeReferenceSeq_actionPerformed()
   {
     if (!ap.av.getAlignment().hasSeqrep())
@@ -1299,8 +1302,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     SequenceGroup sg = ap.av.getSelectionGroup();
     if (sg == null || sg.getSize() < 1)
     {
-      ap.av.hideSequence(new SequenceI[]
-      { seq });
+      ap.av.hideSequence(new SequenceI[] { seq });
       return;
     }
 
@@ -1348,17 +1350,17 @@ public class APopupMenu extends java.awt.PopupMenu implements
   {
     showMenu.removeAll();
     hideMenu.removeAll();
-  
+
     final List all = Arrays.asList(ALL_ANNOTATIONS);
     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
             false);
     showMenu.addSeparator();
     hideMenu.addSeparator();
-  
+
     final AlignmentAnnotation[] annotations = ap.getAlignment()
             .getAlignmentAnnotation();
-  
+
     /*
      * Find shown/hidden annotations types, distinguished by source (calcId),
      * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
@@ -1367,28 +1369,26 @@ public class APopupMenu extends java.awt.PopupMenu implements
      */
     Map>> shownTypes = new LinkedHashMap>>();
     Map>> hiddenTypes = new LinkedHashMap>>();
-    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
-            hiddenTypes,
-            AlignmentAnnotationUtils.asList(annotations),
-            forSequences);
-  
+    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+            AlignmentAnnotationUtils.asList(annotations), forSequences);
+
     for (String calcId : hiddenTypes.keySet())
     {
       for (List type : hiddenTypes.get(calcId))
       {
-        addAnnotationTypeToShowHide(showMenu, forSequences,
-                calcId, type, false, true);
+        addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+                false, true);
       }
     }
     // grey out 'show annotations' if none are hidden
     showMenu.setEnabled(!hiddenTypes.isEmpty());
-  
+
     for (String calcId : shownTypes.keySet())
     {
       for (List type : shownTypes.get(calcId))
       {
-        addAnnotationTypeToShowHide(hideMenu, forSequences,
-                calcId, type, false, false);
+        addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+                false, false);
       }
     }
     // grey out 'hide annotations' if none are shown
@@ -1425,8 +1425,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
-                forSequences, allTypes, actionIsShow);
+        AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+                types, forSequences, allTypes, actionIsShow);
         refresh();
       }
     });
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b490eb6..3996dee 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -139,8 +139,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * @param title
    * @param embedded
    */
-  public AlignFrame(AlignmentI al, JalviewLite applet,
-          String title, boolean embedded)
+  public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+          boolean embedded)
   {
     this(al, applet, title, embedded, true);
   }
@@ -155,8 +155,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * @param embedded
    * @param addToDisplay
    */
-  public AlignFrame(AlignmentI al, JalviewLite applet,
-          String title, boolean embedded, boolean addToDisplay)
+  public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+          boolean embedded, boolean addToDisplay)
   {
     this(al, null, null, applet, title, embedded, addToDisplay);
   }
@@ -365,11 +365,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean featuresFile = false;
     try
     {
-      featuresFile = new jalview.io.FeaturesFile(file, type)
-              .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
-                      .getFeatureRenderer().getFeatureColours(), featureLinks,
-                      true, viewport.applet.getDefaultParameter(
-                              "relaxedidmatch", false));
+      featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
+              .getAlignment(), alignPanel.seqPanel.seqCanvas
+              .getFeatureRenderer().getFeatureColours(), featureLinks,
+              true, viewport.applet.getDefaultParameter("relaxedidmatch",
+                      false));
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -552,8 +552,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     case KeyEvent.VK_F2:
       viewport.cursorMode = !viewport.cursorMode;
       statusBar.setText(MessageManager.formatMessage(
-              "label.keyboard_editing_mode", new String[]
-              { (viewport.cursorMode ? "on" : "off") }));
+              "label.keyboard_editing_mode",
+              new String[] { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
       {
         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
@@ -926,7 +926,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       boolean visible = (aa.sequenceRef == null ? showForAlignment
               : showForSequences);
-        aa.visible = visible;
+      aa.visible = visible;
     }
     alignPanel.validateAnnotationDimensions(true);
     validate();
@@ -1179,8 +1179,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-              "label.alignment_properties", new String[]
-              { getTitle() }), 400, 250);
+              "label.alignment_properties", new String[] { getTitle() }),
+              400, 250);
     }
     else if (source == overviewMenuItem)
     {
@@ -1341,8 +1341,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-            "label.alignment_output_command", new Object[]
-            { e.getActionCommand() }), 600, 500);
+            "label.alignment_output_command",
+            new Object[] { e.getActionCommand() }), 600, 500);
 
     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
@@ -1381,13 +1381,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return annotation;
   }
 
-  private Map getDisplayedFeatureCols()
+  private Map getDisplayedFeatureCols()
   {
     if (alignPanel.getFeatureRenderer() != null
-            && viewport.getFeaturesDisplayed()!= null)
+            && viewport.getFeaturesDisplayed() != null)
     {
       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
-      
+
     }
     return null;
   }
@@ -1570,8 +1570,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       undoMenuItem.setEnabled(true);
       CommandI command = viewport.getHistoryList().peek();
       undoMenuItem.setLabel(MessageManager.formatMessage(
-              "label.undo_command", new Object[]
-              { command.getDescription() }));
+              "label.undo_command",
+              new Object[] { command.getDescription() }));
     }
     else
     {
@@ -1585,8 +1585,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
       CommandI command = viewport.getRedoList().peek();
       redoMenuItem.setLabel(MessageManager.formatMessage(
-              "label.redo_command", new Object[]
-              { command.getDescription() }));
+              "label.redo_command",
+              new Object[] { command.getDescription() }));
     }
     else
     {
@@ -1881,8 +1881,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
       {
-        copiedHiddenColumns.addElement(new int[]
-        { region[0] - hiddenOffset, region[1] - hiddenOffset });
+        copiedHiddenColumns.addElement(new int[] {
+            region[0] - hiddenOffset, region[1] - hiddenOffset });
       }
     }
     else
@@ -1979,14 +1979,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
       if (newAlignment)
       {
-        String newtitle = MessageManager.getString("label.copied_sequences");
-        if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
+        String newtitle = MessageManager
+                .getString("label.copied_sequences");
+        if (getTitle().startsWith(
+                MessageManager.getString("label.copied_sequences")))
         {
           newtitle = getTitle();
         }
         else
         {
-          newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
+          newtitle = newtitle.concat(MessageManager.formatMessage(
+                  "label.from_msname", new String[] { getTitle() }));
         }
         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
                 viewport.applet, newtitle, false);
@@ -2276,8 +2279,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
 
       statusBar.setText(MessageManager.formatMessage(
-              "label.removed_columns", new String[]
-              { Integer.valueOf(trimRegion.getSize()).toString() }));
+              "label.removed_columns",
+              new String[] { Integer.valueOf(trimRegion.getSize())
+                      .toString() }));
       addHistoryItem(trimRegion);
 
       for (SequenceGroup sg : viewport.getAlignment().getGroups())
@@ -2318,8 +2322,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     addHistoryItem(removeGapCols);
 
     statusBar.setText(MessageManager.formatMessage(
-            "label.removed_empty_columns", new String[]
-            { Integer.valueOf(removeGapCols.getSize()).toString() }));
+            "label.removed_empty_columns",
+            new String[] { Integer.valueOf(removeGapCols.getSize())
+                    .toString() }));
 
     // This is to maintain viewport position on first residue
     // of first sequence
@@ -2501,7 +2506,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (alignPanel != null
             && (fr = alignPanel.getFeatureRenderer()) != null)
     {
-      
+
       fr.setGroupVisibility(Arrays.asList(groups), state);
       alignPanel.seqPanel.seqCanvas.repaint();
       if (alignPanel.overviewPanel != null)
@@ -2552,8 +2557,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     frame.add(overview);
     // +50 must allow for applet frame window
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-            "label.overview_params", new String[]
-            { this.getTitle() }), overview.getPreferredSize().width,
+            "label.overview_params", new String[] { this.getTitle() }),
+            overview.getPreferredSize().width,
             overview.getPreferredSize().height + 50);
 
     frame.pack();
@@ -2829,8 +2834,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
     // HistoryItem.SORT));
     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
-            "label.order_by_params", new String[]
-            { title }), oldOrder, viewport.getAlignment()));
+            "label.order_by_params", new String[] { title }), oldOrder,
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -2927,12 +2932,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         // lite and application
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
         g.drawString(MessageManager.formatMessage(
-                "label.jalviewLite_release", new String[]
-                { version }), x, y += fh);
+                "label.jalviewLite_release", new String[] { version }), x,
+                y += fh);
         g.setFont(new Font("Helvetica", Font.BOLD, 12));
         g.drawString(MessageManager.formatMessage(
-                "label.jaview_build_date", new String[]
-                { builddate }), x, y += fh);
+                "label.jaview_build_date", new String[] { builddate }), x,
+                y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
         g.drawString(MessageManager.getString("label.jalview_authors_1"),
                 x, y += fh * 1.5);
@@ -3798,8 +3803,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       add(statusBar, BorderLayout.SOUTH);
       add(alignPanel, BorderLayout.CENTER);
       // and register with the applet so it can pass external API calls to us
-      jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
-              frameWidth,
+      jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
               frameHeight);
     }
   }
@@ -3915,8 +3919,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // TODO: search for a jmv that involves viewer
     if (jmv == null)
     { // create a new viewer/jalview binding.
-      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
-      { seqs });
+      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
     }
     return jmv;
 
@@ -3999,8 +4002,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         if (seqs[i] != null)
         {
-          sequences.addElement(new Object[]
-          { seqs[i], (chains != null) ? chains[i] : null });
+          sequences.addElement(new Object[] { seqs[i],
+              (chains != null) ? chains[i] : null });
         }
       }
       seqs = new SequenceI[sequences.size()];
@@ -4013,8 +4016,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         chains[i] = (String) oj[1];
       }
     }
-    return new Object[]
-    { seqs, chains };
+    return new Object[] { seqs, chains };
 
   }
 
@@ -4202,7 +4204,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     this.splitFrame = sf;
   }
 
-    // may not need this
+  // may not need this
   @Override
   public void setShowSeqFeatures(boolean b)
   {
@@ -4217,6 +4219,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // setMenusFromViewport(viewport);
 
   }
+
   @Override
   public void refreshFeatureUI(boolean enableIfNecessary)
   {
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e4e3e17..e434825 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -287,7 +287,6 @@ public class AlignViewport extends AlignmentViewport implements
     return font;
   }
 
-
   public void resetSeqLimits(int height)
   {
     setEndSeq(height / getCharHeight());
@@ -303,7 +302,6 @@ public class AlignViewport extends AlignmentViewport implements
     return currentTree;
   }
 
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -325,8 +323,8 @@ public class AlignViewport extends AlignmentViewport implements
   public void sendSelection()
   {
     getStructureSelectionManager().sendSelection(
-                    new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
+            new SequenceGroup(getSelectionGroup()),
+            new ColumnSelection(getColumnSelection()), this);
   }
 
   /**
@@ -467,5 +465,4 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
-
 }
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index fd6652b..34e0cc0 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -162,15 +162,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   {
     return av;
   }
+
   public SequenceRenderer getSequenceRenderer()
   {
     return seqPanel.seqCanvas.sr;
   }
+
   @Override
   public jalview.api.FeatureRenderer getFeatureRenderer()
   {
     return seqPanel.seqCanvas.fr;
   }
+
   @Override
   public jalview.api.FeatureRenderer cloneFeatureRenderer()
   {
@@ -178,6 +181,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     nfr.transferSettings(seqPanel.seqCanvas.fr);
     return nfr;
   }
+
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -449,37 +453,37 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       // setScrollValues(start, seqIndex);
       // }
       // logic copied from jalview.gui.AlignmentPanel:
-        if ((startv = av.getStartRes()) >= start)
-        {
-          /*
-           * Scroll left to make start of search results visible
-           */
-          setScrollValues(start - 1, seqIndex);
-        }
-        else if ((endv = av.getEndRes()) <= end)
-        {
-          /*
-           * Scroll right to make end of search results visible
-           */
-          setScrollValues(startv + 1 + end - endv, seqIndex);
-        }
-        else if ((starts = av.getStartSeq()) > seqIndex)
-        {
-          /*
-           * Scroll up to make start of search results visible
-           */
-          setScrollValues(av.getStartRes(), seqIndex);
-        }
-        else if ((ends = av.getEndSeq()) <= seqIndex)
-        {
-          /*
-           * Scroll down to make end of search results visible
-           */
-          setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
-        }
+      if ((startv = av.getStartRes()) >= start)
+      {
+        /*
+         * Scroll left to make start of search results visible
+         */
+        setScrollValues(start - 1, seqIndex);
+      }
+      else if ((endv = av.getEndRes()) <= end)
+      {
+        /*
+         * Scroll right to make end of search results visible
+         */
+        setScrollValues(startv + 1 + end - endv, seqIndex);
+      }
+      else if ((starts = av.getStartSeq()) > seqIndex)
+      {
         /*
-         * Else results are already visible - no need to scroll
+         * Scroll up to make start of search results visible
          */
+        setScrollValues(av.getStartRes(), seqIndex);
+      }
+      else if ((ends = av.getEndSeq()) <= seqIndex)
+      {
+        /*
+         * Scroll down to make end of search results visible
+         */
+        setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+      }
+      /*
+       * Else results are already visible - no need to scroll
+       */
     }
     else
     {
diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 6ad8648..c07dfb4 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -569,8 +569,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     updateView();
   }
 
-  public class FurtherActionPanel extends Panel implements
-          ItemListener
+  public class FurtherActionPanel extends Panel implements ItemListener
   {
     private AnnotationColumnChooser aColChooser;
 
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 67faf11..5727e9c 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -20,6 +20,14 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
+
 import java.awt.Checkbox;
 import java.awt.CheckboxMenuItem;
 import java.awt.Color;
@@ -44,14 +52,6 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Vector;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-import jalview.util.ParseHtmlBodyAndLinks;
-
 public class AnnotationLabels extends Panel implements ActionListener,
         MouseListener, MouseMotionListener
 {
@@ -540,7 +540,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
             if (aaa.groupRef != null)
             {
               final CheckboxMenuItem chist = new CheckboxMenuItem(
-                      MessageManager.getString("label.show_group_histogram"),
+                      MessageManager
+                              .getString("label.show_group_histogram"),
                       aa[selectedRow].groupRef.isShowConsensusHistogram());
               chist.addItemListener(new ItemListener()
               {
@@ -579,7 +580,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
               popup.add(cprofl);
               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
-                      MessageManager.getString("label.normalise_group_logo"),
+                      MessageManager
+                              .getString("label.normalise_group_logo"),
                       aa[selectedRow].groupRef.isNormaliseSequenceLogo());
               cprofn.addItemListener(new ItemListener()
               {
@@ -602,7 +604,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
             else
             {
               final CheckboxMenuItem chist = new CheckboxMenuItem(
-                      MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+                      MessageManager.getString("label.show_histogram"),
+                      av.isShowConsensusHistogram());
               chist.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -624,7 +627,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(chist);
               final CheckboxMenuItem cprof = new CheckboxMenuItem(
-                      MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+                      MessageManager.getString("label.show_logo"),
+                      av.isShowSequenceLogo());
               cprof.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -647,7 +651,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(cprof);
               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
-                      MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+                      MessageManager.getString("label.normalise_logo"),
+                      av.isNormaliseSequenceLogo());
               cprofn.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -710,36 +715,44 @@ public class AnnotationLabels extends Panel implements ActionListener,
         {
           if (evt.getClickCount() == 1)
           {
-            ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
-                    .asList(new SequenceI[]
-                    { aa[selectedRow].sequenceRef }));
+            ap.seqPanel.ap.idPanel
+                    .highlightSearchResults(Arrays
+                            .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
           }
           else if (evt.getClickCount() >= 2)
           {
             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
             SequenceGroup sg = ap.av.getSelectionGroup();
-            if (sg!=null)
+            if (sg != null)
             {
-              // we make a copy rather than edit the current selection if no modifiers pressed
+              // we make a copy rather than edit the current selection if no
+              // modifiers pressed
               // see Enhancement JAL-1557
               if (!(evt.isControlDown() || evt.isShiftDown()))
               {
                 sg = new SequenceGroup(sg);
                 sg.clear();
                 sg.addSequence(aa[selectedRow].sequenceRef, false);
-              } else {
+              }
+              else
+              {
                 if (evt.isControlDown())
                 {
                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
-                } else {
-                  // notionally, we should also add intermediate sequences from last added sequence ?
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
                   sg.addSequence(aa[selectedRow].sequenceRef, true);
                 }
               }
-            } else {
+            }
+            else
+            {
               sg = new SequenceGroup();
               sg.setStartRes(0);
-              sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+              sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
               sg.addSequence(aa[selectedRow].sequenceRef, false);
             }
             ap.av.setSelectionGroup(sg);
@@ -776,8 +789,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
       for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
         jalview.appletgui.AlignFrame.copiedHiddenColumns
-                .addElement(new int[]
-                { region[0], region[1] });
+                .addElement(new int[] { region[0], region[1] });
       }
     }
   }
diff --git a/src/jalview/appletgui/AnnotationRowFilter.java b/src/jalview/appletgui/AnnotationRowFilter.java
index 8a0a44a..b78f273 100644
--- a/src/jalview/appletgui/AnnotationRowFilter.java
+++ b/src/jalview/appletgui/AnnotationRowFilter.java
@@ -13,8 +13,6 @@ import java.awt.TextField;
 import java.awt.event.ActionEvent;
 import java.util.Vector;
 
-
-
 @SuppressWarnings("serial")
 public abstract class AnnotationRowFilter extends Panel
 {
@@ -56,7 +54,6 @@ public abstract class AnnotationRowFilter extends Panel
    */
   protected boolean sliderDragging = false;
 
-
   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
   {
     this.av = av;
@@ -68,7 +65,6 @@ public abstract class AnnotationRowFilter extends Panel
 
   }
 
-
   public Vector getAnnotationItems(boolean isSeqAssociated)
   {
     Vector list = new Vector();
@@ -167,7 +163,6 @@ public abstract class AnnotationRowFilter extends Panel
     }
   }
 
-
   protected void populateThresholdComboBox(Choice threshold)
   {
     threshold.addItem(MessageManager
@@ -178,7 +173,6 @@ public abstract class AnnotationRowFilter extends Panel
             .getString("label.threshold_feature_below_thereshold"));
   }
 
-
   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
   {
     return currentAnnotation;
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 0379615..b9acac0 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -179,10 +179,8 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     this.ap = ap;
     jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
-            new PDBEntry[]
-            { pdbentry }, new SequenceI[][]
-            { seq }, new String[][]
-            { chains }, protocol);
+            new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
+            new String[][] { chains }, protocol);
     jmb.setColourBySequence(true);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
@@ -347,7 +345,9 @@ public class AppletJmol extends EmbmenuFrame implements
           }
           if (freader == null)
           {
-            throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
+            throw new Exception(
+                    MessageManager
+                            .getString("exception.invalid_datasource_couldnt_obtain_reader"));
           }
           jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
                   freader);
diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 535dc62..5617c64 100644
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -204,8 +204,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
       // TODO: JAL-1102 - should have a warning message in dialog, not simply
       // overwrite the broken input data with the exception
       textarea.setText(MessageManager.formatMessage(
-              "label.could_not_parse_newick_file", new Object[]
-              { ex.getMessage() }));
+              "label.could_not_parse_newick_file",
+              new Object[] { ex.getMessage() }));
       return false;
     }
     return false;
@@ -295,7 +295,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
    */
   protected boolean openSplitFrame(AlignmentI al, String format)
   {
-    final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
+    final AlignmentI thisAlignment = this.alignFrame.getAlignViewport()
+            .getAlignment();
     if (thisAlignment.isNucleotide() == al.isNucleotide())
     {
       // both nucleotide or both protein
@@ -324,7 +325,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     dialog.setMainPanel(question);
     dialog.setVisible(true);
     dialog.toFront();
-    
+
     if (!dialog.accept)
     {
       return false;
@@ -341,8 +342,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
             "Cut & Paste input - " + format, false, false);
     AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
-    AlignFrame proteinFrame = al.isNucleotide() ? copyFrame
-            : newFrame;
+    AlignFrame proteinFrame = al.isNucleotide() ? copyFrame : newFrame;
     SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
     sf.addToDisplay(false, applet);
     return true;
@@ -361,8 +361,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
               jalview.io.AppletFormatAdapter.PASTE);
       if (tcf.isValid())
       {
-        if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
-                true))
+        if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
         {
           alignFrame.tcoffeeColour.setEnabled(true);
           alignFrame.alignPanel.fontChanged();
@@ -377,8 +376,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
           // file valid but didn't get added to alignment for some reason
           alignFrame.statusBar.setText(MessageManager.formatMessage(
                   "label.failed_add_tcoffee_scores",
-                  new Object[]
-                  { (tcf.getWarningMessage() != null ? tcf
+                  new Object[] { (tcf.getWarningMessage() != null ? tcf
                           .getWarningMessage() : "") }));
         }
       }
@@ -393,8 +391,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     if (tcf == null)
     {
       if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
-              textarea.getText(),
-              jalview.io.AppletFormatAdapter.PASTE))
+              textarea.getText(), jalview.io.AppletFormatAdapter.PASTE))
       {
         alignFrame.alignPanel.fontChanged();
         alignFrame.alignPanel.setScrollValues(0, 0);
@@ -429,13 +426,13 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
     if (alignFrame.alignPanel.av.applet.jmolAvailable)
     {
-      new jalview.appletgui.AppletJmol(pdb, new SequenceI[]
-      { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+      new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null,
+              alignFrame.alignPanel, AppletFormatAdapter.PASTE);
     }
     else
     {
-      new MCview.AppletPDBViewer(pdb, new SequenceI[]
-      { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+      new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
+              alignFrame.alignPanel, AppletFormatAdapter.PASTE);
     }
   }
 
diff --git a/src/jalview/appletgui/EditNameDialog.java b/src/jalview/appletgui/EditNameDialog.java
index 24a7023..2f6469b 100644
--- a/src/jalview/appletgui/EditNameDialog.java
+++ b/src/jalview/appletgui/EditNameDialog.java
@@ -20,7 +20,12 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.TextField;
 
 public class EditNameDialog extends JVDialog
 {
diff --git a/src/jalview/appletgui/EmbmenuFrame.java b/src/jalview/appletgui/EmbmenuFrame.java
index be4eab6..f61077a 100644
--- a/src/jalview/appletgui/EmbmenuFrame.java
+++ b/src/jalview/appletgui/EmbmenuFrame.java
@@ -51,8 +51,8 @@ import java.util.Map;
  */
 public class EmbmenuFrame extends Frame implements MouseListener
 {
-  protected static final Font FONT_ARIAL_PLAIN_11 = new Font(
-            "Arial", Font.PLAIN, 11);
+  protected static final Font FONT_ARIAL_PLAIN_11 = new Font("Arial",
+          Font.PLAIN, 11);
 
   public static final Font DEFAULT_MENU_FONT = FONT_ARIAL_PLAIN_11;
 
@@ -156,8 +156,7 @@ public class EmbmenuFrame extends Frame implements MouseListener
    * @return the panel instance for convenience.
    */
   protected Panel makeEmbeddedPopupMenu(MenuBar menuBar, Font font,
-          boolean overrideFonts,
-          Panel embeddedMenu,
+          boolean overrideFonts, Panel embeddedMenu,
           MouseListener clickHandler)
   {
     if (overrideFonts)
diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index b4367bf..46a67c4 100644
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -20,15 +20,33 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.GraphLine;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
 import jalview.util.MessageManager;
 
+import java.awt.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.Hashtable;
+
 public class FeatureColourChooser extends Panel implements ActionListener,
         AdjustmentListener, ItemListener, MouseListener
 {
@@ -117,8 +135,8 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     slider.addMouseListener(this);
     owner = (af != null) ? af : fs.frame;
     frame = new JVDialog(owner, MessageManager.formatMessage(
-            "label.graduated_color_for_params", new String[]
-            { type }), true, 480, 248);
+            "label.graduated_color_for_params", new String[] { type }),
+            true, 480, 248);
     frame.setMainPanel(this);
     validate();
     frame.setVisible(true);
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 4536b1a..4655ba5 100644
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -20,6 +20,14 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
 import java.awt.BorderLayout;
 import java.awt.Button;
 import java.awt.Choice;
@@ -37,14 +45,6 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.Hashtable;
 
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-
 /**
  * DOCUMENT ME!
  * 
@@ -326,8 +326,7 @@ public class FeatureRenderer extends
     String title = newFeatures ? MessageManager
             .getString("label.create_new_sequence_features")
             : MessageManager.formatMessage("label.amend_delete_features",
-                    new String[]
-                    { sequences[0].getName() });
+                    new String[] { sequences[0].getName() });
 
     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
             240);
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index f1e9835..1c156dc 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -119,7 +119,8 @@ public class FeatureSettings extends Panel implements ItemListener,
     this.setLayout(new BorderLayout());
     scrollPane = new ScrollPane();
     scrollPane.add(featurePanel);
-    if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+    if (fr.getAllFeatureColours() != null
+            && fr.getAllFeatureColours().size() > 0)
     {
       add(scrollPane, BorderLayout.CENTER);
     }
@@ -150,10 +151,11 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     if (groupPanel != null)
     {
-      groupPanel
-              .setLayout(new GridLayout(
-                      (fr.getFeatureGroupsSize()) / 4 + 1,
-                      4)); // JBPNote - this was scaled on number of visible groups. seems broken
+      groupPanel.setLayout(new GridLayout(
+              (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
+                                                        // scaled on number of
+                                                        // visible groups. seems
+                                                        // broken
       groupPanel.validate();
 
       add(groupPanel, BorderLayout.NORTH);
@@ -180,8 +182,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     int width = 300;
     jalview.bin.JalviewLite.addFrame(frame,
             MessageManager.getString("label.sequence_feature_settings"),
-            width,
-            height);
+            width, height);
   }
 
   public void paint(Graphics g)
@@ -203,8 +204,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     final String type = check.type;
     final Object typeCol = fr.getFeatureStyle(type);
     java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
-            "label.settings_for_type", new String[]
-            { type }));
+            "label.settings_for_type", new String[] { type }));
     java.awt.MenuItem scr = new MenuItem(
             MessageManager.getString("label.sort_by_score"));
     men.add(scr);
@@ -214,8 +214,8 @@ public class FeatureSettings extends Panel implements ItemListener,
 
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]
-        { type });
+        me.ap.alignFrame.avc
+                .sortAlignmentByFeatureScore(new String[] { type });
       }
 
     });
@@ -226,8 +226,8 @@ public class FeatureSettings extends Panel implements ItemListener,
 
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[]
-        { type });
+        me.ap.alignFrame.avc
+                .sortAlignmentByFeatureDensity(new String[] { type });
       }
 
     });
@@ -283,7 +283,8 @@ public class FeatureSettings extends Panel implements ItemListener,
   @Override
   public void discoverAllFeatureData()
   {
-    if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+    if (fr.getAllFeatureColours() != null
+            && fr.getAllFeatureColours().size() > 0)
     {
       rebuildGroups();
 
@@ -308,7 +309,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     // TODO: JAL-964 - smoothly incorporate new group entries if panel already
     // displayed and new groups present
-    for (String group:fr.getFeatureGroups())
+    for (String group : fr.getFeatureGroups())
     {
       boolean vis = fr.checkGroupVisibility(group, false);
       Checkbox check = new MyCheckbox(group, vis,
@@ -326,6 +327,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       groupPanel.validate();
     }
   }
+
   // This routine adds and removes checkboxes depending on
   // Group selection states
   void resetTable(boolean groupsChanged)
@@ -482,11 +484,12 @@ public class FeatureSettings extends Panel implements ItemListener,
     selectionChanged();
   }
 
-  private ItemListener groupItemListener = new ItemListener() {
-    public void itemStateChanged(ItemEvent evt) {
+  private ItemListener groupItemListener = new ItemListener()
+  {
+    public void itemStateChanged(ItemEvent evt)
+    {
       Checkbox source = (Checkbox) evt.getSource();
-      fr.setGroupVisibility(source.getLabel(),
-              source.getState());
+      fr.setGroupVisibility(source.getLabel(), source.getState());
       ap.seqPanel.seqCanvas.repaint();
       if (ap.overviewPanel != null)
       {
@@ -496,6 +499,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       return;
     };
   };
+
   public void itemStateChanged(ItemEvent evt)
   {
     selectionChanged();
@@ -615,7 +619,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     else
     {
-      throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_unsupported_feature_colour_object"));
     }
     refreshTable();
   }
@@ -711,7 +717,9 @@ public class FeatureSettings extends Panel implements ItemListener,
       }
       else
       {
-        throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_colour_for_mycheckbox"));
       }
       if (col != null)
       {
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 5412472..75d9b9e 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -204,16 +204,15 @@ public class Finder extends Panel implements ActionListener
           message += searchResults.getSize() + " subsequence matches.";
         }
         ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
-                "label.search_results", new String[]
-                { searchString, message }));
+                "label.search_results", new String[] { searchString,
+                    message }));
 
       }
       else
       {
         // TODO: indicate sequence and matching position in status bar
         ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
-                "label.found_match_for", new String[]
-                { searchString }));
+                "label.found_match_for", new String[] { searchString }));
       }
     }
   }
diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java
index 6456878..59f6957 100644
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
@@ -20,6 +20,9 @@
  */
 package jalview.appletgui;
 
+import jalview.api.ViewStyleI;
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.Button;
 import java.awt.Checkbox;
@@ -37,9 +40,6 @@ import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 
-import jalview.api.ViewStyleI;
-import jalview.util.MessageManager;
-
 /**
  * This dialog allows the user to try different font settings and related
  * options. Changes are immediately visible on the alignment or tree. The user
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 5204094..16bba0b 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -57,8 +57,7 @@ public class IdCanvas extends Panel
   }
 
   public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
-          int i, int starty,
-          int ypos)
+          int i, int starty, int ypos)
   {
     int charHeight = av.getCharHeight();
 
@@ -187,6 +186,7 @@ public class IdCanvas extends Panel
    * local copy of av.getCharHeight set at top of drawIds
    */
   private int avcharHeight;
+
   void drawIds(int starty, int endy)
   {
     // hardwired italic IDs in applet currently
@@ -356,19 +356,17 @@ public class IdCanvas extends Panel
     gg.setColor(Color.blue);
     if (below)
     {
-      gg.fillPolygon(new int[]
-      { getSize().width - avcharHeight, getSize().width - avcharHeight,
-          getSize().width }, new int[]
-      { (i - starty) * avcharHeight + yoffset,
+      gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+          getSize().width - avcharHeight, getSize().width }, new int[] {
+          (i - starty) * avcharHeight + yoffset,
           (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
           (i - starty) * avcharHeight + yoffset }, 3);
     }
     if (above)
     {
-      gg.fillPolygon(new int[]
-      { getSize().width - avcharHeight, getSize().width - avcharHeight,
-          getSize().width }, new int[]
-      { (i - starty + 1) * avcharHeight + yoffset,
+      gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+          getSize().width - avcharHeight, getSize().width }, new int[] {
+          (i - starty + 1) * avcharHeight + yoffset,
           (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
           (i - starty + 1) * avcharHeight + yoffset }, 3);
 
diff --git a/src/jalview/appletgui/JVDialog.java b/src/jalview/appletgui/JVDialog.java
index 19d7b4c..58c4feb 100644
--- a/src/jalview/appletgui/JVDialog.java
+++ b/src/jalview/appletgui/JVDialog.java
@@ -20,8 +20,14 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Dialog;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Panel;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 
 public class JVDialog extends Dialog implements ActionListener
 {
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index f09bda5..bc64728 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -357,8 +357,8 @@ public class OverviewPanel extends Panel implements Runnable,
         }
 
         if (hiddenRow
-                || (hasHiddenCols && !av.getColumnSelection()
-                        .isVisible(lastcol)))
+                || (hasHiddenCols && !av.getColumnSelection().isVisible(
+                        lastcol)))
         {
           color = color.darker().darker();
         }
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 10969b9..c5ec0c1 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -20,13 +20,31 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 import jalview.viewmodel.PCAModel;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.CheckboxMenuItem;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
 public class PCAPanel extends EmbmenuFrame implements Runnable,
         ActionListener, ItemListener
 {
diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 7b54b1c..7c6fad0 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -20,12 +20,14 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-import java.util.List;
-
-import java.awt.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Component;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index c4a6989..4aea837 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -206,7 +206,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
         }
       }
 
-      EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
+      EditCommand cut = new EditCommand(
+              MessageManager.getString("action.remove_redundancy"),
               Action.CUT, deleted, 0, width, ap.av.getAlignment());
       AlignmentI alignment = ap.av.getAlignment();
       for (int i = 0; i < del.size(); i++)
@@ -223,7 +224,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
       ap.alignFrame.addHistoryItem(cut);
 
       PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
-       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
     }
 
   }
@@ -237,7 +239,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     {
       ap.av.getHistoryList().remove(command);
       ap.alignFrame.updateEditMenuBar();
-      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
     }
 
     ap.paintAlignment(true);
diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 377186a..5c91ea8 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -20,16 +20,28 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
 import jalview.api.RotatableCanvasI;
-import jalview.datamodel.*;
-import jalview.math.*;
-import jalview.util.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+import jalview.util.Format;
+import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
+
 public class RotatableCanvas extends Panel implements MouseListener,
         MouseMotionListener, KeyListener, RotatableCanvasI
 {
diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 3bb676f..769ac8b 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -414,21 +414,17 @@ public class ScalePanel extends Panel implements MouseMotionListener,
           maxX = (i - startx + 1) * avcharWidth + fm.stringWidth(string);
         }
 
-        gg.drawLine(
-((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
+        gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
                 y + 2,
-                ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-                y + (fm.getDescent() * 2));
+                ((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
+                        + (fm.getDescent() * 2));
 
       }
       else
       {
-        gg.drawLine(
-((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-                y + fm.getDescent(),
- ((i - startx - 1) * avcharWidth)
-                + (avcharWidth / 2),
-                y + (fm.getDescent() * 2));
+        gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
+                + fm.getDescent(), ((i - startx - 1) * avcharWidth)
+                + (avcharWidth / 2), y + (fm.getDescent() * 2));
       }
     }
 
@@ -450,12 +446,10 @@ public class ScalePanel extends Panel implements MouseMotionListener,
             continue;
           }
 
-          gg.fillPolygon(new int[]
-          { res * avcharWidth - avcharHeight / 4,
+          gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
               res * avcharWidth + avcharHeight / 4, res * avcharWidth },
-                  new int[]
-                  { y - avcharHeight / 2, y - avcharHeight / 2, y + 8 },
-                  3);
+                  new int[] { y - avcharHeight / 2, y - avcharHeight / 2,
+                      y + 8 }, 3);
 
         }
       }
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 522151c..ce70597 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -473,11 +473,10 @@ public class SeqCanvas extends Panel
             continue;
           }
 
-          gg.fillPolygon(new int[]
-          { res * avcharWidth - avcharHeight / 4,
+          gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
               res * avcharWidth + avcharHeight / 4, res * avcharWidth },
-                  new int[]
-                  { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
+                  new int[] { ypos - (avcharHeight / 2),
+                      ypos - (avcharHeight / 2),
                       ypos - (avcharHeight / 2) + 8 }, 3);
 
         }
@@ -529,11 +528,9 @@ public class SeqCanvas extends Panel
   }
 
   private void drawPanel(Graphics g1, int startRes, int endRes,
-          int startSeq,
-          int endSeq, int offset)
+          int startSeq, int endSeq, int offset)
   {
 
-
     if (!av.hasHiddenColumns())
     {
       draw(g1, startRes, endRes, startSeq, endSeq, offset);
@@ -827,8 +824,7 @@ public class SeqCanvas extends Panel
           break;
         }
 
-        group = av.getAlignment().getGroups()
-                .get(groupIndex);
+        group = av.getAlignment().getGroups().get(groupIndex);
       } while (groupIndex < av.getAlignment().getGroups().size());
 
     }
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 4dd131a..9870e68 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -564,8 +564,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       if (features != null && features.length > 0)
       {
-        seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
-        { sequence }, features, false, ap);
+        seqCanvas.getFeatureRenderer().amendFeatures(
+                new SequenceI[] { sequence }, features, false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -607,8 +607,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
@@ -665,8 +664,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       y -= hgap;
 
@@ -800,8 +798,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      obj = "X".equalsIgnoreCase(ch) ? "X"
-              : ResidueProperties.aa2Triplet.get(ch);
+      obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
+              .get(ch);
       if (obj != null)
       {
         text.append(" Residue: ").append(obj);
@@ -885,13 +883,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       for (int i = 0; i < features.length; i++)
       {
         if (av.getFeaturesDisplayed() == null
-                || !av.getFeaturesDisplayed().isVisible(features[i].getType()))
+                || !av.getFeaturesDisplayed().isVisible(
+                        features[i].getType()))
         {
           continue;
         }
 
         if (features[i].featureGroup != null
-                && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false))
+                && !seqCanvas.fr.checkGroupVisibility(
+                        features[i].featureGroup, false))
         {
           continue;
         }
@@ -1047,8 +1047,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (editCommand == null)
       {
         editCommand = new EditCommand(MessageManager.formatMessage(
-                "label.edit_params", new String[]
-                { label }));
+                "label.edit_params", new String[] { label }));
       }
     }
 
@@ -1282,14 +1281,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           for (int j = lastres; j < startres; j++)
           {
-            insertChar(j, new SequenceI[]
-            { seq }, fixedRight);
+            insertChar(j, new SequenceI[] { seq }, fixedRight);
           }
         }
         else
         {
-          editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
-          { seq }, lastres, startres - lastres, av.getAlignment(), true);
+          editCommand.appendEdit(Action.INSERT_GAP,
+                  new SequenceI[] { seq }, lastres, startres - lastres,
+                  av.getAlignment(), true);
         }
       }
       else
@@ -1304,8 +1303,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
               endEditing();
               break;
             }
-            deleteChar(startres, new SequenceI[]
-            { seq }, fixedRight);
+            deleteChar(startres, new SequenceI[] { seq }, fixedRight);
           }
         }
         else
@@ -1323,8 +1321,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
           if (max > 0)
           {
-            editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
-            { seq }, startres, max, av.getAlignment(), true);
+            editCommand.appendEdit(Action.DELETE_GAP,
+                    new SequenceI[] { seq }, startres, max,
+                    av.getAlignment(), true);
           }
         }
       }
@@ -1929,22 +1928,24 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
           ColumnSelection colsel, SelectionSource source)
   {
-    if (!(source instanceof AlignViewportI)) {
+    if (!(source instanceof AlignViewportI))
+    {
       return false;
     }
     final AlignViewportI sourceAv = (AlignViewportI) source;
-    if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+    if (sourceAv.getCodingComplement() != av
+            && av.getCodingComplement() != sourceAv)
     {
       return false;
     }
-  
+
     /*
      * Map sequence selection
      */
     SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
     av.setSelectionGroup(sg);
     av.isSelectionGroupChanged(true);
-  
+
     /*
      * Map column selection
      */
@@ -1952,10 +1953,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
             av);
     av.setColumnSelection(cs);
     av.isColSelChanged(true);
-  
+
     ap.scalePanelHolder.repaint();
     ap.repaint();
-  
+
     return true;
   }
 
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index e07fcb2..09b50c4 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -256,8 +256,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (currentSequenceGroup.getShowNonconserved())
         {
-          s = getDisplayChar(srep, i, s,
-                  '.');
+          s = getDisplayChar(srep, i, s, '.');
         }
       }
       else
@@ -281,8 +280,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (av.getShowUnconserved())
         {
-          s = getDisplayChar(srep, i, s,
-                  '.');
+          s = getDisplayChar(srep, i, s, '.');
 
         }
       }
@@ -314,13 +312,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
   }
 
-  private char getDisplayChar(final boolean usesrep, int position,
-          char s, char c)
+  private char getDisplayChar(final boolean usesrep, int position, char s,
+          char c)
   {
     // TODO - use currentSequenceGroup rather than alignment
     // currentSequenceGroup.getConsensus()
-    char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
-            .charAt(0);
+    char conschar = (usesrep) ? av.getAlignment().getSeqrep()
+            .getCharAt(position)
+            : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+                    .charAt(0);
     if (!jalview.util.Comparison.isGap(conschar) && s == conschar)
     {
       s = c;
diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 65622aa..2fc15d0 100644
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -74,7 +74,10 @@ public class SliderPanel extends Panel implements ActionListener,
       sp.cs = cs;
     }
 
-    conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));
+    conservationSlider
+            .setTitle(MessageManager.formatMessage(
+                    "label.conservation_colour_increment",
+                    new String[] { source }));
     if (ap.av.getAlignment().getGroups() != null)
     {
       sp.setAllGroupsCheckEnabled(true);
@@ -128,7 +131,9 @@ public class SliderPanel extends Panel implements ActionListener,
       pid = (SliderPanel) PIDSlider.getComponent(0);
       pid.cs = cs;
     }
-    PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));
+    PIDSlider.setTitle(MessageManager
+            .formatMessage("label.percentage_identity_thereshold",
+                    new String[] { source }));
 
     if (ap.av.getAlignment().getGroups() != null)
     {
diff --git a/src/jalview/appletgui/SplitFrame.java b/src/jalview/appletgui/SplitFrame.java
index 888208a..bdda465 100644
--- a/src/jalview/appletgui/SplitFrame.java
+++ b/src/jalview/appletgui/SplitFrame.java
@@ -1,10 +1,5 @@
 package jalview.appletgui;
 
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-import java.awt.Panel;
-
 import jalview.analysis.AlignmentUtils;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
@@ -13,6 +8,11 @@ import jalview.datamodel.AlignmentI;
 import jalview.structure.StructureSelectionManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.Panel;
+
 public class SplitFrame extends EmbmenuFrame
 {
   private static final long serialVersionUID = 1L;
diff --git a/src/jalview/appletgui/Tooltip.java b/src/jalview/appletgui/Tooltip.java
index c9df482..7a65ec3 100755
--- a/src/jalview/appletgui/Tooltip.java
+++ b/src/jalview/appletgui/Tooltip.java
@@ -20,11 +20,20 @@
  */
 package jalview.appletgui;
 
-import java.applet.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
+import java.applet.Applet;
+import java.awt.Canvas;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.LayoutManager;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.StringTokenizer;
 
 public class Tooltip extends Canvas implements MouseListener,
         MouseMotionListener
diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 277bd55..57cf669 100644
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -20,6 +20,13 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
+
 import java.awt.Button;
 import java.awt.Color;
 import java.awt.Component;
@@ -42,13 +49,6 @@ import java.awt.event.FocusListener;
 import java.awt.event.MouseEvent;
 import java.util.Vector;
 
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.GraduatedColor;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.util.MessageManager;
-
 public class UserDefinedColours extends Panel implements ActionListener,
         AdjustmentListener, FocusListener
 {
@@ -189,7 +189,8 @@ public class UserDefinedColours extends Panel implements ActionListener,
     setTargetColour(colour);
 
     okcancelPanel.setBounds(new Rectangle(0, 113, 400, 35));
-    frame.setTitle(MessageManager.getString("label.user_defined_colours") + " - " + label);
+    frame.setTitle(MessageManager.getString("label.user_defined_colours")
+            + " - " + label);
     frame.setSize(420, 200);
   }
 
@@ -208,7 +209,9 @@ public class UserDefinedColours extends Panel implements ActionListener,
       // // not 1.1 compatible!
       // dialog = new Dialog(((JVDialog)alignframe), title, true);
       // } else {
-      throw new Error(MessageManager.getString("label.error_unsupported_owwner_user_colour_scheme"));
+      throw new Error(
+              MessageManager
+                      .getString("label.error_unsupported_owwner_user_colour_scheme"));
     }
 
     dialog.add(this);
diff --git a/src/jalview/bin/BuildDetails.java b/src/jalview/bin/BuildDetails.java
index 0a1e227..2ead42f 100644
--- a/src/jalview/bin/BuildDetails.java
+++ b/src/jalview/bin/BuildDetails.java
@@ -2,7 +2,6 @@ package jalview.bin;
 
 import jalview.api.BuildDetailsI;
 
-
 public class BuildDetails implements BuildDetailsI
 {
   private static String buildDate;
@@ -53,6 +52,4 @@ public class BuildDetails implements BuildDetailsI
     BuildDetails.installation = installation;
   }
 
-
-
 }
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 641815d..ee46581 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -222,11 +222,13 @@ public class Cache
   public static Logger log;
 
   /** Jalview Properties */
-  public static Properties applicationProperties = new Properties() {
+  public static Properties applicationProperties = new Properties()
+  {
     // override results in properties output in alphabetical order
     @Override
-    public synchronized Enumeration keys() {
-        return Collections.enumeration(new TreeSet(super.keySet()));
+    public synchronized Enumeration keys()
+    {
+      return Collections.enumeration(new TreeSet(super.keySet()));
     }
   };
 
@@ -315,9 +317,9 @@ public class Cache
         fis = new FileInputStream(propertiesFile);
       }
       applicationProperties.load(fis);
-      
+
       // remove any old build properties
-      
+
       deleteBuildProperties();
       fis.close();
     } catch (Exception ex)
@@ -718,21 +720,22 @@ public class Cache
       try
       {
         // Google analytics tracking code for Library Finder
-        tracker = jgoogleanalyticstracker.getConstructor(new Class[]
-        { String.class, String.class, String.class }).newInstance(
-                new Object[]
-                {
-                    "Jalview Desktop",
-                    (vrs = jalview.bin.Cache.getProperty("VERSION")
-                            + "_"
-                            + jalview.bin.Cache.getDefault("BUILD_DATE",
-                                    "unknown")), "UA-9060947-1" });
+        tracker = jgoogleanalyticstracker.getConstructor(
+                new Class[] { String.class, String.class, String.class })
+                .newInstance(
+                        new Object[] {
+                            "Jalview Desktop",
+                            (vrs = jalview.bin.Cache.getProperty("VERSION")
+                                    + "_"
+                                    + jalview.bin.Cache.getDefault(
+                                            "BUILD_DATE", "unknown")),
+                            "UA-9060947-1" });
         jgoogleanalyticstracker.getMethod("trackAsynchronously",
-                new Class[]
-                { trackerfocus }).invoke(tracker, new Object[]
-        { trackerfocus.getConstructor(new Class[]
-        { String.class }).newInstance(new Object[]
-        { "Application Started." }) });
+                new Class[] { trackerfocus }).invoke(
+                tracker,
+                new Object[] { trackerfocus.getConstructor(
+                        new Class[] { String.class }).newInstance(
+                        new Object[] { "Application Started." }) });
       } catch (RuntimeException e)
       {
         re = e;
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 177d56f..dfd0924 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -240,8 +240,7 @@ public class Jalview
       }
       else
       {
-        System.err
-.println("CMD [-noquestionnaire] executed successfully!");
+        System.err.println("CMD [-noquestionnaire] executed successfully!");
       }
       desktop.checkForNews();
     }
@@ -358,7 +357,8 @@ public class Jalview
     {
       if (!headless)
       {
-        desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
+        desktop.setProgressBar(MessageManager
+                .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
@@ -445,8 +445,7 @@ public class Jalview
           af.getViewport().setSortByTree(true);
           if (af.getViewport().getSortByTree())
           {
-            System.out
-.println("CMD [-sortbytree] executed successfully!");
+            System.out.println("CMD [-sortbytree] executed successfully!");
           }
         }
         if (aparser.contains("no-annotation"))
@@ -454,8 +453,7 @@ public class Jalview
           af.getViewport().setShowAnnotation(false);
           if (!af.getViewport().isShowAnnotation())
           {
-            System.out
-.println("CMD no-annotation executed successfully!");
+            System.out.println("CMD no-annotation executed successfully!");
           }
         }
         if (aparser.contains("nosortbytree"))
@@ -519,8 +517,7 @@ public class Jalview
           if (jalview.bin.Cache.groovyJarsPresent())
           {
             System.out.println("Executing script " + groovyscript);
-            executeGroovyScript(groovyscript, new Object[]
-            { desktop, af });
+            executeGroovyScript(groovyscript, new Object[] { desktop, af });
 
             System.out.println("CMD groovy[" + groovyscript
                     + "] executed successfully!");
@@ -655,8 +652,8 @@ public class Jalview
       if (jalview.bin.Cache.groovyJarsPresent())
       {
         System.out.println("Executing script " + groovyscript);
-        executeGroovyScript(groovyscript, new Object[]
-        { desktop, startUpAlframe });
+        executeGroovyScript(groovyscript, new Object[] { desktop,
+            startUpAlframe });
       }
       else
       {
@@ -865,8 +862,7 @@ public class Jalview
       Object[] binding;
       int blen = ((jalviewContext[0] == null) ? 0 : 1)
               + ((jalviewContext[1] == null) ? 0 : 1);
-      String cnames[] = new String[]
-      { "Jalview", "currentAlFrame" };
+      String cnames[] = new String[] { "Jalview", "currentAlFrame" };
       bspec = new Class[blen * 2];
       binding = new Object[blen * 2];
       blen = 0;
@@ -907,15 +903,15 @@ public class Jalview
       }
 
       Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
-      Constructor gseccons = gsec.getConstructor(new Class[]
-      { URL[].class }); // String[].class });
-      Object gse = gseccons.newInstance(new Object[]
-      { new URL[]
-      { sfile } }); // .toString() } });
-      java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
-      { String.class, gbindingc });
-      run.invoke(gse, new Object[]
-      { sfile.toString(), gbinding });
+      Constructor gseccons = gsec
+              .getConstructor(new Class[] { URL[].class }); // String[].class
+                                                            // });
+      Object gse = gseccons
+              .newInstance(new Object[] { new URL[] { sfile } }); // .toString()
+                                                                  // } });
+      java.lang.reflect.Method run = gsec.getMethod("run", new Class[] {
+          String.class, gbindingc });
+      run.invoke(gse, new Object[] { sfile.toString(), gbinding });
       success = true;
     } catch (Exception e)
     {
@@ -1181,7 +1177,8 @@ class FeatureFetcher
           running++;
         }
 
-        af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
+        af.setProgressBar(MessageManager
+                .getString("status.das_features_being_retrived"), id);
         af.featureSettings_actionPerformed(null);
         af.featureSettings.fetchDasFeatures(dasSources, true);
         af.setProgressBar(null, id);
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index d0c3829..3024e66 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1385,8 +1385,7 @@ public class JalviewLite extends Applet implements
     String externalsviewer = getParameter("externalstructureviewer");
     if (externalsviewer != null)
     {
-      useXtrnalSviewer = externalsviewer.trim().toLowerCase()
-              .equals(TRUE);
+      useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
     }
     /**
      * if true disable the check for jmol
@@ -1412,7 +1411,9 @@ public class JalviewLite extends Applet implements
       }
       else
       {
-        throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_separator_parameter"));
       }
     }
     int r = 255;
@@ -1921,7 +1922,8 @@ public class JalviewLite extends Applet implements
       AlignmentI al = null;
       try
       {
-        al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format);
+        al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
+                format);
         if ((al != null) && (al.getHeight() > 0))
         {
           dbgMsg("Successfully loaded file.");
@@ -1939,13 +1941,13 @@ public class JalviewLite extends Applet implements
           if (protocol == AppletFormatAdapter.PASTE)
           {
             newAlignFrame.setTitle(MessageManager.formatMessage(
-                    "label.sequences_from", new Object[]
-                    { applet.getDocumentBase().toString() }));
+                    "label.sequences_from", new Object[] { applet
+                            .getDocumentBase().toString() }));
           }
 
           newAlignFrame.statusBar.setText(MessageManager.formatMessage(
-                  "label.successfully_loaded_file", new Object[]
-                  { resolvedFile }));
+                  "label.successfully_loaded_file",
+                  new Object[] { resolvedFile }));
 
           return newAlignFrame;
         }
@@ -2040,10 +2042,9 @@ public class JalviewLite extends Applet implements
             String sequence = applet.getParameter("PDBSEQ");
             if (sequence != null)
             {
-              seqs = new SequenceI[]
-              { matcher == null ? (Sequence) alignFrame.getAlignViewport()
-                      .getAlignment().findName(sequence) : matcher
-                      .findIdMatch(sequence) };
+              seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
+                      .getAlignViewport().getAlignment().findName(sequence)
+                      : matcher.findIdMatch(sequence) };
             }
 
           }
@@ -2125,8 +2126,8 @@ public class JalviewLite extends Applet implements
             }
             else
             {
-              pdbs.addElement(new Object[]
-              { pdb, seqs, chains, new String(protocol) });
+              pdbs.addElement(new Object[] { pdb, seqs, chains,
+                  new String(protocol) });
             }
           }
         }
@@ -2401,8 +2402,7 @@ public class JalviewLite extends Applet implements
         if (debug)
         {
           System.err.println("Prepended document base '" + documentBase
-                  + "' to make: '" + url
-                  + "'");
+                  + "' to make: '" + url + "'");
         }
         return url;
       }
@@ -2911,8 +2911,7 @@ public class JalviewLite extends Applet implements
     if (url.indexOf("/") == 0)
     {
       String localfile = localref.getFile();
-      url = codebase.substring(0, codebase.length()
-              - localfile.length())
+      url = codebase.substring(0, codebase.length() - localfile.length())
               + url;
     }
     else
diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 5b107b5..b8fcb2c 100644
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,151 +19,162 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Alignment implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _annotation.
-     */
-    private jalview.binding.Annotation _annotation;
-
-    /**
-     * Field _sequenceSet.
-     */
-    private jalview.binding.SequenceSet _sequenceSet;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Alignment() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'annotation'.
-     * 
-     * @return the value of field 'Annotation'.
-     */
-    public jalview.binding.Annotation getAnnotation(
-    ) {
-        return this._annotation;
-    }
-
-    /**
-     * Returns the value of field 'sequenceSet'.
-     * 
-     * @return the value of field 'SequenceSet'.
-     */
-    public jalview.binding.SequenceSet getSequenceSet(
-    ) {
-        return this._sequenceSet;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'annotation'.
-     * 
-     * @param annotation the value of field 'annotation'.
-     */
-    public void setAnnotation(
-            final jalview.binding.Annotation annotation) {
-        this._annotation = annotation;
-    }
-
-    /**
-     * Sets the value of field 'sequenceSet'.
-     * 
-     * @param sequenceSet the value of field 'sequenceSet'.
-     */
-    public void setSequenceSet(
-            final jalview.binding.SequenceSet sequenceSet) {
-        this._sequenceSet = sequenceSet;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Alignment
-     */
-    public static jalview.binding.Alignment unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Alignment implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _annotation.
+   */
+  private jalview.binding.Annotation _annotation;
+
+  /**
+   * Field _sequenceSet.
+   */
+  private jalview.binding.SequenceSet _sequenceSet;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Alignment()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'annotation'.
+   * 
+   * @return the value of field 'Annotation'.
+   */
+  public jalview.binding.Annotation getAnnotation()
+  {
+    return this._annotation;
+  }
+
+  /**
+   * Returns the value of field 'sequenceSet'.
+   * 
+   * @return the value of field 'SequenceSet'.
+   */
+  public jalview.binding.SequenceSet getSequenceSet()
+  {
+    return this._sequenceSet;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'annotation'.
+   * 
+   * @param annotation
+   *          the value of field 'annotation'.
+   */
+  public void setAnnotation(final jalview.binding.Annotation annotation)
+  {
+    this._annotation = annotation;
+  }
+
+  /**
+   * Sets the value of field 'sequenceSet'.
+   * 
+   * @param sequenceSet
+   *          the value of field 'sequenceSet'.
+   */
+  public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet)
+  {
+    this._sequenceSet = sequenceSet;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Alignment
+   */
+  public static jalview.binding.Alignment unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Alignment) Unmarshaller.unmarshal(
+            jalview.binding.Alignment.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java
index 108d3ad..86f1a63 100644
--- a/src/jalview/binding/Annotation.java
+++ b/src/jalview/binding/Annotation.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,414 +19,441 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Annotation implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _graph.
-     */
-    private boolean _graph;
-
-    /**
-     * keeps track of state for field: _graph
-     */
-    private boolean _has_graph;
-
-    /**
-     * Field _graphType.
-     */
-    private int _graphType;
-
-    /**
-     * keeps track of state for field: _graphType
-     */
-    private boolean _has_graphType;
-
-    /**
-     * Field _annotationElementList.
-     */
-    private java.util.Vector _annotationElementList;
-
-    /**
-     * Field _label.
-     */
-    private java.lang.String _label;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Annotation() {
-        super();
-        this._annotationElementList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotationElement(
-            final jalview.binding.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationElementList.addElement(vAnnotationElement);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotationElement(
-            final int index,
-            final jalview.binding.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationElementList.add(index, vAnnotationElement);
-    }
-
-    /**
-     */
-    public void deleteGraph(
-    ) {
-        this._has_graph= false;
-    }
-
-    /**
-     */
-    public void deleteGraphType(
-    ) {
-        this._has_graphType= false;
-    }
-
-    /**
-     * Method enumerateAnnotationElement.
-     * 
-     * @return an Enumeration over all
-     * jalview.binding.AnnotationElement elements
-     */
-    public java.util.Enumeration enumerateAnnotationElement(
-    ) {
-        return this._annotationElementList.elements();
-    }
-
-    /**
-     * Method getAnnotationElement.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.AnnotationElement
-     * at the given index
-     */
-    public jalview.binding.AnnotationElement getAnnotationElement(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationElementList.size()) {
-            throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.AnnotationElement) _annotationElementList.get(index);
-    }
-
-    /**
-     * Method getAnnotationElement.Returns the contents of the
-     * collection in an Array.  
Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we know that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.AnnotationElement[] getAnnotationElement(
-    ) {
-        jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
-        return (jalview.binding.AnnotationElement[]) this._annotationElementList.toArray(array);
-    }
-
-    /**
-     * Method getAnnotationElementCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAnnotationElementCount(
-    ) {
-        return this._annotationElementList.size();
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return the value of field 'Graph'.
-     */
-    public boolean getGraph(
-    ) {
-        return this._graph;
+public class Annotation implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _graph.
+   */
+  private boolean _graph;
+
+  /**
+   * keeps track of state for field: _graph
+   */
+  private boolean _has_graph;
+
+  /**
+   * Field _graphType.
+   */
+  private int _graphType;
+
+  /**
+   * keeps track of state for field: _graphType
+   */
+  private boolean _has_graphType;
+
+  /**
+   * Field _annotationElementList.
+   */
+  private java.util.Vector _annotationElementList;
+
+  /**
+   * Field _label.
+   */
+  private java.lang.String _label;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Annotation()
+  {
+    super();
+    this._annotationElementList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAnnotationElement(
+          final jalview.binding.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationElementList.addElement(vAnnotationElement);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAnnotationElement(final int index,
+          final jalview.binding.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationElementList.add(index, vAnnotationElement);
+  }
+
+  /**
+     */
+  public void deleteGraph()
+  {
+    this._has_graph = false;
+  }
+
+  /**
+     */
+  public void deleteGraphType()
+  {
+    this._has_graphType = false;
+  }
+
+  /**
+   * Method enumerateAnnotationElement.
+   * 
+   * @return an Enumeration over all jalview.binding.AnnotationElement elements
+   */
+  public java.util.Enumeration enumerateAnnotationElement()
+  {
+    return this._annotationElementList.elements();
+  }
+
+  /**
+   * Method getAnnotationElement.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.AnnotationElement at the given
+   *         index
+   */
+  public jalview.binding.AnnotationElement getAnnotationElement(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationElementList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getAnnotationElement: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._annotationElementList.size() - 1) + "]");
     }
 
-    /**
-     * Returns the value of field 'graphType'.
-     * 
-     * @return the value of field 'GraphType'.
-     */
-    public int getGraphType(
-    ) {
-        return this._graphType;
-    }
-
-    /**
-     * Returns the value of field 'label'.
-     * 
-     * @return the value of field 'Label'.
-     */
-    public java.lang.String getLabel(
-    ) {
-        return this._label;
-    }
-
-    /**
-     * Method hasGraph.
-     * 
-     * @return true if at least one Graph has been added
-     */
-    public boolean hasGraph(
-    ) {
-        return this._has_graph;
-    }
-
-    /**
-     * Method hasGraphType.
-     * 
-     * @return true if at least one GraphType has been added
-     */
-    public boolean hasGraphType(
-    ) {
-        return this._has_graphType;
-    }
-
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return the value of field 'Graph'.
-     */
-    public boolean isGraph(
-    ) {
-        return this._graph;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllAnnotationElement(
-    ) {
-        this._annotationElementList.clear();
-    }
-
-    /**
-     * Method removeAnnotationElement.
-     * 
-     * @param vAnnotationElement
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAnnotationElement(
-            final jalview.binding.AnnotationElement vAnnotationElement) {
-        boolean removed = _annotationElementList.remove(vAnnotationElement);
-        return removed;
-    }
-
-    /**
-     * Method removeAnnotationElementAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.AnnotationElement removeAnnotationElementAt(
-            final int index) {
-        java.lang.Object obj = this._annotationElementList.remove(index);
-        return (jalview.binding.AnnotationElement) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAnnotationElement(
-            final int index,
-            final jalview.binding.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationElementList.size()) {
-            throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
-        }
-        
-        this._annotationElementList.set(index, vAnnotationElement);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotationElementArray
-     */
-    public void setAnnotationElement(
-            final jalview.binding.AnnotationElement[] vAnnotationElementArray) {
-        //-- copy array
-        _annotationElementList.clear();
-        
-        for (int i = 0; i < vAnnotationElementArray.length; i++) {
-                this._annotationElementList.add(vAnnotationElementArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
+    return (jalview.binding.AnnotationElement) _annotationElementList
+            .get(index);
+  }
+
+  /**
+   * Method getAnnotationElement.Returns the contents of the collection in an
+   * Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.AnnotationElement[] getAnnotationElement()
+  {
+    jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
+    return (jalview.binding.AnnotationElement[]) this._annotationElementList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAnnotationElementCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAnnotationElementCount()
+  {
+    return this._annotationElementList.size();
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'graph'.
+   * 
+   * @return the value of field 'Graph'.
+   */
+  public boolean getGraph()
+  {
+    return this._graph;
+  }
+
+  /**
+   * Returns the value of field 'graphType'.
+   * 
+   * @return the value of field 'GraphType'.
+   */
+  public int getGraphType()
+  {
+    return this._graphType;
+  }
+
+  /**
+   * Returns the value of field 'label'.
+   * 
+   * @return the value of field 'Label'.
+   */
+  public java.lang.String getLabel()
+  {
+    return this._label;
+  }
+
+  /**
+   * Method hasGraph.
+   * 
+   * @return true if at least one Graph has been added
+   */
+  public boolean hasGraph()
+  {
+    return this._has_graph;
+  }
+
+  /**
+   * Method hasGraphType.
+   * 
+   * @return true if at least one GraphType has been added
+   */
+  public boolean hasGraphType()
+  {
+    return this._has_graphType;
+  }
+
+  /**
+   * Returns the value of field 'graph'.
+   * 
+   * @return the value of field 'Graph'.
+   */
+  public boolean isGraph()
+  {
+    return this._graph;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Sets the value of field 'graph'.
-     * 
-     * @param graph the value of field 'graph'.
-     */
-    public void setGraph(
-            final boolean graph) {
-        this._graph = graph;
-        this._has_graph = true;
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllAnnotationElement()
+  {
+    this._annotationElementList.clear();
+  }
+
+  /**
+   * Method removeAnnotationElement.
+   * 
+   * @param vAnnotationElement
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAnnotationElement(
+          final jalview.binding.AnnotationElement vAnnotationElement)
+  {
+    boolean removed = _annotationElementList.remove(vAnnotationElement);
+    return removed;
+  }
+
+  /**
+   * Method removeAnnotationElementAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.AnnotationElement removeAnnotationElementAt(
+          final int index)
+  {
+    java.lang.Object obj = this._annotationElementList.remove(index);
+    return (jalview.binding.AnnotationElement) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAnnotationElement(final int index,
+          final jalview.binding.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationElementList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setAnnotationElement: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._annotationElementList.size() - 1) + "]");
     }
 
-    /**
-     * Sets the value of field 'graphType'.
-     * 
-     * @param graphType the value of field 'graphType'.
-     */
-    public void setGraphType(
-            final int graphType) {
-        this._graphType = graphType;
-        this._has_graphType = true;
-    }
-
-    /**
-     * Sets the value of field 'label'.
-     * 
-     * @param label the value of field 'label'.
-     */
-    public void setLabel(
-            final java.lang.String label) {
-        this._label = label;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Annotation
-     */
-    public static jalview.binding.Annotation unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._annotationElementList.set(index, vAnnotationElement);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotationElementArray
+   */
+  public void setAnnotationElement(
+          final jalview.binding.AnnotationElement[] vAnnotationElementArray)
+  {
+    // -- copy array
+    _annotationElementList.clear();
+
+    for (int i = 0; i < vAnnotationElementArray.length; i++)
+    {
+      this._annotationElementList.add(vAnnotationElementArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *          the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'graph'.
+   * 
+   * @param graph
+   *          the value of field 'graph'.
+   */
+  public void setGraph(final boolean graph)
+  {
+    this._graph = graph;
+    this._has_graph = true;
+  }
+
+  /**
+   * Sets the value of field 'graphType'.
+   * 
+   * @param graphType
+   *          the value of field 'graphType'.
+   */
+  public void setGraphType(final int graphType)
+  {
+    this._graphType = graphType;
+    this._has_graphType = true;
+  }
+
+  /**
+   * Sets the value of field 'label'.
+   * 
+   * @param label
+   *          the value of field 'label'.
+   */
+  public void setLabel(final java.lang.String label)
+  {
+    this._label = label;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Annotation
+   */
+  public static jalview.binding.Annotation unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Annotation) Unmarshaller.unmarshal(
+            jalview.binding.Annotation.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java
index d133fe0..1f583c7 100644
--- a/src/jalview/binding/AnnotationElement.java
+++ b/src/jalview/binding/AnnotationElement.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,273 +19,287 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationElement implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _position.
-     */
-    private int _position;
-
-    /**
-     * keeps track of state for field: _position
-     */
-    private boolean _has_position;
-
-    /**
-     * Field _displayCharacter.
-     */
-    private java.lang.String _displayCharacter;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _secondaryStructure.
-     */
-    private java.lang.String _secondaryStructure;
-
-    /**
-     * Field _value.
-     */
-    private float _value;
-
-    /**
-     * keeps track of state for field: _value
-     */
-    private boolean _has_value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationElement() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deletePosition(
-    ) {
-        this._has_position= false;
-    }
-
-    /**
-     */
-    public void deleteValue(
-    ) {
-        this._has_value= false;
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'displayCharacter'.
-     * 
-     * @return the value of field 'DisplayCharacter'.
-     */
-    public java.lang.String getDisplayCharacter(
-    ) {
-        return this._displayCharacter;
-    }
-
-    /**
-     * Returns the value of field 'position'.
-     * 
-     * @return the value of field 'Position'.
-     */
-    public int getPosition(
-    ) {
-        return this._position;
-    }
-
-    /**
-     * Returns the value of field 'secondaryStructure'.
-     * 
-     * @return the value of field 'SecondaryStructure'.
-     */
-    public java.lang.String getSecondaryStructure(
-    ) {
-        return this._secondaryStructure;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public float getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method hasPosition.
-     * 
-     * @return true if at least one Position has been added
-     */
-    public boolean hasPosition(
-    ) {
-        return this._has_position;
-    }
-
-    /**
-     * Method hasValue.
-     * 
-     * @return true if at least one Value has been added
-     */
-    public boolean hasValue(
-    ) {
-        return this._has_value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
+public class AnnotationElement implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _position.
+   */
+  private int _position;
+
+  /**
+   * keeps track of state for field: _position
+   */
+  private boolean _has_position;
+
+  /**
+   * Field _displayCharacter.
+   */
+  private java.lang.String _displayCharacter;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _secondaryStructure.
+   */
+  private java.lang.String _secondaryStructure;
+
+  /**
+   * Field _value.
+   */
+  private float _value;
+
+  /**
+   * keeps track of state for field: _value
+   */
+  private boolean _has_value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationElement()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
      */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'displayCharacter'.
-     * 
-     * @param displayCharacter the value of field 'displayCharacter'
-     */
-    public void setDisplayCharacter(
-            final java.lang.String displayCharacter) {
-        this._displayCharacter = displayCharacter;
-    }
-
-    /**
-     * Sets the value of field 'position'.
-     * 
-     * @param position the value of field 'position'.
-     */
-    public void setPosition(
-            final int position) {
-        this._position = position;
-        this._has_position = true;
-    }
-
-    /**
-     * Sets the value of field 'secondaryStructure'.
-     * 
-     * @param secondaryStructure the value of field
-     * 'secondaryStructure'.
-     */
-    public void setSecondaryStructure(
-            final java.lang.String secondaryStructure) {
-        this._secondaryStructure = secondaryStructure;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final float value) {
-        this._value = value;
-        this._has_value = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.AnnotationElement
-     */
-    public static jalview.binding.AnnotationElement unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);
-    }
+  public void deletePosition()
+  {
+    this._has_position = false;
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+  /**
      */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+  public void deleteValue()
+  {
+    this._has_value = false;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'displayCharacter'.
+   * 
+   * @return the value of field 'DisplayCharacter'.
+   */
+  public java.lang.String getDisplayCharacter()
+  {
+    return this._displayCharacter;
+  }
+
+  /**
+   * Returns the value of field 'position'.
+   * 
+   * @return the value of field 'Position'.
+   */
+  public int getPosition()
+  {
+    return this._position;
+  }
+
+  /**
+   * Returns the value of field 'secondaryStructure'.
+   * 
+   * @return the value of field 'SecondaryStructure'.
+   */
+  public java.lang.String getSecondaryStructure()
+  {
+    return this._secondaryStructure;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public float getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method hasPosition.
+   * 
+   * @return true if at least one Position has been added
+   */
+  public boolean hasPosition()
+  {
+    return this._has_position;
+  }
+
+  /**
+   * Method hasValue.
+   * 
+   * @return true if at least one Value has been added
+   */
+  public boolean hasValue()
+  {
+    return this._has_value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *          the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'displayCharacter'.
+   * 
+   * @param displayCharacter
+   *          the value of field 'displayCharacter'
+   */
+  public void setDisplayCharacter(final java.lang.String displayCharacter)
+  {
+    this._displayCharacter = displayCharacter;
+  }
+
+  /**
+   * Sets the value of field 'position'.
+   * 
+   * @param position
+   *          the value of field 'position'.
+   */
+  public void setPosition(final int position)
+  {
+    this._position = position;
+    this._has_position = true;
+  }
+
+  /**
+   * Sets the value of field 'secondaryStructure'.
+   * 
+   * @param secondaryStructure
+   *          the value of field 'secondaryStructure'.
+   */
+  public void setSecondaryStructure(
+          final java.lang.String secondaryStructure)
+  {
+    this._secondaryStructure = secondaryStructure;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *          the value of field 'value'.
+   */
+  public void setValue(final float value)
+  {
+    this._value = value;
+    this._has_value = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.AnnotationElement
+   */
+  public static jalview.binding.AnnotationElement unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(
+            jalview.binding.AnnotationElement.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
index c041723..c1de152 100644
--- a/src/jalview/binding/Colour.java
+++ b/src/jalview/binding/Colour.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,465 +19,480 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Colour implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _RGB.
-     */
-    private java.lang.String _RGB;
-
-    /**
-     * Field _minRGB.
-     */
-    private java.lang.String _minRGB;
-
-    /**
-     * loosely specified enumeration: NONE,ABOVE, or BELOW
-     */
-    private java.lang.String _threshType;
-
-    /**
-     * Field _threshold.
-     */
-    private float _threshold;
-
-    /**
-     * keeps track of state for field: _threshold
-     */
-    private boolean _has_threshold;
-
-    /**
-     * Field _max.
-     */
-    private float _max;
-
-    /**
-     * keeps track of state for field: _max
-     */
-    private boolean _has_max;
-
-    /**
-     * Field _min.
-     */
-    private float _min;
-
-    /**
-     * keeps track of state for field: _min
-     */
-    private boolean _has_min;
-
-    /**
-     * Field _colourByLabel.
-     */
-    private boolean _colourByLabel;
-
-    /**
-     * keeps track of state for field: _colourByLabel
-     */
-    private boolean _has_colourByLabel;
-
-    /**
-     * Field _autoScale.
-     */
-    private boolean _autoScale;
-
-    /**
-     * keeps track of state for field: _autoScale
-     */
-    private boolean _has_autoScale;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Colour() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteAutoScale(
-    ) {
-        this._has_autoScale= false;
-    }
-
-    /**
-     */
-    public void deleteColourByLabel(
-    ) {
-        this._has_colourByLabel= false;
-    }
-
-    /**
-     */
-    public void deleteMax(
-    ) {
-        this._has_max= false;
-    }
-
-    /**
-     */
-    public void deleteMin(
-    ) {
-        this._has_min= false;
-    }
-
-    /**
-     */
-    public void deleteThreshold(
-    ) {
-        this._has_threshold= false;
-    }
-
-    /**
-     * Returns the value of field 'autoScale'.
-     * 
-     * @return the value of field 'AutoScale'.
-     */
-    public boolean getAutoScale(
-    ) {
-        return this._autoScale;
-    }
-
-    /**
-     * Returns the value of field 'colourByLabel'.
-     * 
-     * @return the value of field 'ColourByLabel'.
-     */
-    public boolean getColourByLabel(
-    ) {
-        return this._colourByLabel;
-    }
-
-    /**
-     * Returns the value of field 'max'.
-     * 
-     * @return the value of field 'Max'.
-     */
-    public float getMax(
-    ) {
-        return this._max;
-    }
-
-    /**
-     * Returns the value of field 'min'.
-     * 
-     * @return the value of field 'Min'.
-     */
-    public float getMin(
-    ) {
-        return this._min;
-    }
-
-    /**
-     * Returns the value of field 'minRGB'.
-     * 
-     * @return the value of field 'MinRGB'.
-     */
-    public java.lang.String getMinRGB(
-    ) {
-        return this._minRGB;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'RGB'.
-     * 
-     * @return the value of field 'RGB'.
-     */
-    public java.lang.String getRGB(
-    ) {
-        return this._RGB;
-    }
-
-    /**
-     * Returns the value of field 'threshType'. The field
-     * 'threshType' has the following description: loosely
-     * specified enumeration: NONE,ABOVE, or BELOW
-     * 
-     * @return the value of field 'ThreshType'.
-     */
-    public java.lang.String getThreshType(
-    ) {
-        return this._threshType;
-    }
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return the value of field 'Threshold'.
-     */
-    public float getThreshold(
-    ) {
-        return this._threshold;
-    }
-
-    /**
-     * Method hasAutoScale.
-     * 
-     * @return true if at least one AutoScale has been added
-     */
-    public boolean hasAutoScale(
-    ) {
-        return this._has_autoScale;
-    }
-
-    /**
-     * Method hasColourByLabel.
-     * 
-     * @return true if at least one ColourByLabel has been added
-     */
-    public boolean hasColourByLabel(
-    ) {
-        return this._has_colourByLabel;
-    }
-
-    /**
-     * Method hasMax.
-     * 
-     * @return true if at least one Max has been added
-     */
-    public boolean hasMax(
-    ) {
-        return this._has_max;
-    }
-
-    /**
-     * Method hasMin.
-     * 
-     * @return true if at least one Min has been added
-     */
-    public boolean hasMin(
-    ) {
-        return this._has_min;
-    }
-
-    /**
-     * Method hasThreshold.
-     * 
-     * @return true if at least one Threshold has been added
-     */
-    public boolean hasThreshold(
-    ) {
-        return this._has_threshold;
-    }
-
-    /**
-     * Returns the value of field 'autoScale'.
-     * 
-     * @return the value of field 'AutoScale'.
-     */
-    public boolean isAutoScale(
-    ) {
-        return this._autoScale;
-    }
-
-    /**
-     * Returns the value of field 'colourByLabel'.
-     * 
-     * @return the value of field 'ColourByLabel'.
-     */
-    public boolean isColourByLabel(
-    ) {
-        return this._colourByLabel;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'autoScale'.
-     * 
-     * @param autoScale the value of field 'autoScale'.
-     */
-    public void setAutoScale(
-            final boolean autoScale) {
-        this._autoScale = autoScale;
-        this._has_autoScale = true;
-    }
-
-    /**
-     * Sets the value of field 'colourByLabel'.
-     * 
-     * @param colourByLabel the value of field 'colourByLabel'.
-     */
-    public void setColourByLabel(
-            final boolean colourByLabel) {
-        this._colourByLabel = colourByLabel;
-        this._has_colourByLabel = true;
-    }
-
-    /**
-     * Sets the value of field 'max'.
-     * 
-     * @param max the value of field 'max'.
-     */
-    public void setMax(
-            final float max) {
-        this._max = max;
-        this._has_max = true;
-    }
-
-    /**
-     * Sets the value of field 'min'.
-     * 
-     * @param min the value of field 'min'.
-     */
-    public void setMin(
-            final float min) {
-        this._min = min;
-        this._has_min = true;
-    }
-
-    /**
-     * Sets the value of field 'minRGB'.
-     * 
-     * @param minRGB the value of field 'minRGB'.
-     */
-    public void setMinRGB(
-            final java.lang.String minRGB) {
-        this._minRGB = minRGB;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'RGB'.
-     * 
-     * @param RGB the value of field 'RGB'.
-     */
-    public void setRGB(
-            final java.lang.String RGB) {
-        this._RGB = RGB;
-    }
-
-    /**
-     * Sets the value of field 'threshType'. The field 'threshType'
-     * has the following description: loosely specified
-     * enumeration: NONE,ABOVE, or BELOW
-     * 
-     * @param threshType the value of field 'threshType'.
-     */
-    public void setThreshType(
-            final java.lang.String threshType) {
-        this._threshType = threshType;
-    }
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(
-            final float threshold) {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Colour
-     */
-    public static jalview.binding.Colour unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Colour implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _RGB.
+   */
+  private java.lang.String _RGB;
+
+  /**
+   * Field _minRGB.
+   */
+  private java.lang.String _minRGB;
+
+  /**
+   * loosely specified enumeration: NONE,ABOVE, or BELOW
+   */
+  private java.lang.String _threshType;
+
+  /**
+   * Field _threshold.
+   */
+  private float _threshold;
+
+  /**
+   * keeps track of state for field: _threshold
+   */
+  private boolean _has_threshold;
+
+  /**
+   * Field _max.
+   */
+  private float _max;
+
+  /**
+   * keeps track of state for field: _max
+   */
+  private boolean _has_max;
+
+  /**
+   * Field _min.
+   */
+  private float _min;
+
+  /**
+   * keeps track of state for field: _min
+   */
+  private boolean _has_min;
+
+  /**
+   * Field _colourByLabel.
+   */
+  private boolean _colourByLabel;
+
+  /**
+   * keeps track of state for field: _colourByLabel
+   */
+  private boolean _has_colourByLabel;
+
+  /**
+   * Field _autoScale.
+   */
+  private boolean _autoScale;
+
+  /**
+   * keeps track of state for field: _autoScale
+   */
+  private boolean _has_autoScale;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Colour()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteAutoScale()
+  {
+    this._has_autoScale = false;
+  }
+
+  /**
+     */
+  public void deleteColourByLabel()
+  {
+    this._has_colourByLabel = false;
+  }
+
+  /**
+     */
+  public void deleteMax()
+  {
+    this._has_max = false;
+  }
+
+  /**
+     */
+  public void deleteMin()
+  {
+    this._has_min = false;
+  }
+
+  /**
+     */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  }
+
+  /**
+   * Returns the value of field 'autoScale'.
+   * 
+   * @return the value of field 'AutoScale'.
+   */
+  public boolean getAutoScale()
+  {
+    return this._autoScale;
+  }
+
+  /**
+   * Returns the value of field 'colourByLabel'.
+   * 
+   * @return the value of field 'ColourByLabel'.
+   */
+  public boolean getColourByLabel()
+  {
+    return this._colourByLabel;
+  }
+
+  /**
+   * Returns the value of field 'max'.
+   * 
+   * @return the value of field 'Max'.
+   */
+  public float getMax()
+  {
+    return this._max;
+  }
+
+  /**
+   * Returns the value of field 'min'.
+   * 
+   * @return the value of field 'Min'.
+   */
+  public float getMin()
+  {
+    return this._min;
+  }
+
+  /**
+   * Returns the value of field 'minRGB'.
+   * 
+   * @return the value of field 'MinRGB'.
+   */
+  public java.lang.String getMinRGB()
+  {
+    return this._minRGB;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'RGB'.
+   * 
+   * @return the value of field 'RGB'.
+   */
+  public java.lang.String getRGB()
+  {
+    return this._RGB;
+  }
+
+  /**
+   * Returns the value of field 'threshType'. The field 'threshType' has the
+   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * 
+   * @return the value of field 'ThreshType'.
+   */
+  public java.lang.String getThreshType()
+  {
+    return this._threshType;
+  }
+
+  /**
+   * Returns the value of field 'threshold'.
+   * 
+   * @return the value of field 'Threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  }
+
+  /**
+   * Method hasAutoScale.
+   * 
+   * @return true if at least one AutoScale has been added
+   */
+  public boolean hasAutoScale()
+  {
+    return this._has_autoScale;
+  }
+
+  /**
+   * Method hasColourByLabel.
+   * 
+   * @return true if at least one ColourByLabel has been added
+   */
+  public boolean hasColourByLabel()
+  {
+    return this._has_colourByLabel;
+  }
+
+  /**
+   * Method hasMax.
+   * 
+   * @return true if at least one Max has been added
+   */
+  public boolean hasMax()
+  {
+    return this._has_max;
+  }
+
+  /**
+   * Method hasMin.
+   * 
+   * @return true if at least one Min has been added
+   */
+  public boolean hasMin()
+  {
+    return this._has_min;
+  }
+
+  /**
+   * Method hasThreshold.
+   * 
+   * @return true if at least one Threshold has been added
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  }
+
+  /**
+   * Returns the value of field 'autoScale'.
+   * 
+   * @return the value of field 'AutoScale'.
+   */
+  public boolean isAutoScale()
+  {
+    return this._autoScale;
+  }
+
+  /**
+   * Returns the value of field 'colourByLabel'.
+   * 
+   * @return the value of field 'ColourByLabel'.
+   */
+  public boolean isColourByLabel()
+  {
+    return this._colourByLabel;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'autoScale'.
+   * 
+   * @param autoScale
+   *          the value of field 'autoScale'.
+   */
+  public void setAutoScale(final boolean autoScale)
+  {
+    this._autoScale = autoScale;
+    this._has_autoScale = true;
+  }
+
+  /**
+   * Sets the value of field 'colourByLabel'.
+   * 
+   * @param colourByLabel
+   *          the value of field 'colourByLabel'.
+   */
+  public void setColourByLabel(final boolean colourByLabel)
+  {
+    this._colourByLabel = colourByLabel;
+    this._has_colourByLabel = true;
+  }
+
+  /**
+   * Sets the value of field 'max'.
+   * 
+   * @param max
+   *          the value of field 'max'.
+   */
+  public void setMax(final float max)
+  {
+    this._max = max;
+    this._has_max = true;
+  }
+
+  /**
+   * Sets the value of field 'min'.
+   * 
+   * @param min
+   *          the value of field 'min'.
+   */
+  public void setMin(final float min)
+  {
+    this._min = min;
+    this._has_min = true;
+  }
+
+  /**
+   * Sets the value of field 'minRGB'.
+   * 
+   * @param minRGB
+   *          the value of field 'minRGB'.
+   */
+  public void setMinRGB(final java.lang.String minRGB)
+  {
+    this._minRGB = minRGB;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'RGB'.
+   * 
+   * @param RGB
+   *          the value of field 'RGB'.
+   */
+  public void setRGB(final java.lang.String RGB)
+  {
+    this._RGB = RGB;
+  }
+
+  /**
+   * Sets the value of field 'threshType'. The field 'threshType' has the
+   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * 
+   * @param threshType
+   *          the value of field 'threshType'.
+   */
+  public void setThreshType(final java.lang.String threshType)
+  {
+    this._threshType = threshType;
+  }
+
+  /**
+   * Sets the value of field 'threshold'.
+   * 
+   * @param threshold
+   *          the value of field 'threshold'.
+   */
+  public void setThreshold(final float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Colour
+   */
+  public static jalview.binding.Colour unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Colour) Unmarshaller.unmarshal(
+            jalview.binding.Colour.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java
index d429df3..1cb6eee 100644
--- a/src/jalview/binding/Feature.java
+++ b/src/jalview/binding/Feature.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,272 +19,286 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Feature implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _begin.
-     */
-    private int _begin;
-
-    /**
-     * keeps track of state for field: _begin
-     */
-    private boolean _has_begin;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _status.
-     */
-    private java.lang.String _status;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Feature() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteBegin(
-    ) {
-        this._has_begin= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     * Returns the value of field 'begin'.
-     * 
-     * @return the value of field 'Begin'.
-     */
-    public int getBegin(
-    ) {
-        return this._begin;
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'status'.
-     * 
-     * @return the value of field 'Status'.
-     */
-    public java.lang.String getStatus(
-    ) {
-        return this._status;
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method hasBegin.
-     * 
-     * @return true if at least one Begin has been added
-     */
-    public boolean hasBegin(
-    ) {
-        return this._has_begin;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
+public class Feature implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _begin.
+   */
+  private int _begin;
+
+  /**
+   * keeps track of state for field: _begin
+   */
+  private boolean _has_begin;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _status.
+   */
+  private java.lang.String _status;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Feature()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
      */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'begin'.
-     * 
-     * @param begin the value of field 'begin'.
-     */
-    public void setBegin(
-            final int begin) {
-        this._begin = begin;
-        this._has_begin = true;
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'status'.
-     * 
-     * @param status the value of field 'status'.
-     */
-    public void setStatus(
-            final java.lang.String status) {
-        this._status = status;
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Feature
-     */
-    public static jalview.binding.Feature unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.class, reader);
-    }
+  public void deleteBegin()
+  {
+    this._has_begin = false;
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+  /**
      */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   * Returns the value of field 'begin'.
+   * 
+   * @return the value of field 'Begin'.
+   */
+  public int getBegin()
+  {
+    return this._begin;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'status'.
+   * 
+   * @return the value of field 'Status'.
+   */
+  public java.lang.String getStatus()
+  {
+    return this._status;
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method hasBegin.
+   * 
+   * @return true if at least one Begin has been added
+   */
+  public boolean hasBegin()
+  {
+    return this._has_begin;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'begin'.
+   * 
+   * @param begin
+   *          the value of field 'begin'.
+   */
+  public void setBegin(final int begin)
+  {
+    this._begin = begin;
+    this._has_begin = true;
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *          the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'status'.
+   * 
+   * @param status
+   *          the value of field 'status'.
+   */
+  public void setStatus(final java.lang.String status)
+  {
+    this._status = status;
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *          the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Feature
+   */
+  public static jalview.binding.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Feature) Unmarshaller.unmarshal(
+            jalview.binding.Feature.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java
index f3d06be..c4d5c4f 100644
--- a/src/jalview/binding/FeatureSettings.java
+++ b/src/jalview/binding/FeatureSettings.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,257 +19,271 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class FeatureSettings implements java.io.Serializable {
+public class FeatureSettings implements java.io.Serializable
+{
 
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _settingList.
+   */
+  private java.util.Vector _settingList;
 
-    /**
-     * Field _settingList.
-     */
-    private java.util.Vector _settingList;
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
+  public FeatureSettings()
+  {
+    super();
+    this._settingList = new java.util.Vector();
+  }
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    public FeatureSettings() {
-        super();
-        this._settingList = new java.util.Vector();
-    }
+  /**
+   * 
+   * 
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSetting(final jalview.binding.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.addElement(vSetting);
+  }
 
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSetting(final int index,
+          final jalview.binding.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.add(index, vSetting);
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method enumerateSetting.
+   * 
+   * @return an Enumeration over all jalview.binding.Setting elements
+   */
+  public java.util.Enumeration enumerateSetting()
+  {
+    return this._settingList.elements();
+  }
 
-    /**
-     * 
-     * 
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final jalview.binding.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.addElement(vSetting);
+  /**
+   * Method getSetting.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Setting at the given index
+   */
+  public jalview.binding.Setting getSetting(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("getSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final int index,
-            final jalview.binding.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.add(index, vSetting);
-    }
+    return (jalview.binding.Setting) _settingList.get(index);
+  }
 
-    /**
-     * Method enumerateSetting.
-     * 
-     * @return an Enumeration over all jalview.binding.Setting
-     * elements
-     */
-    public java.util.Enumeration enumerateSetting(
-    ) {
-        return this._settingList.elements();
-    }
+  /**
+   * Method getSetting.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Setting[] getSetting()
+  {
+    jalview.binding.Setting[] array = new jalview.binding.Setting[0];
+    return (jalview.binding.Setting[]) this._settingList.toArray(array);
+  }
 
-    /**
-     * Method getSetting.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Setting at the
-     * given index
-     */
-    public jalview.binding.Setting getSetting(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Setting) _settingList.get(index);
-    }
+  /**
+   * Method getSettingCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSettingCount()
+  {
+    return this._settingList.size();
+  }
 
-    /**
-     * Method getSetting.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Setting[] getSetting(
-    ) {
-        jalview.binding.Setting[] array = new jalview.binding.Setting[0];
-        return (jalview.binding.Setting[]) this._settingList.toArray(array);
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * Method getSettingCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSettingCount(
-    ) {
-        return this._settingList.size();
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+  /**
      */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  public void removeAllSetting()
+  {
+    this._settingList.clear();
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * Method removeSetting.
+   * 
+   * @param vSetting
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSetting(final jalview.binding.Setting vSetting)
+  {
+    boolean removed = _settingList.remove(vSetting);
+    return removed;
+  }
 
-    /**
-     */
-    public void removeAllSetting(
-    ) {
-        this._settingList.clear();
-    }
+  /**
+   * Method removeSettingAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Setting removeSettingAt(final int index)
+  {
+    java.lang.Object obj = this._settingList.remove(index);
+    return (jalview.binding.Setting) obj;
+  }
 
-    /**
-     * Method removeSetting.
-     * 
-     * @param vSetting
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSetting(
-            final jalview.binding.Setting vSetting) {
-        boolean removed = _settingList.remove(vSetting);
-        return removed;
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSetting(final int index,
+          final jalview.binding.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("setSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeSettingAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Setting removeSettingAt(
-            final int index) {
-        java.lang.Object obj = this._settingList.remove(index);
-        return (jalview.binding.Setting) obj;
-    }
+    this._settingList.set(index, vSetting);
+  }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSetting(
-            final int index,
-            final jalview.binding.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        this._settingList.set(index, vSetting);
-    }
+  /**
+   * 
+   * 
+   * @param vSettingArray
+   */
+  public void setSetting(final jalview.binding.Setting[] vSettingArray)
+  {
+    // -- copy array
+    _settingList.clear();
 
-    /**
-     * 
-     * 
-     * @param vSettingArray
-     */
-    public void setSetting(
-            final jalview.binding.Setting[] vSettingArray) {
-        //-- copy array
-        _settingList.clear();
-        
-        for (int i = 0; i < vSettingArray.length; i++) {
-                this._settingList.add(vSettingArray[i]);
-        }
+    for (int i = 0; i < vSettingArray.length; i++)
+    {
+      this._settingList.add(vSettingArray[i]);
     }
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.FeatureSettings
-     */
-    public static jalview.binding.FeatureSettings unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.FeatureSettings
+   */
+  public static jalview.binding.FeatureSettings unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(
+            jalview.binding.FeatureSettings.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Features.java b/src/jalview/binding/Features.java
index e50ae7c..c730f4b 100644
--- a/src/jalview/binding/Features.java
+++ b/src/jalview/binding/Features.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,98 +19,106 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Features extends Feature 
-implements java.io.Serializable
+public class Features extends Feature implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Features() {
-        super();
-    }
-
+  public Features()
+  {
+    super();
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Feature
-     */
-    public static jalview.binding.Feature unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Features.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Feature
+   */
+  public static jalview.binding.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Feature) Unmarshaller.unmarshal(
+            jalview.binding.Features.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java
index 862eebd..477cc30 100644
--- a/src/jalview/binding/JGroup.java
+++ b/src/jalview/binding/JGroup.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,721 +19,742 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JGroup implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _colour.
-     */
-    private java.lang.String _colour;
-
-    /**
-     * Field _consThreshold.
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold.
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _outlineColour.
-     */
-    private int _outlineColour;
-
-    /**
-     * keeps track of state for field: _outlineColour
-     */
-    private boolean _has_outlineColour;
-
-    /**
-     * Field _displayBoxes.
-     */
-    private boolean _displayBoxes;
-
-    /**
-     * keeps track of state for field: _displayBoxes
-     */
-    private boolean _has_displayBoxes;
-
-    /**
-     * Field _displayText.
-     */
-    private boolean _displayText;
-
-    /**
-     * keeps track of state for field: _displayText
-     */
-    private boolean _has_displayText;
-
-    /**
-     * Field _colourText.
-     */
-    private boolean _colourText;
-
-    /**
-     * keeps track of state for field: _colourText
-     */
-    private boolean _has_colourText;
-
-    /**
-     * Field _seqList.
-     */
-    private java.util.Vector _seqList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JGroup() {
-        super();
-        this._seqList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeq(
-            final int vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._seqList.addElement(new java.lang.Integer(vSeq));
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeq(
-            final int index,
-            final int vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._seqList.add(index, new java.lang.Integer(vSeq));
-    }
-
-    /**
-     */
-    public void deleteColourText(
-    ) {
-        this._has_colourText= false;
-    }
-
-    /**
-     */
-    public void deleteConsThreshold(
-    ) {
-        this._has_consThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteDisplayBoxes(
-    ) {
-        this._has_displayBoxes= false;
-    }
-
-    /**
-     */
-    public void deleteDisplayText(
-    ) {
-        this._has_displayText= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteOutlineColour(
-    ) {
-        this._has_outlineColour= false;
-    }
-
-    /**
-     */
-    public void deletePidThreshold(
-    ) {
-        this._has_pidThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Method enumerateSeq.
-     * 
-     * @return an Enumeration over all int elements
-     */
-    public java.util.Enumeration enumerateSeq(
-    ) {
-        return this._seqList.elements();
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public java.lang.String getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return the value of field 'ColourText'.
-     */
-    public boolean getColourText(
-    ) {
-        return this._colourText;
-    }
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return the value of field 'ConsThreshold'.
-     */
-    public int getConsThreshold(
-    ) {
-        return this._consThreshold;
-    }
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return the value of field 'DisplayBoxes'.
-     */
-    public boolean getDisplayBoxes(
-    ) {
-        return this._displayBoxes;
-    }
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return the value of field 'DisplayText'.
-     */
-    public boolean getDisplayText(
-    ) {
-        return this._displayText;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'outlineColour'.
-     * 
-     * @return the value of field 'OutlineColour'.
-     */
-    public int getOutlineColour(
-    ) {
-        return this._outlineColour;
-    }
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return the value of field 'PidThreshold'.
-     */
-    public int getPidThreshold(
-    ) {
-        return this._pidThreshold;
-    }
-
-    /**
-     * Method getSeq.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the int at the given index
-     */
-    public int getSeq(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._seqList.size()) {
-            throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
-        }
-        
-        return ((java.lang.Integer) _seqList.get(index)).intValue();
-    }
-
-    /**
-     * Method getSeq.Returns the contents of the collection in an
-     * Array.  
-     * 
-     * @return this collection as an Array
-     */
-    public int[] getSeq(
-    ) {
-        int size = this._seqList.size();
-        int[] array = new int[size];
-        java.util.Iterator iter = _seqList.iterator();
-        for (int index = 0; index < size; index++) {
-            array[index] = ((java.lang.Integer) iter.next()).intValue();
-        }
-        return array;
-    }
-
-    /**
-     * Method getSeqCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSeqCount(
-    ) {
-        return this._seqList.size();
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasColourText.
-     * 
-     * @return true if at least one ColourText has been added
-     */
-    public boolean hasColourText(
-    ) {
-        return this._has_colourText;
-    }
-
-    /**
-     * Method hasConsThreshold.
-     * 
-     * @return true if at least one ConsThreshold has been added
-     */
-    public boolean hasConsThreshold(
-    ) {
-        return this._has_consThreshold;
-    }
-
-    /**
-     * Method hasDisplayBoxes.
-     * 
-     * @return true if at least one DisplayBoxes has been added
-     */
-    public boolean hasDisplayBoxes(
-    ) {
-        return this._has_displayBoxes;
-    }
-
-    /**
-     * Method hasDisplayText.
-     * 
-     * @return true if at least one DisplayText has been added
-     */
-    public boolean hasDisplayText(
-    ) {
-        return this._has_displayText;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasOutlineColour.
-     * 
-     * @return true if at least one OutlineColour has been added
-     */
-    public boolean hasOutlineColour(
-    ) {
-        return this._has_outlineColour;
-    }
-
-    /**
-     * Method hasPidThreshold.
-     * 
-     * @return true if at least one PidThreshold has been added
-     */
-    public boolean hasPidThreshold(
-    ) {
-        return this._has_pidThreshold;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return the value of field 'ColourText'.
-     */
-    public boolean isColourText(
-    ) {
-        return this._colourText;
-    }
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return the value of field 'DisplayBoxes'.
-     */
-    public boolean isDisplayBoxes(
-    ) {
-        return this._displayBoxes;
-    }
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return the value of field 'DisplayText'.
-     */
-    public boolean isDisplayText(
-    ) {
-        return this._displayText;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllSeq(
-    ) {
-        this._seqList.clear();
-    }
-
-    /**
-     * Method removeSeq.
-     * 
-     * @param vSeq
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSeq(
-            final int vSeq) {
-        boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
-        return removed;
-    }
-
-    /**
-     * Method removeSeqAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public int removeSeqAt(
-            final int index) {
-        java.lang.Object obj = this._seqList.remove(index);
-        return ((java.lang.Integer) obj).intValue();
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final java.lang.String colour) {
-        this._colour = colour;
-    }
-
-    /**
-     * Sets the value of field 'colourText'.
-     * 
-     * @param colourText the value of field 'colourText'.
-     */
-    public void setColourText(
-            final boolean colourText) {
-        this._colourText = colourText;
-        this._has_colourText = true;
-    }
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(
-            final int consThreshold) {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'displayBoxes'.
-     * 
-     * @param displayBoxes the value of field 'displayBoxes'.
-     */
-    public void setDisplayBoxes(
-            final boolean displayBoxes) {
-        this._displayBoxes = displayBoxes;
-        this._has_displayBoxes = true;
-    }
-
-    /**
-     * Sets the value of field 'displayText'.
-     * 
-     * @param displayText the value of field 'displayText'.
-     */
-    public void setDisplayText(
-            final boolean displayText) {
-        this._displayText = displayText;
-        this._has_displayText = true;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'outlineColour'.
-     * 
-     * @param outlineColour the value of field 'outlineColour'.
-     */
-    public void setOutlineColour(
-            final int outlineColour) {
-        this._outlineColour = outlineColour;
-        this._has_outlineColour = true;
-    }
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(
-            final int pidThreshold) {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSeq(
-            final int index,
-            final int vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._seqList.size()) {
-            throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
-        }
-        
-        this._seqList.set(index, new java.lang.Integer(vSeq));
-    }
-
-    /**
-     * 
-     * 
-     * @param vSeqArray
-     */
-    public void setSeq(
-            final int[] vSeqArray) {
-        //-- copy array
-        _seqList.clear();
-        
-        for (int i = 0; i < vSeqArray.length; i++) {
-                this._seqList.add(new java.lang.Integer(vSeqArray[i]));
-        }
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JGroup
-     */
-    public static jalview.binding.JGroup unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JGroup implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _colour.
+   */
+  private java.lang.String _colour;
+
+  /**
+   * Field _consThreshold.
+   */
+  private int _consThreshold;
+
+  /**
+   * keeps track of state for field: _consThreshold
+   */
+  private boolean _has_consThreshold;
+
+  /**
+   * Field _pidThreshold.
+   */
+  private int _pidThreshold;
+
+  /**
+   * keeps track of state for field: _pidThreshold
+   */
+  private boolean _has_pidThreshold;
+
+  /**
+   * Field _outlineColour.
+   */
+  private int _outlineColour;
+
+  /**
+   * keeps track of state for field: _outlineColour
+   */
+  private boolean _has_outlineColour;
+
+  /**
+   * Field _displayBoxes.
+   */
+  private boolean _displayBoxes;
+
+  /**
+   * keeps track of state for field: _displayBoxes
+   */
+  private boolean _has_displayBoxes;
+
+  /**
+   * Field _displayText.
+   */
+  private boolean _displayText;
+
+  /**
+   * keeps track of state for field: _displayText
+   */
+  private boolean _has_displayText;
+
+  /**
+   * Field _colourText.
+   */
+  private boolean _colourText;
+
+  /**
+   * keeps track of state for field: _colourText
+   */
+  private boolean _has_colourText;
+
+  /**
+   * Field _seqList.
+   */
+  private java.util.Vector _seqList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JGroup()
+  {
+    super();
+    this._seqList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSeq(final int vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._seqList.addElement(new java.lang.Integer(vSeq));
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSeq(final int index, final int vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._seqList.add(index, new java.lang.Integer(vSeq));
+  }
+
+  /**
+     */
+  public void deleteColourText()
+  {
+    this._has_colourText = false;
+  }
+
+  /**
+     */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  }
+
+  /**
+     */
+  public void deleteDisplayBoxes()
+  {
+    this._has_displayBoxes = false;
+  }
+
+  /**
+     */
+  public void deleteDisplayText()
+  {
+    this._has_displayText = false;
+  }
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+     */
+  public void deleteOutlineColour()
+  {
+    this._has_outlineColour = false;
+  }
+
+  /**
+     */
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  }
+
+  /**
+     */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Method enumerateSeq.
+   * 
+   * @return an Enumeration over all int elements
+   */
+  public java.util.Enumeration enumerateSeq()
+  {
+    return this._seqList.elements();
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public java.lang.String getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'colourText'.
+   * 
+   * @return the value of field 'ColourText'.
+   */
+  public boolean getColourText()
+  {
+    return this._colourText;
+  }
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   * 
+   * @return the value of field 'ConsThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  }
+
+  /**
+   * Returns the value of field 'displayBoxes'.
+   * 
+   * @return the value of field 'DisplayBoxes'.
+   */
+  public boolean getDisplayBoxes()
+  {
+    return this._displayBoxes;
+  }
+
+  /**
+   * Returns the value of field 'displayText'.
+   * 
+   * @return the value of field 'DisplayText'.
+   */
+  public boolean getDisplayText()
+  {
+    return this._displayText;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'outlineColour'.
+   * 
+   * @return the value of field 'OutlineColour'.
+   */
+  public int getOutlineColour()
+  {
+    return this._outlineColour;
+  }
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   * 
+   * @return the value of field 'PidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  }
+
+  /**
+   * Method getSeq.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the int at the given index
+   */
+  public int getSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
+    {
+      throw new IndexOutOfBoundsException("getSeq: Index value '" + index
+              + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+    }
+
+    return ((java.lang.Integer) _seqList.get(index)).intValue();
+  }
+
+  /**
+   * Method getSeq.Returns the contents of the collection in an Array.
+   * 
+   * @return this collection as an Array
+   */
+  public int[] getSeq()
+  {
+    int size = this._seqList.size();
+    int[] array = new int[size];
+    java.util.Iterator iter = _seqList.iterator();
+    for (int index = 0; index < size; index++)
+    {
+      array[index] = ((java.lang.Integer) iter.next()).intValue();
+    }
+    return array;
+  }
+
+  /**
+   * Method getSeqCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSeqCount()
+  {
+    return this._seqList.size();
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasColourText.
+   * 
+   * @return true if at least one ColourText has been added
+   */
+  public boolean hasColourText()
+  {
+    return this._has_colourText;
+  }
+
+  /**
+   * Method hasConsThreshold.
+   * 
+   * @return true if at least one ConsThreshold has been added
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  }
+
+  /**
+   * Method hasDisplayBoxes.
+   * 
+   * @return true if at least one DisplayBoxes has been added
+   */
+  public boolean hasDisplayBoxes()
+  {
+    return this._has_displayBoxes;
+  }
+
+  /**
+   * Method hasDisplayText.
+   * 
+   * @return true if at least one DisplayText has been added
+   */
+  public boolean hasDisplayText()
+  {
+    return this._has_displayText;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasOutlineColour.
+   * 
+   * @return true if at least one OutlineColour has been added
+   */
+  public boolean hasOutlineColour()
+  {
+    return this._has_outlineColour;
+  }
+
+  /**
+   * Method hasPidThreshold.
+   * 
+   * @return true if at least one PidThreshold has been added
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Returns the value of field 'colourText'.
+   * 
+   * @return the value of field 'ColourText'.
+   */
+  public boolean isColourText()
+  {
+    return this._colourText;
+  }
+
+  /**
+   * Returns the value of field 'displayBoxes'.
+   * 
+   * @return the value of field 'DisplayBoxes'.
+   */
+  public boolean isDisplayBoxes()
+  {
+    return this._displayBoxes;
+  }
+
+  /**
+   * Returns the value of field 'displayText'.
+   * 
+   * @return the value of field 'DisplayText'.
+   */
+  public boolean isDisplayText()
+  {
+    return this._displayText;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllSeq()
+  {
+    this._seqList.clear();
+  }
+
+  /**
+   * Method removeSeq.
+   * 
+   * @param vSeq
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSeq(final int vSeq)
+  {
+    boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+    return removed;
+  }
+
+  /**
+   * Method removeSeqAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public int removeSeqAt(final int index)
+  {
+    java.lang.Object obj = this._seqList.remove(index);
+    return ((java.lang.Integer) obj).intValue();
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *          the value of field 'colour'.
+   */
+  public void setColour(final java.lang.String colour)
+  {
+    this._colour = colour;
+  }
+
+  /**
+   * Sets the value of field 'colourText'.
+   * 
+   * @param colourText
+   *          the value of field 'colourText'.
+   */
+  public void setColourText(final boolean colourText)
+  {
+    this._colourText = colourText;
+    this._has_colourText = true;
+  }
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   * 
+   * @param consThreshold
+   *          the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(final int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'displayBoxes'.
+   * 
+   * @param displayBoxes
+   *          the value of field 'displayBoxes'.
+   */
+  public void setDisplayBoxes(final boolean displayBoxes)
+  {
+    this._displayBoxes = displayBoxes;
+    this._has_displayBoxes = true;
+  }
+
+  /**
+   * Sets the value of field 'displayText'.
+   * 
+   * @param displayText
+   *          the value of field 'displayText'.
+   */
+  public void setDisplayText(final boolean displayText)
+  {
+    this._displayText = displayText;
+    this._has_displayText = true;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'outlineColour'.
+   * 
+   * @param outlineColour
+   *          the value of field 'outlineColour'.
+   */
+  public void setOutlineColour(final int outlineColour)
+  {
+    this._outlineColour = outlineColour;
+    this._has_outlineColour = true;
+  }
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   * 
+   * @param pidThreshold
+   *          the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(final int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSeq(final int index, final int vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
+    {
+      throw new IndexOutOfBoundsException("setSeq: Index value '" + index
+              + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+    }
+
+    this._seqList.set(index, new java.lang.Integer(vSeq));
+  }
+
+  /**
+   * 
+   * 
+   * @param vSeqArray
+   */
+  public void setSeq(final int[] vSeqArray)
+  {
+    // -- copy array
+    _seqList.clear();
+
+    for (int i = 0; i < vSeqArray.length; i++)
+    {
+      this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+    }
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *          the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.JGroup
+   */
+  public static jalview.binding.JGroup unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JGroup) Unmarshaller.unmarshal(
+            jalview.binding.JGroup.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
index 14b1f2f..996a807 100644
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,605 +19,627 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JSeq implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _id.
-     */
-    private int _id;
-
-    /**
-     * keeps track of state for field: _id
-     */
-    private boolean _has_id;
-
-    /**
-     * Field _featuresList.
-     */
-    private java.util.Vector _featuresList;
-
-    /**
-     * Field _pdbidsList.
-     */
-    private java.util.Vector _pdbidsList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JSeq() {
-        super();
-        this._featuresList = new java.util.Vector();
-        this._pdbidsList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addFeatures(
-            final jalview.binding.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        this._featuresList.addElement(vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addFeatures(
-            final int index,
-            final jalview.binding.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        this._featuresList.add(index, vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbids(
-            final jalview.binding.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        this._pdbidsList.addElement(vPdbids);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbids(
-            final int index,
-            final jalview.binding.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        this._pdbidsList.add(index, vPdbids);
-    }
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteId(
-    ) {
-        this._has_id= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Method enumerateFeatures.
-     * 
-     * @return an Enumeration over all jalview.binding.Features
-     * elements
-     */
-    public java.util.Enumeration enumerateFeatures(
-    ) {
-        return this._featuresList.elements();
-    }
-
-    /**
-     * Method enumeratePdbids.
-     * 
-     * @return an Enumeration over all jalview.binding.Pdbids
-     * elements
-     */
-    public java.util.Enumeration enumeratePdbids(
-    ) {
-        return this._pdbidsList.elements();
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Method getFeatures.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Features at the
-     * given index
-     */
-    public jalview.binding.Features getFeatures(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._featuresList.size()) {
-            throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Features) _featuresList.get(index);
-    }
-
-    /**
-     * Method getFeatures.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Features[] getFeatures(
-    ) {
-        jalview.binding.Features[] array = new jalview.binding.Features[0];
-        return (jalview.binding.Features[]) this._featuresList.toArray(array);
-    }
-
-    /**
-     * Method getFeaturesCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getFeaturesCount(
-    ) {
-        return this._featuresList.size();
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public int getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Method getPdbids.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Pdbids at the given
-     * index
-     */
-    public jalview.binding.Pdbids getPdbids(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._pdbidsList.size()) {
-            throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Pdbids) _pdbidsList.get(index);
-    }
-
-    /**
-     * Method getPdbids.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Pdbids[] getPdbids(
-    ) {
-        jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
-        return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
-    }
-
-    /**
-     * Method getPdbidsCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPdbidsCount(
-    ) {
-        return this._pdbidsList.size();
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasId.
-     * 
-     * @return true if at least one Id has been added
-     */
-    public boolean hasId(
-    ) {
-        return this._has_id;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllFeatures(
-    ) {
-        this._featuresList.clear();
-    }
-
-    /**
-     */
-    public void removeAllPdbids(
-    ) {
-        this._pdbidsList.clear();
-    }
-
-    /**
-     * Method removeFeatures.
-     * 
-     * @param vFeatures
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeFeatures(
-            final jalview.binding.Features vFeatures) {
-        boolean removed = _featuresList.remove(vFeatures);
-        return removed;
-    }
-
-    /**
-     * Method removeFeaturesAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Features removeFeaturesAt(
-            final int index) {
-        java.lang.Object obj = this._featuresList.remove(index);
-        return (jalview.binding.Features) obj;
-    }
-
-    /**
-     * Method removePdbids.
-     * 
-     * @param vPdbids
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePdbids(
-            final jalview.binding.Pdbids vPdbids) {
-        boolean removed = _pdbidsList.remove(vPdbids);
-        return removed;
-    }
-
-    /**
-     * Method removePdbidsAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Pdbids removePdbidsAt(
-            final int index) {
-        java.lang.Object obj = this._pdbidsList.remove(index);
-        return (jalview.binding.Pdbids) obj;
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setFeatures(
-            final int index,
-            final jalview.binding.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._featuresList.size()) {
-            throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
-        }
-        
-        this._featuresList.set(index, vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param vFeaturesArray
-     */
-    public void setFeatures(
-            final jalview.binding.Features[] vFeaturesArray) {
-        //-- copy array
-        _featuresList.clear();
-        
-        for (int i = 0; i < vFeaturesArray.length; i++) {
-                this._featuresList.add(vFeaturesArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final int id) {
-        this._id = id;
-        this._has_id = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setPdbids(
-            final int index,
-            final jalview.binding.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._pdbidsList.size()) {
-            throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
-        }
-        
-        this._pdbidsList.set(index, vPdbids);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbidsArray
-     */
-    public void setPdbids(
-            final jalview.binding.Pdbids[] vPdbidsArray) {
-        //-- copy array
-        _pdbidsList.clear();
-        
-        for (int i = 0; i < vPdbidsArray.length; i++) {
-                this._pdbidsList.add(vPdbidsArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JSeq
-     */
-    public static jalview.binding.JSeq unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JSeq implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _id.
+   */
+  private int _id;
+
+  /**
+   * keeps track of state for field: _id
+   */
+  private boolean _has_id;
+
+  /**
+   * Field _featuresList.
+   */
+  private java.util.Vector _featuresList;
+
+  /**
+   * Field _pdbidsList.
+   */
+  private java.util.Vector _pdbidsList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JSeq()
+  {
+    super();
+    this._featuresList = new java.util.Vector();
+    this._pdbidsList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(final jalview.binding.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.addElement(vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(final int index,
+          final jalview.binding.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.add(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final jalview.binding.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.addElement(vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final int index,
+          final jalview.binding.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.add(index, vPdbids);
+  }
+
+  /**
+     */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+     */
+  public void deleteId()
+  {
+    this._has_id = false;
+  }
+
+  /**
+     */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Method enumerateFeatures.
+   * 
+   * @return an Enumeration over all jalview.binding.Features elements
+   */
+  public java.util.Enumeration enumerateFeatures()
+  {
+    return this._featuresList.elements();
+  }
+
+  /**
+   * Method enumeratePdbids.
+   * 
+   * @return an Enumeration over all jalview.binding.Pdbids elements
+   */
+  public java.util.Enumeration enumeratePdbids()
+  {
+    return this._pdbidsList.elements();
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Method getFeatures.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Features at the given index
+   */
+  public jalview.binding.Features getFeatures(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("getFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Features) _featuresList.get(index);
+  }
+
+  /**
+   * Method getFeatures.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Features[] getFeatures()
+  {
+    jalview.binding.Features[] array = new jalview.binding.Features[0];
+    return (jalview.binding.Features[]) this._featuresList.toArray(array);
+  }
+
+  /**
+   * Method getFeaturesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getFeaturesCount()
+  {
+    return this._featuresList.size();
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public int getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbids.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Pdbids at the given index
+   */
+  public jalview.binding.Pdbids getPdbids(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Pdbids) _pdbidsList.get(index);
+  }
+
+  /**
+   * Method getPdbids.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Pdbids[] getPdbids()
+  {
+    jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
+    return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
+  }
+
+  /**
+   * Method getPdbidsCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbidsCount()
+  {
+    return this._pdbidsList.size();
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasId.
+   * 
+   * @return true if at least one Id has been added
+   */
+  public boolean hasId()
+  {
+    return this._has_id;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllFeatures()
+  {
+    this._featuresList.clear();
+  }
+
+  /**
+     */
+  public void removeAllPdbids()
+  {
+    this._pdbidsList.clear();
+  }
+
+  /**
+   * Method removeFeatures.
+   * 
+   * @param vFeatures
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeFeatures(final jalview.binding.Features vFeatures)
+  {
+    boolean removed = _featuresList.remove(vFeatures);
+    return removed;
+  }
+
+  /**
+   * Method removeFeaturesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Features removeFeaturesAt(final int index)
+  {
+    java.lang.Object obj = this._featuresList.remove(index);
+    return (jalview.binding.Features) obj;
+  }
+
+  /**
+   * Method removePdbids.
+   * 
+   * @param vPdbids
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbids(final jalview.binding.Pdbids vPdbids)
+  {
+    boolean removed = _pdbidsList.remove(vPdbids);
+    return removed;
+  }
+
+  /**
+   * Method removePdbidsAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Pdbids removePdbidsAt(final int index)
+  {
+    java.lang.Object obj = this._pdbidsList.remove(index);
+    return (jalview.binding.Pdbids) obj;
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *          the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setFeatures(final int index,
+          final jalview.binding.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("setFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    this._featuresList.set(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vFeaturesArray
+   */
+  public void setFeatures(final jalview.binding.Features[] vFeaturesArray)
+  {
+    // -- copy array
+    _featuresList.clear();
+
+    for (int i = 0; i < vFeaturesArray.length; i++)
+    {
+      this._featuresList.add(vFeaturesArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final int id)
+  {
+    this._id = id;
+    this._has_id = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setPdbids(final int index,
+          final jalview.binding.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    this._pdbidsList.set(index, vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbidsArray
+   */
+  public void setPdbids(final jalview.binding.Pdbids[] vPdbidsArray)
+  {
+    // -- copy array
+    _pdbidsList.clear();
+
+    for (int i = 0; i < vPdbidsArray.length; i++)
+    {
+      this._pdbidsList.add(vPdbidsArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *          the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.JSeq
+   */
+  public static jalview.binding.JSeq unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JSeq) Unmarshaller.unmarshal(
+            jalview.binding.JSeq.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java
index 21f8be9..7141b27 100644
--- a/src/jalview/binding/JalviewModel.java
+++ b/src/jalview/binding/JalviewModel.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,202 +19,215 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModel implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _creationDate.
-     */
-    private java.util.Date _creationDate;
-
-    /**
-     * Field _version.
-     */
-    private java.lang.String _version;
-
-    /**
-     * Field _vamsasModel.
-     */
-    private jalview.binding.VamsasModel _vamsasModel;
-
-    /**
-     * Field _jalviewModelSequence.
-     */
-    private jalview.binding.JalviewModelSequence _jalviewModelSequence;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModel() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'creationDate'.
-     * 
-     * @return the value of field 'CreationDate'.
-     */
-    public java.util.Date getCreationDate(
-    ) {
-        return this._creationDate;
-    }
-
-    /**
-     * Returns the value of field 'jalviewModelSequence'.
-     * 
-     * @return the value of field 'JalviewModelSequence'.
-     */
-    public jalview.binding.JalviewModelSequence getJalviewModelSequence(
-    ) {
-        return this._jalviewModelSequence;
-    }
-
-    /**
-     * Returns the value of field 'vamsasModel'.
-     * 
-     * @return the value of field 'VamsasModel'.
-     */
-    public jalview.binding.VamsasModel getVamsasModel(
-    ) {
-        return this._vamsasModel;
-    }
-
-    /**
-     * Returns the value of field 'version'.
-     * 
-     * @return the value of field 'Version'.
-     */
-    public java.lang.String getVersion(
-    ) {
-        return this._version;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'creationDate'.
-     * 
-     * @param creationDate the value of field 'creationDate'.
-     */
-    public void setCreationDate(
-            final java.util.Date creationDate) {
-        this._creationDate = creationDate;
-    }
-
-    /**
-     * Sets the value of field 'jalviewModelSequence'.
-     * 
-     * @param jalviewModelSequence the value of field
-     * 'jalviewModelSequence'.
-     */
-    public void setJalviewModelSequence(
-            final jalview.binding.JalviewModelSequence jalviewModelSequence) {
-        this._jalviewModelSequence = jalviewModelSequence;
-    }
-
-    /**
-     * Sets the value of field 'vamsasModel'.
-     * 
-     * @param vamsasModel the value of field 'vamsasModel'.
-     */
-    public void setVamsasModel(
-            final jalview.binding.VamsasModel vamsasModel) {
-        this._vamsasModel = vamsasModel;
-    }
-
-    /**
-     * Sets the value of field 'version'.
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(
-            final java.lang.String version) {
-        this._version = version;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JalviewModel
-     */
-    public static jalview.binding.JalviewModel unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class JalviewModel implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _creationDate.
+   */
+  private java.util.Date _creationDate;
+
+  /**
+   * Field _version.
+   */
+  private java.lang.String _version;
+
+  /**
+   * Field _vamsasModel.
+   */
+  private jalview.binding.VamsasModel _vamsasModel;
+
+  /**
+   * Field _jalviewModelSequence.
+   */
+  private jalview.binding.JalviewModelSequence _jalviewModelSequence;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModel()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'creationDate'.
+   * 
+   * @return the value of field 'CreationDate'.
+   */
+  public java.util.Date getCreationDate()
+  {
+    return this._creationDate;
+  }
+
+  /**
+   * Returns the value of field 'jalviewModelSequence'.
+   * 
+   * @return the value of field 'JalviewModelSequence'.
+   */
+  public jalview.binding.JalviewModelSequence getJalviewModelSequence()
+  {
+    return this._jalviewModelSequence;
+  }
+
+  /**
+   * Returns the value of field 'vamsasModel'.
+   * 
+   * @return the value of field 'VamsasModel'.
+   */
+  public jalview.binding.VamsasModel getVamsasModel()
+  {
+    return this._vamsasModel;
+  }
+
+  /**
+   * Returns the value of field 'version'.
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'creationDate'.
+   * 
+   * @param creationDate
+   *          the value of field 'creationDate'.
+   */
+  public void setCreationDate(final java.util.Date creationDate)
+  {
+    this._creationDate = creationDate;
+  }
+
+  /**
+   * Sets the value of field 'jalviewModelSequence'.
+   * 
+   * @param jalviewModelSequence
+   *          the value of field 'jalviewModelSequence'.
+   */
+  public void setJalviewModelSequence(
+          final jalview.binding.JalviewModelSequence jalviewModelSequence)
+  {
+    this._jalviewModelSequence = jalviewModelSequence;
+  }
+
+  /**
+   * Sets the value of field 'vamsasModel'.
+   * 
+   * @param vamsasModel
+   *          the value of field 'vamsasModel'.
+   */
+  public void setVamsasModel(final jalview.binding.VamsasModel vamsasModel)
+  {
+    this._vamsasModel = vamsasModel;
+  }
+
+  /**
+   * Sets the value of field 'version'.
+   * 
+   * @param version
+   *          the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.JalviewModel
+   */
+  public static jalview.binding.JalviewModel unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(
+            jalview.binding.JalviewModel.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 5ebcee6..eb0716d 100644
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,904 +19,937 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequence implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _JSeqList.
-     */
-    private java.util.Vector _JSeqList;
-
-    /**
-     * Field _JGroupList.
-     */
-    private java.util.Vector _JGroupList;
-
-    /**
-     * Field _viewportList.
-     */
-    private java.util.Vector _viewportList;
-
-    /**
-     * Field _userColoursList.
-     */
-    private java.util.Vector _userColoursList;
-
-    /**
-     * Field _treeList.
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _featureSettings.
-     */
-    private jalview.binding.FeatureSettings _featureSettings;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelSequence() {
-        super();
-        this._JSeqList = new java.util.Vector();
-        this._JGroupList = new java.util.Vector();
-        this._viewportList = new java.util.Vector();
-        this._userColoursList = new java.util.Vector();
-        this._treeList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJGroup(
-            final jalview.binding.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JGroupList.addElement(vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJGroup(
-            final int index,
-            final jalview.binding.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JGroupList.add(index, vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJSeq(
-            final jalview.binding.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JSeqList.addElement(vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJSeq(
-            final int index,
-            final jalview.binding.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JSeqList.add(index, vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final jalview.binding.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.addElement(vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final int index,
-            final jalview.binding.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.add(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addUserColours(
-            final jalview.binding.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        this._userColoursList.addElement(vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addUserColours(
-            final int index,
-            final jalview.binding.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        this._userColoursList.add(index, vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addViewport(
-            final jalview.binding.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        this._viewportList.addElement(vViewport);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addViewport(
-            final int index,
-            final jalview.binding.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        this._viewportList.add(index, vViewport);
-    }
-
-    /**
-     * Method enumerateJGroup.
-     * 
-     * @return an Enumeration over all jalview.binding.JGroup
-     * elements
-     */
-    public java.util.Enumeration enumerateJGroup(
-    ) {
-        return this._JGroupList.elements();
-    }
-
-    /**
-     * Method enumerateJSeq.
-     * 
-     * @return an Enumeration over all jalview.binding.JSeq elements
-     */
-    public java.util.Enumeration enumerateJSeq(
-    ) {
-        return this._JSeqList.elements();
-    }
-
-    /**
-     * Method enumerateTree.
-     * 
-     * @return an Enumeration over all jalview.binding.Tree elements
-     */
-    public java.util.Enumeration enumerateTree(
-    ) {
-        return this._treeList.elements();
-    }
-
-    /**
-     * Method enumerateUserColours.
-     * 
-     * @return an Enumeration over all jalview.binding.UserColours
-     * elements
-     */
-    public java.util.Enumeration enumerateUserColours(
-    ) {
-        return this._userColoursList.elements();
-    }
-
-    /**
-     * Method enumerateViewport.
-     * 
-     * @return an Enumeration over all jalview.binding.Viewport
-     * elements
-     */
-    public java.util.Enumeration enumerateViewport(
-    ) {
-        return this._viewportList.elements();
-    }
-
-    /**
-     * Returns the value of field 'featureSettings'.
-     * 
-     * @return the value of field 'FeatureSettings'.
-     */
-    public jalview.binding.FeatureSettings getFeatureSettings(
-    ) {
-        return this._featureSettings;
-    }
-
-    /**
-     * Method getJGroup.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.JGroup at the given
-     * index
-     */
-    public jalview.binding.JGroup getJGroup(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JGroupList.size()) {
-            throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.JGroup) _JGroupList.get(index);
-    }
-
-    /**
-     * Method getJGroup.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.JGroup[] getJGroup(
-    ) {
-        jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
-        return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
-    }
-
-    /**
-     * Method getJGroupCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getJGroupCount(
-    ) {
-        return this._JGroupList.size();
-    }
-
-    /**
-     * Method getJSeq.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.JSeq at the given
-     * index
-     */
-    public jalview.binding.JSeq getJSeq(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JSeqList.size()) {
-            throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.JSeq) _JSeqList.get(index);
-    }
-
-    /**
-     * Method getJSeq.Returns the contents of the collection in an
-     * Array.  
Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.JSeq[] getJSeq(
-    ) {
-        jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
-        return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
-    }
-
-    /**
-     * Method getJSeqCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getJSeqCount(
-    ) {
-        return this._JSeqList.size();
-    }
-
-    /**
-     * Method getTree.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Tree at the given
-     * index
-     */
-    public jalview.binding.Tree getTree(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Tree) _treeList.get(index);
-    }
-
-    /**
-     * Method getTree.Returns the contents of the collection in an
-     * Array.  
Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Tree[] getTree(
-    ) {
-        jalview.binding.Tree[] array = new jalview.binding.Tree[0];
-        return (jalview.binding.Tree[]) this._treeList.toArray(array);
-    }
-
-    /**
-     * Method getTreeCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getTreeCount(
-    ) {
-        return this._treeList.size();
-    }
-
-    /**
-     * Method getUserColours.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.UserColours at the
-     * given index
-     */
-    public jalview.binding.UserColours getUserColours(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._userColoursList.size()) {
-            throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.UserColours) _userColoursList.get(index);
-    }
-
-    /**
-     * Method getUserColours.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.UserColours[] getUserColours(
-    ) {
-        jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
-        return (jalview.binding.UserColours[]) this._userColoursList.toArray(array);
-    }
-
-    /**
-     * Method getUserColoursCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getUserColoursCount(
-    ) {
-        return this._userColoursList.size();
-    }
-
-    /**
-     * Method getViewport.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Viewport at the
-     * given index
-     */
-    public jalview.binding.Viewport getViewport(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._viewportList.size()) {
-            throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Viewport) _viewportList.get(index);
-    }
-
-    /**
-     * Method getViewport.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Viewport[] getViewport(
-    ) {
-        jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
-        return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
-    }
-
-    /**
-     * Method getViewportCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getViewportCount(
-    ) {
-        return this._viewportList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllJGroup(
-    ) {
-        this._JGroupList.clear();
-    }
-
-    /**
-     */
-    public void removeAllJSeq(
-    ) {
-        this._JSeqList.clear();
-    }
-
-    /**
-     */
-    public void removeAllTree(
-    ) {
-        this._treeList.clear();
-    }
-
-    /**
-     */
-    public void removeAllUserColours(
-    ) {
-        this._userColoursList.clear();
-    }
-
-    /**
-     */
-    public void removeAllViewport(
-    ) {
-        this._viewportList.clear();
-    }
-
-    /**
-     * Method removeJGroup.
-     * 
-     * @param vJGroup
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeJGroup(
-            final jalview.binding.JGroup vJGroup) {
-        boolean removed = _JGroupList.remove(vJGroup);
-        return removed;
-    }
-
-    /**
-     * Method removeJGroupAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.JGroup removeJGroupAt(
-            final int index) {
-        java.lang.Object obj = this._JGroupList.remove(index);
-        return (jalview.binding.JGroup) obj;
-    }
-
-    /**
-     * Method removeJSeq.
-     * 
-     * @param vJSeq
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeJSeq(
-            final jalview.binding.JSeq vJSeq) {
-        boolean removed = _JSeqList.remove(vJSeq);
-        return removed;
-    }
-
-    /**
-     * Method removeJSeqAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.JSeq removeJSeqAt(
-            final int index) {
-        java.lang.Object obj = this._JSeqList.remove(index);
-        return (jalview.binding.JSeq) obj;
-    }
-
-    /**
-     * Method removeTree.
-     * 
-     * @param vTree
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeTree(
-            final jalview.binding.Tree vTree) {
-        boolean removed = _treeList.remove(vTree);
-        return removed;
-    }
-
-    /**
-     * Method removeTreeAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Tree removeTreeAt(
-            final int index) {
-        java.lang.Object obj = this._treeList.remove(index);
-        return (jalview.binding.Tree) obj;
-    }
-
-    /**
-     * Method removeUserColours.
-     * 
-     * @param vUserColours
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeUserColours(
-            final jalview.binding.UserColours vUserColours) {
-        boolean removed = _userColoursList.remove(vUserColours);
-        return removed;
-    }
-
-    /**
-     * Method removeUserColoursAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.UserColours removeUserColoursAt(
-            final int index) {
-        java.lang.Object obj = this._userColoursList.remove(index);
-        return (jalview.binding.UserColours) obj;
-    }
-
-    /**
-     * Method removeViewport.
-     * 
-     * @param vViewport
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeViewport(
-            final jalview.binding.Viewport vViewport) {
-        boolean removed = _viewportList.remove(vViewport);
-        return removed;
-    }
-
-    /**
-     * Method removeViewportAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Viewport removeViewportAt(
-            final int index) {
-        java.lang.Object obj = this._viewportList.remove(index);
-        return (jalview.binding.Viewport) obj;
-    }
-
-    /**
-     * Sets the value of field 'featureSettings'.
-     * 
-     * @param featureSettings the value of field 'featureSettings'.
-     */
-    public void setFeatureSettings(
-            final jalview.binding.FeatureSettings featureSettings) {
-        this._featureSettings = featureSettings;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setJGroup(
-            final int index,
-            final jalview.binding.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JGroupList.size()) {
-            throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
-        }
-        
-        this._JGroupList.set(index, vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJGroupArray
-     */
-    public void setJGroup(
-            final jalview.binding.JGroup[] vJGroupArray) {
-        //-- copy array
-        _JGroupList.clear();
-        
-        for (int i = 0; i < vJGroupArray.length; i++) {
-                this._JGroupList.add(vJGroupArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setJSeq(
-            final int index,
-            final jalview.binding.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JSeqList.size()) {
-            throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-        }
-        
-        this._JSeqList.set(index, vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJSeqArray
-     */
-    public void setJSeq(
-            final jalview.binding.JSeq[] vJSeqArray) {
-        //-- copy array
-        _JSeqList.clear();
-        
-        for (int i = 0; i < vJSeqArray.length; i++) {
-                this._JSeqList.add(vJSeqArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setTree(
-            final int index,
-            final jalview.binding.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        this._treeList.set(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTreeArray
-     */
-    public void setTree(
-            final jalview.binding.Tree[] vTreeArray) {
-        //-- copy array
-        _treeList.clear();
-        
-        for (int i = 0; i < vTreeArray.length; i++) {
-                this._treeList.add(vTreeArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setUserColours(
-            final int index,
-            final jalview.binding.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._userColoursList.size()) {
-            throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
-        }
-        
-        this._userColoursList.set(index, vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param vUserColoursArray
-     */
-    public void setUserColours(
-            final jalview.binding.UserColours[] vUserColoursArray) {
-        //-- copy array
-        _userColoursList.clear();
-        
-        for (int i = 0; i < vUserColoursArray.length; i++) {
-                this._userColoursList.add(vUserColoursArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setViewport(
-            final int index,
-            final jalview.binding.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._viewportList.size()) {
-            throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
-        }
-        
-        this._viewportList.set(index, vViewport);
-    }
-
-    /**
-     * 
-     * 
-     * @param vViewportArray
-     */
-    public void setViewport(
-            final jalview.binding.Viewport[] vViewportArray) {
-        //-- copy array
-        _viewportList.clear();
-        
-        for (int i = 0; i < vViewportArray.length; i++) {
-                this._viewportList.add(vViewportArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JalviewModelSequence
-     */
-    public static jalview.binding.JalviewModelSequence unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JalviewModelSequence implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _JSeqList.
+   */
+  private java.util.Vector _JSeqList;
+
+  /**
+   * Field _JGroupList.
+   */
+  private java.util.Vector _JGroupList;
+
+  /**
+   * Field _viewportList.
+   */
+  private java.util.Vector _viewportList;
+
+  /**
+   * Field _userColoursList.
+   */
+  private java.util.Vector _userColoursList;
+
+  /**
+   * Field _treeList.
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _featureSettings.
+   */
+  private jalview.binding.FeatureSettings _featureSettings;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModelSequence()
+  {
+    super();
+    this._JSeqList = new java.util.Vector();
+    this._JGroupList = new java.util.Vector();
+    this._viewportList = new java.util.Vector();
+    this._userColoursList = new java.util.Vector();
+    this._treeList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addJGroup(final jalview.binding.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JGroupList.addElement(vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addJGroup(final int index,
+          final jalview.binding.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JGroupList.add(index, vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addJSeq(final jalview.binding.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JSeqList.addElement(vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addJSeq(final int index, final jalview.binding.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JSeqList.add(index, vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final jalview.binding.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.addElement(vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final int index, final jalview.binding.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.add(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addUserColours(final jalview.binding.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._userColoursList.addElement(vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addUserColours(final int index,
+          final jalview.binding.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._userColoursList.add(index, vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addViewport(final jalview.binding.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._viewportList.addElement(vViewport);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addViewport(final int index,
+          final jalview.binding.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._viewportList.add(index, vViewport);
+  }
+
+  /**
+   * Method enumerateJGroup.
+   * 
+   * @return an Enumeration over all jalview.binding.JGroup elements
+   */
+  public java.util.Enumeration enumerateJGroup()
+  {
+    return this._JGroupList.elements();
+  }
+
+  /**
+   * Method enumerateJSeq.
+   * 
+   * @return an Enumeration over all jalview.binding.JSeq elements
+   */
+  public java.util.Enumeration enumerateJSeq()
+  {
+    return this._JSeqList.elements();
+  }
+
+  /**
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all jalview.binding.Tree elements
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return this._treeList.elements();
+  }
+
+  /**
+   * Method enumerateUserColours.
+   * 
+   * @return an Enumeration over all jalview.binding.UserColours elements
+   */
+  public java.util.Enumeration enumerateUserColours()
+  {
+    return this._userColoursList.elements();
+  }
+
+  /**
+   * Method enumerateViewport.
+   * 
+   * @return an Enumeration over all jalview.binding.Viewport elements
+   */
+  public java.util.Enumeration enumerateViewport()
+  {
+    return this._viewportList.elements();
+  }
+
+  /**
+   * Returns the value of field 'featureSettings'.
+   * 
+   * @return the value of field 'FeatureSettings'.
+   */
+  public jalview.binding.FeatureSettings getFeatureSettings()
+  {
+    return this._featureSettings;
+  }
+
+  /**
+   * Method getJGroup.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.JGroup at the given index
+   */
+  public jalview.binding.JGroup getJGroup(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
+    {
+      throw new IndexOutOfBoundsException("getJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.JGroup) _JGroupList.get(index);
+  }
+
+  /**
+   * Method getJGroup.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.JGroup[] getJGroup()
+  {
+    jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
+    return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
+  }
+
+  /**
+   * Method getJGroupCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getJGroupCount()
+  {
+    return this._JGroupList.size();
+  }
+
+  /**
+   * Method getJSeq.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.JSeq at the given index
+   */
+  public jalview.binding.JSeq getJSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
+    {
+      throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.JSeq) _JSeqList.get(index);
+  }
+
+  /**
+   * Method getJSeq.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.JSeq[] getJSeq()
+  {
+    jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
+    return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
+  }
+
+  /**
+   * Method getJSeqCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getJSeqCount()
+  {
+    return this._JSeqList.size();
+  }
+
+  /**
+   * Method getTree.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Tree at the given index
+   */
+  public jalview.binding.Tree getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Tree) _treeList.get(index);
+  }
+
+  /**
+   * Method getTree.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Tree[] getTree()
+  {
+    jalview.binding.Tree[] array = new jalview.binding.Tree[0];
+    return (jalview.binding.Tree[]) this._treeList.toArray(array);
+  }
+
+  /**
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getTreeCount()
+  {
+    return this._treeList.size();
+  }
+
+  /**
+   * Method getUserColours.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.UserColours at the given index
+   */
+  public jalview.binding.UserColours getUserColours(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
+    {
+      throw new IndexOutOfBoundsException("getUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.UserColours) _userColoursList.get(index);
+  }
+
+  /**
+   * Method getUserColours.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.UserColours[] getUserColours()
+  {
+    jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
+    return (jalview.binding.UserColours[]) this._userColoursList
+            .toArray(array);
+  }
+
+  /**
+   * Method getUserColoursCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getUserColoursCount()
+  {
+    return this._userColoursList.size();
+  }
+
+  /**
+   * Method getViewport.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Viewport at the given index
+   */
+  public jalview.binding.Viewport getViewport(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
+    {
+      throw new IndexOutOfBoundsException("getViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Viewport) _viewportList.get(index);
+  }
+
+  /**
+   * Method getViewport.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Viewport[] getViewport()
+  {
+    jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
+    return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
+  }
+
+  /**
+   * Method getViewportCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getViewportCount()
+  {
+    return this._viewportList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllJGroup()
+  {
+    this._JGroupList.clear();
+  }
+
+  /**
+     */
+  public void removeAllJSeq()
+  {
+    this._JSeqList.clear();
+  }
+
+  /**
+     */
+  public void removeAllTree()
+  {
+    this._treeList.clear();
+  }
+
+  /**
+     */
+  public void removeAllUserColours()
+  {
+    this._userColoursList.clear();
+  }
+
+  /**
+     */
+  public void removeAllViewport()
+  {
+    this._viewportList.clear();
+  }
+
+  /**
+   * Method removeJGroup.
+   * 
+   * @param vJGroup
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJGroup(final jalview.binding.JGroup vJGroup)
+  {
+    boolean removed = _JGroupList.remove(vJGroup);
+    return removed;
+  }
+
+  /**
+   * Method removeJGroupAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.JGroup removeJGroupAt(final int index)
+  {
+    java.lang.Object obj = this._JGroupList.remove(index);
+    return (jalview.binding.JGroup) obj;
+  }
+
+  /**
+   * Method removeJSeq.
+   * 
+   * @param vJSeq
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJSeq(final jalview.binding.JSeq vJSeq)
+  {
+    boolean removed = _JSeqList.remove(vJSeq);
+    return removed;
+  }
+
+  /**
+   * Method removeJSeqAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.JSeq removeJSeqAt(final int index)
+  {
+    java.lang.Object obj = this._JSeqList.remove(index);
+    return (jalview.binding.JSeq) obj;
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final jalview.binding.Tree vTree)
+  {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
+
+  /**
+   * Method removeTreeAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Tree removeTreeAt(final int index)
+  {
+    java.lang.Object obj = this._treeList.remove(index);
+    return (jalview.binding.Tree) obj;
+  }
+
+  /**
+   * Method removeUserColours.
+   * 
+   * @param vUserColours
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeUserColours(
+          final jalview.binding.UserColours vUserColours)
+  {
+    boolean removed = _userColoursList.remove(vUserColours);
+    return removed;
+  }
+
+  /**
+   * Method removeUserColoursAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.UserColours removeUserColoursAt(final int index)
+  {
+    java.lang.Object obj = this._userColoursList.remove(index);
+    return (jalview.binding.UserColours) obj;
+  }
+
+  /**
+   * Method removeViewport.
+   * 
+   * @param vViewport
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeViewport(final jalview.binding.Viewport vViewport)
+  {
+    boolean removed = _viewportList.remove(vViewport);
+    return removed;
+  }
+
+  /**
+   * Method removeViewportAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Viewport removeViewportAt(final int index)
+  {
+    java.lang.Object obj = this._viewportList.remove(index);
+    return (jalview.binding.Viewport) obj;
+  }
+
+  /**
+   * Sets the value of field 'featureSettings'.
+   * 
+   * @param featureSettings
+   *          the value of field 'featureSettings'.
+   */
+  public void setFeatureSettings(
+          final jalview.binding.FeatureSettings featureSettings)
+  {
+    this._featureSettings = featureSettings;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setJGroup(final int index,
+          final jalview.binding.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
+    {
+      throw new IndexOutOfBoundsException("setJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
+    }
+
+    this._JGroupList.set(index, vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJGroupArray
+   */
+  public void setJGroup(final jalview.binding.JGroup[] vJGroupArray)
+  {
+    // -- copy array
+    _JGroupList.clear();
+
+    for (int i = 0; i < vJGroupArray.length; i++)
+    {
+      this._JGroupList.add(vJGroupArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setJSeq(final int index, final jalview.binding.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
+    {
+      throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+    }
+
+    this._JSeqList.set(index, vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJSeqArray
+   */
+  public void setJSeq(final jalview.binding.JSeq[] vJSeqArray)
+  {
+    // -- copy array
+    _JSeqList.clear();
+
+    for (int i = 0; i < vJSeqArray.length; i++)
+    {
+      this._JSeqList.add(vJSeqArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setTree(final int index, final jalview.binding.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    this._treeList.set(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTreeArray
+   */
+  public void setTree(final jalview.binding.Tree[] vTreeArray)
+  {
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
+    {
+      this._treeList.add(vTreeArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setUserColours(final int index,
+          final jalview.binding.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
+    {
+      throw new IndexOutOfBoundsException("setUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
+    }
+
+    this._userColoursList.set(index, vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param vUserColoursArray
+   */
+  public void setUserColours(
+          final jalview.binding.UserColours[] vUserColoursArray)
+  {
+    // -- copy array
+    _userColoursList.clear();
+
+    for (int i = 0; i < vUserColoursArray.length; i++)
+    {
+      this._userColoursList.add(vUserColoursArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setViewport(final int index,
+          final jalview.binding.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
+    {
+      throw new IndexOutOfBoundsException("setViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
+    }
+
+    this._viewportList.set(index, vViewport);
+  }
+
+  /**
+   * 
+   * 
+   * @param vViewportArray
+   */
+  public void setViewport(final jalview.binding.Viewport[] vViewportArray)
+  {
+    // -- copy array
+    _viewportList.clear();
+
+    for (int i = 0; i < vViewportArray.length; i++)
+    {
+      this._viewportList.add(vViewportArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.JalviewModelSequence
+   */
+  public static jalview.binding.JalviewModelSequence unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(
+            jalview.binding.JalviewModelSequence.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java
index 9a6465b..02bb12e 100644
--- a/src/jalview/binding/JalviewUserColours.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,312 +19,326 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewUserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _schemeName.
-     */
-    private java.lang.String _schemeName;
-
-    /**
-     * Jalview colour scheme document version.
-     *  
-     */
-    private java.lang.String _version;
-
-    /**
-     * Field _colourList.
-     */
-    private java.util.Vector _colourList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewUserColours() {
-        super();
-        this._colourList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addColour(
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        this._colourList.addElement(vColour);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addColour(
-            final int index,
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        this._colourList.add(index, vColour);
-    }
-
-    /**
-     * Method enumerateColour.
-     * 
-     * @return an Enumeration over all Colour elements
-     */
-    public java.util.Enumeration enumerateColour(
-    ) {
-        return this._colourList.elements();
-    }
-
-    /**
-     * Method getColour.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the Colour at the given index
-     */
-    public Colour getColour(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._colourList.size()) {
-            throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
-        }
-        
-        return (Colour) _colourList.get(index);
-    }
-
-    /**
-     * Method getColour.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public Colour[] getColour(
-    ) {
-        Colour[] array = new Colour[0];
-        return (Colour[]) this._colourList.toArray(array);
-    }
-
-    /**
-     * Method getColourCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getColourCount(
-    ) {
-        return this._colourList.size();
-    }
-
-    /**
-     * Returns the value of field 'schemeName'.
-     * 
-     * @return the value of field 'SchemeName'.
-     */
-    public java.lang.String getSchemeName(
-    ) {
-        return this._schemeName;
-    }
-
-    /**
-     * Returns the value of field 'version'. The field 'version'
-     * has the following description: Jalview colour scheme
-     * document version.
-     *  
-     * 
-     * @return the value of field 'Version'.
-     */
-    public java.lang.String getVersion(
-    ) {
-        return this._version;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllColour(
-    ) {
-        this._colourList.clear();
-    }
-
-    /**
-     * Method removeColour.
-     * 
-     * @param vColour
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeColour(
-            final Colour vColour) {
-        boolean removed = _colourList.remove(vColour);
-        return removed;
+public class JalviewUserColours implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _schemeName.
+   */
+  private java.lang.String _schemeName;
+
+  /**
+   * Jalview colour scheme document version.
+   * 
+   */
+  private java.lang.String _version;
+
+  /**
+   * Field _colourList.
+   */
+  private java.util.Vector _colourList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewUserColours()
+  {
+    super();
+    this._colourList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addColour(final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._colourList.addElement(vColour);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._colourList.add(index, vColour);
+  }
+
+  /**
+   * Method enumerateColour.
+   * 
+   * @return an Enumeration over all Colour elements
+   */
+  public java.util.Enumeration enumerateColour()
+  {
+    return this._colourList.elements();
+  }
+
+  /**
+   * Method getColour.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the Colour at the given index
+   */
+  public Colour getColour(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
+    {
+      throw new IndexOutOfBoundsException("getColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeColourAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public Colour removeColourAt(
-            final int index) {
-        java.lang.Object obj = this._colourList.remove(index);
-        return (Colour) obj;
+    return (Colour) _colourList.get(index);
+  }
+
+  /**
+   * Method getColour.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public Colour[] getColour()
+  {
+    Colour[] array = new Colour[0];
+    return (Colour[]) this._colourList.toArray(array);
+  }
+
+  /**
+   * Method getColourCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getColourCount()
+  {
+    return this._colourList.size();
+  }
+
+  /**
+   * Returns the value of field 'schemeName'.
+   * 
+   * @return the value of field 'SchemeName'.
+   */
+  public java.lang.String getSchemeName()
+  {
+    return this._schemeName;
+  }
+
+  /**
+   * Returns the value of field 'version'. The field 'version' has the following
+   * description: Jalview colour scheme document version.
+   * 
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
      */
-    public void setColour(
-            final int index,
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._colourList.size()) {
-            throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
-        }
-        
-        this._colourList.set(index, vColour);
+  public void removeAllColour()
+  {
+    this._colourList.clear();
+  }
+
+  /**
+   * Method removeColour.
+   * 
+   * @param vColour
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeColour(final Colour vColour)
+  {
+    boolean removed = _colourList.remove(vColour);
+    return removed;
+  }
+
+  /**
+   * Method removeColourAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public Colour removeColourAt(final int index)
+  {
+    java.lang.Object obj = this._colourList.remove(index);
+    return (Colour) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
+    {
+      throw new IndexOutOfBoundsException("setColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param vColourArray
-     */
-    public void setColour(
-            final Colour[] vColourArray) {
-        //-- copy array
-        _colourList.clear();
-        
-        for (int i = 0; i < vColourArray.length; i++) {
-                this._colourList.add(vColourArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'schemeName'.
-     * 
-     * @param schemeName the value of field 'schemeName'.
-     */
-    public void setSchemeName(
-            final java.lang.String schemeName) {
-        this._schemeName = schemeName;
-    }
-
-    /**
-     * Sets the value of field 'version'. The field 'version' has
-     * the following description: Jalview colour scheme document
-     * version.
-     *  
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(
-            final java.lang.String version) {
-        this._version = version;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JalviewUserColours
-     */
-    public static jalview.binding.JalviewUserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._colourList.set(index, vColour);
+  }
+
+  /**
+   * 
+   * 
+   * @param vColourArray
+   */
+  public void setColour(final Colour[] vColourArray)
+  {
+    // -- copy array
+    _colourList.clear();
+
+    for (int i = 0; i < vColourArray.length; i++)
+    {
+      this._colourList.add(vColourArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'schemeName'.
+   * 
+   * @param schemeName
+   *          the value of field 'schemeName'.
+   */
+  public void setSchemeName(final java.lang.String schemeName)
+  {
+    this._schemeName = schemeName;
+  }
+
+  /**
+   * Sets the value of field 'version'. The field 'version' has the following
+   * description: Jalview colour scheme document version.
+   * 
+   * 
+   * @param version
+   *          the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.JalviewUserColours
+   */
+  public static jalview.binding.JalviewUserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
+            jalview.binding.JalviewUserColours.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java
index cac4cf6..6c0e745 100644
--- a/src/jalview/binding/Pdbentry.java
+++ b/src/jalview/binding/Pdbentry.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,308 +19,326 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbentry implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _items.
-     */
-    private java.util.Vector _items;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Pdbentry() {
-        super();
-        this._items = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final jalview.binding.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.addElement(vPdbentryItem);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final int index,
-            final jalview.binding.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.add(index, vPdbentryItem);
-    }
-
-    /**
-     * Method enumeratePdbentryItem.
-     * 
-     * @return an Enumeration over all jalview.binding.PdbentryItem
-     * elements
-     */
-    public java.util.Enumeration enumeratePdbentryItem(
-    ) {
-        return this._items.elements();
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Method getPdbentryItem.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.PdbentryItem at the
-     * given index
-     */
-    public jalview.binding.PdbentryItem getPdbentryItem(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.PdbentryItem) _items.get(index);
-    }
-
-    /**
-     * Method getPdbentryItem.Returns the contents of the
-     * collection in an Array.  
Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we know that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.PdbentryItem[] getPdbentryItem(
-    ) {
-        jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
-        return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
-    }
-
-    /**
-     * Method getPdbentryItemCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPdbentryItemCount(
-    ) {
-        return this._items.size();
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllPdbentryItem(
-    ) {
-        this._items.clear();
-    }
-
-    /**
-     * Method removePdbentryItem.
-     * 
-     * @param vPdbentryItem
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePdbentryItem(
-            final jalview.binding.PdbentryItem vPdbentryItem) {
-        boolean removed = _items.remove(vPdbentryItem);
-        return removed;
+public class Pdbentry implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _items.
+   */
+  private java.util.Vector _items;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Pdbentry()
+  {
+    super();
+    this._items = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(
+          final jalview.binding.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.addElement(vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(final int index,
+          final jalview.binding.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.add(index, vPdbentryItem);
+  }
+
+  /**
+   * Method enumeratePdbentryItem.
+   * 
+   * @return an Enumeration over all jalview.binding.PdbentryItem elements
+   */
+  public java.util.Enumeration enumeratePdbentryItem()
+  {
+    return this._items.elements();
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbentryItem.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.PdbentryItem at the given index
+   */
+  public jalview.binding.PdbentryItem getPdbentryItem(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    /**
-     * Method removePdbentryItemAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.PdbentryItem removePdbentryItemAt(
-            final int index) {
-        java.lang.Object obj = this._items.remove(index);
-        return (jalview.binding.PdbentryItem) obj;
+    return (jalview.binding.PdbentryItem) _items.get(index);
+  }
+
+  /**
+   * Method getPdbentryItem.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.PdbentryItem[] getPdbentryItem()
+  {
+    jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
+    return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
+  }
+
+  /**
+   * Method getPdbentryItemCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbentryItemCount()
+  {
+    return this._items.size();
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
      */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
+  public void removeAllPdbentryItem()
+  {
+    this._items.clear();
+  }
+
+  /**
+   * Method removePdbentryItem.
+   * 
+   * @param vPdbentryItem
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbentryItem(
+          final jalview.binding.PdbentryItem vPdbentryItem)
+  {
+    boolean removed = _items.remove(vPdbentryItem);
+    return removed;
+  }
+
+  /**
+   * Method removePdbentryItemAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.PdbentryItem removePdbentryItemAt(final int index)
+  {
+    java.lang.Object obj = this._items.remove(index);
+    return (jalview.binding.PdbentryItem) obj;
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setPdbentryItem(final int index,
+          final jalview.binding.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setPdbentryItem(
-            final int index,
-            final jalview.binding.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        this._items.set(index, vPdbentryItem);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbentryItemArray
-     */
-    public void setPdbentryItem(
-            final jalview.binding.PdbentryItem[] vPdbentryItemArray) {
-        //-- copy array
-        _items.clear();
-        
-        for (int i = 0; i < vPdbentryItemArray.length; i++) {
-                this._items.add(vPdbentryItemArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Pdbentry
-     */
-    public static jalview.binding.Pdbentry unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._items.set(index, vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItemArray
+   */
+  public void setPdbentryItem(
+          final jalview.binding.PdbentryItem[] vPdbentryItemArray)
+  {
+    // -- copy array
+    _items.clear();
+
+    for (int i = 0; i < vPdbentryItemArray.length; i++)
+    {
+      this._items.add(vPdbentryItemArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *          the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Pdbentry
+   */
+  public static jalview.binding.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
+            jalview.binding.Pdbentry.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java
index 83bc40a..93c46e0 100644
--- a/src/jalview/binding/PdbentryItem.java
+++ b/src/jalview/binding/PdbentryItem.java
@@ -12,181 +12,185 @@ package jalview.binding;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbentryItem implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _propertyList.
-     */
-    private java.util.Vector _propertyList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryItem() {
-        super();
-        this._propertyList = new java.util.Vector();
+public class PdbentryItem implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _propertyList.
+   */
+  private java.util.Vector _propertyList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PdbentryItem()
+  {
+    super();
+    this._propertyList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addProperty(final jalview.binding.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.addElement(vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addProperty(final int index,
+          final jalview.binding.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.add(index, vProperty);
+  }
+
+  /**
+   * Method enumerateProperty.
+   * 
+   * @return an Enumeration over all jalview.binding.Property elements
+   */
+  public java.util.Enumeration enumerateProperty()
+  {
+    return this._propertyList.elements();
+  }
+
+  /**
+   * Method getProperty.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Property at the given index
+   */
+  public jalview.binding.Property getProperty(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("getProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
     }
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
+    return (jalview.binding.Property) _propertyList.get(index);
+  }
+
+  /**
+   * Method getProperty.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Property[] getProperty()
+  {
+    jalview.binding.Property[] array = new jalview.binding.Property[0];
+    return (jalview.binding.Property[]) this._propertyList.toArray(array);
+  }
+
+  /**
+   * Method getPropertyCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPropertyCount()
+  {
+    return this._propertyList.size();
+  }
+
+  /**
      */
-    public void addProperty(
-            final jalview.binding.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.addElement(vProperty);
+  public void removeAllProperty()
+  {
+    this._propertyList.clear();
+  }
+
+  /**
+   * Method removeProperty.
+   * 
+   * @param vProperty
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeProperty(final jalview.binding.Property vProperty)
+  {
+    boolean removed = _propertyList.remove(vProperty);
+    return removed;
+  }
+
+  /**
+   * Method removePropertyAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Property removePropertyAt(final int index)
+  {
+    java.lang.Object obj = this._propertyList.remove(index);
+    return (jalview.binding.Property) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setProperty(final int index,
+          final jalview.binding.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("setProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addProperty(
-            final int index,
-            final jalview.binding.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.add(index, vProperty);
-    }
-
-    /**
-     * Method enumerateProperty.
-     * 
-     * @return an Enumeration over all jalview.binding.Property
-     * elements
-     */
-    public java.util.Enumeration enumerateProperty(
-    ) {
-        return this._propertyList.elements();
-    }
-
-    /**
-     * Method getProperty.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Property at the
-     * given index
-     */
-    public jalview.binding.Property getProperty(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Property) _propertyList.get(index);
-    }
-
-    /**
-     * Method getProperty.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Property[] getProperty(
-    ) {
-        jalview.binding.Property[] array = new jalview.binding.Property[0];
-        return (jalview.binding.Property[]) this._propertyList.toArray(array);
-    }
-
-    /**
-     * Method getPropertyCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPropertyCount(
-    ) {
-        return this._propertyList.size();
-    }
-
-    /**
-     */
-    public void removeAllProperty(
-    ) {
-        this._propertyList.clear();
-    }
-
-    /**
-     * Method removeProperty.
-     * 
-     * @param vProperty
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeProperty(
-            final jalview.binding.Property vProperty) {
-        boolean removed = _propertyList.remove(vProperty);
-        return removed;
-    }
-
-    /**
-     * Method removePropertyAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Property removePropertyAt(
-            final int index) {
-        java.lang.Object obj = this._propertyList.remove(index);
-        return (jalview.binding.Property) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setProperty(
-            final int index,
-            final jalview.binding.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        this._propertyList.set(index, vProperty);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPropertyArray
-     */
-    public void setProperty(
-            final jalview.binding.Property[] vPropertyArray) {
-        //-- copy array
-        _propertyList.clear();
-        
-        for (int i = 0; i < vPropertyArray.length; i++) {
-                this._propertyList.add(vPropertyArray[i]);
-        }
+    this._propertyList.set(index, vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPropertyArray
+   */
+  public void setProperty(final jalview.binding.Property[] vPropertyArray)
+  {
+    // -- copy array
+    _propertyList.clear();
+
+    for (int i = 0; i < vPropertyArray.length; i++)
+    {
+      this._propertyList.add(vPropertyArray[i]);
     }
+  }
 
 }
diff --git a/src/jalview/binding/Pdbids.java b/src/jalview/binding/Pdbids.java
index b4745a2..d821a6a 100644
--- a/src/jalview/binding/Pdbids.java
+++ b/src/jalview/binding/Pdbids.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,98 +19,106 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbids extends Pdbentry 
-implements java.io.Serializable
+public class Pdbids extends Pdbentry implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Pdbids() {
-        super();
-    }
-
+  public Pdbids()
+  {
+    super();
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Pdbentry
-     */
-    public static jalview.binding.Pdbentry unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbids.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Pdbentry
+   */
+  public static jalview.binding.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
+            jalview.binding.Pdbids.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Property.java b/src/jalview/binding/Property.java
index f1114f7..df3decf 100644
--- a/src/jalview/binding/Property.java
+++ b/src/jalview/binding/Property.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,151 +19,162 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Property implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _value.
-     */
-    private java.lang.String _value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Property() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public java.lang.String getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final java.lang.String value) {
-        this._value = value;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Property
-     */
-    public static jalview.binding.Property unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Property implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Property()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *          the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Property
+   */
+  public static jalview.binding.Property unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Property) Unmarshaller.unmarshal(
+            jalview.binding.Property.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java
index 9c8cbc2..5ab8a37 100644
--- a/src/jalview/binding/Sequence.java
+++ b/src/jalview/binding/Sequence.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,98 +19,106 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Sequence extends SequenceType 
-implements java.io.Serializable
+public class Sequence extends SequenceType implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Sequence() {
-        super();
-    }
-
+  public Sequence()
+  {
+    super();
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.SequenceType
-     */
-    public static jalview.binding.SequenceType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.SequenceType
+   */
+  public static jalview.binding.SequenceType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
+            jalview.binding.Sequence.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
index 13a9020..c12934d 100644
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,496 +19,520 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _gapChar.
-     */
-    private java.lang.String _gapChar;
-
-    /**
-     * Field _aligned.
-     */
-    private boolean _aligned;
-
-    /**
-     * keeps track of state for field: _aligned
-     */
-    private boolean _has_aligned;
-
-    /**
-     * Field _sequenceList.
-     */
-    private java.util.Vector _sequenceList;
-
-    /**
-     * Field _annotationList.
-     */
-    private java.util.Vector _annotationList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSet() {
-        super();
-        this._sequenceList = new java.util.Vector();
-        this._annotationList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotation(
-            final jalview.binding.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationList.addElement(vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotation(
-            final int index,
-            final jalview.binding.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationList.add(index, vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequence(
-            final jalview.binding.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceList.addElement(vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequence(
-            final int index,
-            final jalview.binding.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceList.add(index, vSequence);
-    }
-
-    /**
-     */
-    public void deleteAligned(
-    ) {
-        this._has_aligned= false;
-    }
-
-    /**
-     * Method enumerateAnnotation.
-     * 
-     * @return an Enumeration over all jalview.binding.Annotation
-     * elements
-     */
-    public java.util.Enumeration enumerateAnnotation(
-    ) {
-        return this._annotationList.elements();
-    }
-
-    /**
-     * Method enumerateSequence.
-     * 
-     * @return an Enumeration over all jalview.binding.Sequence
-     * elements
-     */
-    public java.util.Enumeration enumerateSequence(
-    ) {
-        return this._sequenceList.elements();
-    }
-
-    /**
-     * Returns the value of field 'aligned'.
-     * 
-     * @return the value of field 'Aligned'.
-     */
-    public boolean getAligned(
-    ) {
-        return this._aligned;
-    }
-
-    /**
-     * Method getAnnotation.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Annotation at the
-     * given index
-     */
-    public jalview.binding.Annotation getAnnotation(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationList.size()) {
-            throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Annotation) _annotationList.get(index);
-    }
-
-    /**
-     * Method getAnnotation.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Annotation[] getAnnotation(
-    ) {
-        jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
-        return (jalview.binding.Annotation[]) this._annotationList.toArray(array);
-    }
-
-    /**
-     * Method getAnnotationCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAnnotationCount(
-    ) {
-        return this._annotationList.size();
-    }
-
-    /**
-     * Returns the value of field 'gapChar'.
-     * 
-     * @return the value of field 'GapChar'.
-     */
-    public java.lang.String getGapChar(
-    ) {
-        return this._gapChar;
-    }
-
-    /**
-     * Method getSequence.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Sequence at the
-     * given index
-     */
-    public jalview.binding.Sequence getSequence(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceList.size()) {
-            throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Sequence) _sequenceList.get(index);
-    }
-
-    /**
-     * Method getSequence.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Sequence[] getSequence(
-    ) {
-        jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
-        return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
-    }
-
-    /**
-     * Method getSequenceCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceCount(
-    ) {
-        return this._sequenceList.size();
-    }
-
-    /**
-     * Method hasAligned.
-     * 
-     * @return true if at least one Aligned has been added
-     */
-    public boolean hasAligned(
-    ) {
-        return this._has_aligned;
-    }
-
-    /**
-     * Returns the value of field 'aligned'.
-     * 
-     * @return the value of field 'Aligned'.
-     */
-    public boolean isAligned(
-    ) {
-        return this._aligned;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllAnnotation(
-    ) {
-        this._annotationList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSequence(
-    ) {
-        this._sequenceList.clear();
-    }
-
-    /**
-     * Method removeAnnotation.
-     * 
-     * @param vAnnotation
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAnnotation(
-            final jalview.binding.Annotation vAnnotation) {
-        boolean removed = _annotationList.remove(vAnnotation);
-        return removed;
-    }
-
-    /**
-     * Method removeAnnotationAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Annotation removeAnnotationAt(
-            final int index) {
-        java.lang.Object obj = this._annotationList.remove(index);
-        return (jalview.binding.Annotation) obj;
-    }
-
-    /**
-     * Method removeSequence.
-     * 
-     * @param vSequence
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequence(
-            final jalview.binding.Sequence vSequence) {
-        boolean removed = _sequenceList.remove(vSequence);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Sequence removeSequenceAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceList.remove(index);
-        return (jalview.binding.Sequence) obj;
-    }
-
-    /**
-     * Sets the value of field 'aligned'.
-     * 
-     * @param aligned the value of field 'aligned'.
-     */
-    public void setAligned(
-            final boolean aligned) {
-        this._aligned = aligned;
-        this._has_aligned = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAnnotation(
-            final int index,
-            final jalview.binding.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationList.size()) {
-            throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
-        }
-        
-        this._annotationList.set(index, vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotationArray
-     */
-    public void setAnnotation(
-            final jalview.binding.Annotation[] vAnnotationArray) {
-        //-- copy array
-        _annotationList.clear();
-        
-        for (int i = 0; i < vAnnotationArray.length; i++) {
-                this._annotationList.add(vAnnotationArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'gapChar'.
-     * 
-     * @param gapChar the value of field 'gapChar'.
-     */
-    public void setGapChar(
-            final java.lang.String gapChar) {
-        this._gapChar = gapChar;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequence(
-            final int index,
-            final jalview.binding.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceList.size()) {
-            throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
-        }
-        
-        this._sequenceList.set(index, vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceArray
-     */
-    public void setSequence(
-            final jalview.binding.Sequence[] vSequenceArray) {
-        //-- copy array
-        _sequenceList.clear();
-        
-        for (int i = 0; i < vSequenceArray.length; i++) {
-                this._sequenceList.add(vSequenceArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.SequenceSet
-     */
-    public static jalview.binding.SequenceSet unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class SequenceSet implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _gapChar.
+   */
+  private java.lang.String _gapChar;
+
+  /**
+   * Field _aligned.
+   */
+  private boolean _aligned;
+
+  /**
+   * keeps track of state for field: _aligned
+   */
+  private boolean _has_aligned;
+
+  /**
+   * Field _sequenceList.
+   */
+  private java.util.Vector _sequenceList;
+
+  /**
+   * Field _annotationList.
+   */
+  private java.util.Vector _annotationList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSet()
+  {
+    super();
+    this._sequenceList = new java.util.Vector();
+    this._annotationList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAnnotation(final jalview.binding.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationList.addElement(vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAnnotation(final int index,
+          final jalview.binding.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationList.add(index, vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequence(final jalview.binding.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceList.addElement(vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequence(final int index,
+          final jalview.binding.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceList.add(index, vSequence);
+  }
+
+  /**
+     */
+  public void deleteAligned()
+  {
+    this._has_aligned = false;
+  }
+
+  /**
+   * Method enumerateAnnotation.
+   * 
+   * @return an Enumeration over all jalview.binding.Annotation elements
+   */
+  public java.util.Enumeration enumerateAnnotation()
+  {
+    return this._annotationList.elements();
+  }
+
+  /**
+   * Method enumerateSequence.
+   * 
+   * @return an Enumeration over all jalview.binding.Sequence elements
+   */
+  public java.util.Enumeration enumerateSequence()
+  {
+    return this._sequenceList.elements();
+  }
+
+  /**
+   * Returns the value of field 'aligned'.
+   * 
+   * @return the value of field 'Aligned'.
+   */
+  public boolean getAligned()
+  {
+    return this._aligned;
+  }
+
+  /**
+   * Method getAnnotation.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Annotation at the given index
+   */
+  public jalview.binding.Annotation getAnnotation(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationList.size())
+    {
+      throw new IndexOutOfBoundsException("getAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Annotation) _annotationList.get(index);
+  }
+
+  /**
+   * Method getAnnotation.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Annotation[] getAnnotation()
+  {
+    jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
+    return (jalview.binding.Annotation[]) this._annotationList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAnnotationCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAnnotationCount()
+  {
+    return this._annotationList.size();
+  }
+
+  /**
+   * Returns the value of field 'gapChar'.
+   * 
+   * @return the value of field 'GapChar'.
+   */
+  public java.lang.String getGapChar()
+  {
+    return this._gapChar;
+  }
+
+  /**
+   * Method getSequence.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Sequence at the given index
+   */
+  public jalview.binding.Sequence getSequence(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceList.size())
+    {
+      throw new IndexOutOfBoundsException("getSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.Sequence) _sequenceList.get(index);
+  }
+
+  /**
+   * Method getSequence.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Sequence[] getSequence()
+  {
+    jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
+    return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
+  }
+
+  /**
+   * Method getSequenceCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceCount()
+  {
+    return this._sequenceList.size();
+  }
+
+  /**
+   * Method hasAligned.
+   * 
+   * @return true if at least one Aligned has been added
+   */
+  public boolean hasAligned()
+  {
+    return this._has_aligned;
+  }
+
+  /**
+   * Returns the value of field 'aligned'.
+   * 
+   * @return the value of field 'Aligned'.
+   */
+  public boolean isAligned()
+  {
+    return this._aligned;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllAnnotation()
+  {
+    this._annotationList.clear();
+  }
+
+  /**
+     */
+  public void removeAllSequence()
+  {
+    this._sequenceList.clear();
+  }
+
+  /**
+   * Method removeAnnotation.
+   * 
+   * @param vAnnotation
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAnnotation(
+          final jalview.binding.Annotation vAnnotation)
+  {
+    boolean removed = _annotationList.remove(vAnnotation);
+    return removed;
+  }
+
+  /**
+   * Method removeAnnotationAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Annotation removeAnnotationAt(final int index)
+  {
+    java.lang.Object obj = this._annotationList.remove(index);
+    return (jalview.binding.Annotation) obj;
+  }
+
+  /**
+   * Method removeSequence.
+   * 
+   * @param vSequence
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequence(final jalview.binding.Sequence vSequence)
+  {
+    boolean removed = _sequenceList.remove(vSequence);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Sequence removeSequenceAt(final int index)
+  {
+    java.lang.Object obj = this._sequenceList.remove(index);
+    return (jalview.binding.Sequence) obj;
+  }
+
+  /**
+   * Sets the value of field 'aligned'.
+   * 
+   * @param aligned
+   *          the value of field 'aligned'.
+   */
+  public void setAligned(final boolean aligned)
+  {
+    this._aligned = aligned;
+    this._has_aligned = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAnnotation(final int index,
+          final jalview.binding.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationList.size())
+    {
+      throw new IndexOutOfBoundsException("setAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
+    }
+
+    this._annotationList.set(index, vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotationArray
+   */
+  public void setAnnotation(
+          final jalview.binding.Annotation[] vAnnotationArray)
+  {
+    // -- copy array
+    _annotationList.clear();
+
+    for (int i = 0; i < vAnnotationArray.length; i++)
+    {
+      this._annotationList.add(vAnnotationArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'gapChar'.
+   * 
+   * @param gapChar
+   *          the value of field 'gapChar'.
+   */
+  public void setGapChar(final java.lang.String gapChar)
+  {
+    this._gapChar = gapChar;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSequence(final int index,
+          final jalview.binding.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceList.size())
+    {
+      throw new IndexOutOfBoundsException("setSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
+    }
+
+    this._sequenceList.set(index, vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceArray
+   */
+  public void setSequence(final jalview.binding.Sequence[] vSequenceArray)
+  {
+    // -- copy array
+    _sequenceList.clear();
+
+    for (int i = 0; i < vSequenceArray.length; i++)
+    {
+      this._sequenceList.add(vSequenceArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.SequenceSet
+   */
+  public static jalview.binding.SequenceSet unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(
+            jalview.binding.SequenceSet.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java
index 1bb2a62..d725405 100644
--- a/src/jalview/binding/SequenceType.java
+++ b/src/jalview/binding/SequenceType.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,176 +19,188 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceType implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _sequence.
-     */
-    private java.lang.String _sequence;
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceType() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'sequence'.
-     * 
-     * @return the value of field 'Sequence'.
-     */
-    public java.lang.String getSequence(
-    ) {
-        return this._sequence;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'sequence'.
-     * 
-     * @param sequence the value of field 'sequence'.
-     */
-    public void setSequence(
-            final java.lang.String sequence) {
-        this._sequence = sequence;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.SequenceType
-     */
-    public static jalview.binding.SequenceType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class SequenceType implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _sequence.
+   */
+  private java.lang.String _sequence;
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceType()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'sequence'.
+   * 
+   * @return the value of field 'Sequence'.
+   */
+  public java.lang.String getSequence()
+  {
+    return this._sequence;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'sequence'.
+   * 
+   * @param sequence
+   *          the value of field 'sequence'.
+   */
+  public void setSequence(final java.lang.String sequence)
+  {
+    this._sequence = sequence;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.SequenceType
+   */
+  public static jalview.binding.SequenceType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
+            jalview.binding.SequenceType.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java
index 9cd84b4..6641429 100644
--- a/src/jalview/binding/Setting.java
+++ b/src/jalview/binding/Setting.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,232 +19,244 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Setting implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _display.
-     */
-    private boolean _display;
-
-    /**
-     * keeps track of state for field: _display
-     */
-    private boolean _has_display;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Setting() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteDisplay(
-    ) {
-        this._has_display= false;
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean getDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
+public class Setting implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _display.
+   */
+  private boolean _display;
+
+  /**
+   * keeps track of state for field: _display
+   */
+  private boolean _has_display;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Setting()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
      */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasDisplay.
-     * 
-     * @return true if at least one Display has been added
-     */
-    public boolean hasDisplay(
-    ) {
-        return this._has_display;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean isDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'display'.
-     * 
-     * @param display the value of field 'display'.
-     */
-    public void setDisplay(
-            final boolean display) {
-        this._display = display;
-        this._has_display = true;
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Setting
-     */
-    public static jalview.binding.Setting unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader);
-    }
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+  /**
      */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+  public void deleteDisplay()
+  {
+    this._has_display = false;
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean getDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasDisplay.
+   * 
+   * @return true if at least one Display has been added
+   */
+  public boolean hasDisplay()
+  {
+    return this._has_display;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean isDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *          the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'display'.
+   * 
+   * @param display
+   *          the value of field 'display'.
+   */
+  public void setDisplay(final boolean display)
+  {
+    this._display = display;
+    this._has_display = true;
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *          the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Setting
+   */
+  public static jalview.binding.Setting unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Setting) Unmarshaller.unmarshal(
+            jalview.binding.Setting.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java
index 5f138d0..04ea0a4 100644
--- a/src/jalview/binding/Tree.java
+++ b/src/jalview/binding/Tree.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,802 +19,825 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Tree implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _width.
-     */
-    private int _width;
-
-    /**
-     * keeps track of state for field: _width
-     */
-    private boolean _has_width;
-
-    /**
-     * Field _height.
-     */
-    private int _height;
-
-    /**
-     * keeps track of state for field: _height
-     */
-    private boolean _has_height;
-
-    /**
-     * Field _xpos.
-     */
-    private int _xpos;
-
-    /**
-     * keeps track of state for field: _xpos
-     */
-    private boolean _has_xpos;
-
-    /**
-     * Field _ypos.
-     */
-    private int _ypos;
-
-    /**
-     * keeps track of state for field: _ypos
-     */
-    private boolean _has_ypos;
-
-    /**
-     * Field _fontName.
-     */
-    private java.lang.String _fontName;
-
-    /**
-     * Field _fontSize.
-     */
-    private int _fontSize;
-
-    /**
-     * keeps track of state for field: _fontSize
-     */
-    private boolean _has_fontSize;
-
-    /**
-     * Field _fontStyle.
-     */
-    private int _fontStyle;
-
-    /**
-     * keeps track of state for field: _fontStyle
-     */
-    private boolean _has_fontStyle;
-
-    /**
-     * Field _threshold.
-     */
-    private float _threshold;
-
-    /**
-     * keeps track of state for field: _threshold
-     */
-    private boolean _has_threshold;
-
-    /**
-     * Field _showBootstrap.
-     */
-    private boolean _showBootstrap;
-
-    /**
-     * keeps track of state for field: _showBootstrap
-     */
-    private boolean _has_showBootstrap;
-
-    /**
-     * Field _showDistances.
-     */
-    private boolean _showDistances;
-
-    /**
-     * keeps track of state for field: _showDistances
-     */
-    private boolean _has_showDistances;
-
-    /**
-     * Field _markUnlinked.
-     */
-    private boolean _markUnlinked;
-
-    /**
-     * keeps track of state for field: _markUnlinked
-     */
-    private boolean _has_markUnlinked;
-
-    /**
-     * Field _fitToWindow.
-     */
-    private boolean _fitToWindow;
-
-    /**
-     * keeps track of state for field: _fitToWindow
-     */
-    private boolean _has_fitToWindow;
-
-    /**
-     * Field _currentTree.
-     */
-    private boolean _currentTree;
-
-    /**
-     * keeps track of state for field: _currentTree
-     */
-    private boolean _has_currentTree;
-
-    /**
-     * Field _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * Field _newick.
-     */
-    private java.lang.String _newick;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Tree() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteCurrentTree(
-    ) {
-        this._has_currentTree= false;
-    }
-
-    /**
-     */
-    public void deleteFitToWindow(
-    ) {
-        this._has_fitToWindow= false;
-    }
-
-    /**
-     */
-    public void deleteFontSize(
-    ) {
-        this._has_fontSize= false;
-    }
-
-    /**
-     */
-    public void deleteFontStyle(
-    ) {
-        this._has_fontStyle= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deleteMarkUnlinked(
-    ) {
-        this._has_markUnlinked= false;
-    }
-
-    /**
-     */
-    public void deleteShowBootstrap(
-    ) {
-        this._has_showBootstrap= false;
-    }
-
-    /**
-     */
-    public void deleteShowDistances(
-    ) {
-        this._has_showDistances= false;
-    }
-
-    /**
-     */
-    public void deleteThreshold(
-    ) {
-        this._has_threshold= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Returns the value of field 'currentTree'.
-     * 
-     * @return the value of field 'CurrentTree'.
-     */
-    public boolean getCurrentTree(
-    ) {
-        return this._currentTree;
-    }
-
-    /**
-     * Returns the value of field 'fitToWindow'.
-     * 
-     * @return the value of field 'FitToWindow'.
-     */
-    public boolean getFitToWindow(
-    ) {
-        return this._fitToWindow;
-    }
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return the value of field 'FontName'.
-     */
-    public java.lang.String getFontName(
-    ) {
-        return this._fontName;
-    }
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return the value of field 'FontSize'.
-     */
-    public int getFontSize(
-    ) {
-        return this._fontSize;
-    }
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return the value of field 'FontStyle'.
-     */
-    public int getFontStyle(
-    ) {
-        return this._fontStyle;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Returns the value of field 'markUnlinked'.
-     * 
-     * @return the value of field 'MarkUnlinked'.
-     */
-    public boolean getMarkUnlinked(
-    ) {
-        return this._markUnlinked;
-    }
-
-    /**
-     * Returns the value of field 'newick'.
-     * 
-     * @return the value of field 'Newick'.
-     */
-    public java.lang.String getNewick(
-    ) {
-        return this._newick;
-    }
-
-    /**
-     * Returns the value of field 'showBootstrap'.
-     * 
-     * @return the value of field 'ShowBootstrap'.
-     */
-    public boolean getShowBootstrap(
-    ) {
-        return this._showBootstrap;
-    }
-
-    /**
-     * Returns the value of field 'showDistances'.
-     * 
-     * @return the value of field 'ShowDistances'.
-     */
-    public boolean getShowDistances(
-    ) {
-        return this._showDistances;
-    }
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return the value of field 'Threshold'.
-     */
-    public float getThreshold(
-    ) {
-        return this._threshold;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasCurrentTree.
-     * 
-     * @return true if at least one CurrentTree has been added
-     */
-    public boolean hasCurrentTree(
-    ) {
-        return this._has_currentTree;
-    }
-
-    /**
-     * Method hasFitToWindow.
-     * 
-     * @return true if at least one FitToWindow has been added
-     */
-    public boolean hasFitToWindow(
-    ) {
-        return this._has_fitToWindow;
-    }
-
-    /**
-     * Method hasFontSize.
-     * 
-     * @return true if at least one FontSize has been added
-     */
-    public boolean hasFontSize(
-    ) {
-        return this._has_fontSize;
-    }
-
-    /**
-     * Method hasFontStyle.
-     * 
-     * @return true if at least one FontStyle has been added
-     */
-    public boolean hasFontStyle(
-    ) {
-        return this._has_fontStyle;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasMarkUnlinked.
-     * 
-     * @return true if at least one MarkUnlinked has been added
-     */
-    public boolean hasMarkUnlinked(
-    ) {
-        return this._has_markUnlinked;
-    }
-
-    /**
-     * Method hasShowBootstrap.
-     * 
-     * @return true if at least one ShowBootstrap has been added
-     */
-    public boolean hasShowBootstrap(
-    ) {
-        return this._has_showBootstrap;
-    }
-
-    /**
-     * Method hasShowDistances.
-     * 
-     * @return true if at least one ShowDistances has been added
-     */
-    public boolean hasShowDistances(
-    ) {
-        return this._has_showDistances;
-    }
-
-    /**
-     * Method hasThreshold.
-     * 
-     * @return true if at least one Threshold has been added
-     */
-    public boolean hasThreshold(
-    ) {
-        return this._has_threshold;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Returns the value of field 'currentTree'.
-     * 
-     * @return the value of field 'CurrentTree'.
-     */
-    public boolean isCurrentTree(
-    ) {
-        return this._currentTree;
-    }
-
-    /**
-     * Returns the value of field 'fitToWindow'.
-     * 
-     * @return the value of field 'FitToWindow'.
-     */
-    public boolean isFitToWindow(
-    ) {
-        return this._fitToWindow;
-    }
-
-    /**
-     * Returns the value of field 'markUnlinked'.
-     * 
-     * @return the value of field 'MarkUnlinked'.
-     */
-    public boolean isMarkUnlinked(
-    ) {
-        return this._markUnlinked;
-    }
-
-    /**
-     * Returns the value of field 'showBootstrap'.
-     * 
-     * @return the value of field 'ShowBootstrap'.
-     */
-    public boolean isShowBootstrap(
-    ) {
-        return this._showBootstrap;
-    }
-
-    /**
-     * Returns the value of field 'showDistances'.
-     * 
-     * @return the value of field 'ShowDistances'.
-     */
-    public boolean isShowDistances(
-    ) {
-        return this._showDistances;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'currentTree'.
-     * 
-     * @param currentTree the value of field 'currentTree'.
-     */
-    public void setCurrentTree(
-            final boolean currentTree) {
-        this._currentTree = currentTree;
-        this._has_currentTree = true;
-    }
-
-    /**
-     * Sets the value of field 'fitToWindow'.
-     * 
-     * @param fitToWindow the value of field 'fitToWindow'.
-     */
-    public void setFitToWindow(
-            final boolean fitToWindow) {
-        this._fitToWindow = fitToWindow;
-        this._has_fitToWindow = true;
-    }
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(
-            final java.lang.String fontName) {
-        this._fontName = fontName;
-    }
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(
-            final int fontSize) {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    }
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(
-            final int fontStyle) {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * Sets the value of field 'markUnlinked'.
-     * 
-     * @param markUnlinked the value of field 'markUnlinked'.
-     */
-    public void setMarkUnlinked(
-            final boolean markUnlinked) {
-        this._markUnlinked = markUnlinked;
-        this._has_markUnlinked = true;
-    }
-
-    /**
-     * Sets the value of field 'newick'.
-     * 
-     * @param newick the value of field 'newick'.
-     */
-    public void setNewick(
-            final java.lang.String newick) {
-        this._newick = newick;
-    }
-
-    /**
-     * Sets the value of field 'showBootstrap'.
-     * 
-     * @param showBootstrap the value of field 'showBootstrap'.
-     */
-    public void setShowBootstrap(
-            final boolean showBootstrap) {
-        this._showBootstrap = showBootstrap;
-        this._has_showBootstrap = true;
-    }
-
-    /**
-     * Sets the value of field 'showDistances'.
-     * 
-     * @param showDistances the value of field 'showDistances'.
-     */
-    public void setShowDistances(
-            final boolean showDistances) {
-        this._showDistances = showDistances;
-        this._has_showDistances = true;
-    }
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(
-            final float threshold) {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Tree
-     */
-    public static jalview.binding.Tree unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Tree implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _width.
+   */
+  private int _width;
+
+  /**
+   * keeps track of state for field: _width
+   */
+  private boolean _has_width;
+
+  /**
+   * Field _height.
+   */
+  private int _height;
+
+  /**
+   * keeps track of state for field: _height
+   */
+  private boolean _has_height;
+
+  /**
+   * Field _xpos.
+   */
+  private int _xpos;
+
+  /**
+   * keeps track of state for field: _xpos
+   */
+  private boolean _has_xpos;
+
+  /**
+   * Field _ypos.
+   */
+  private int _ypos;
+
+  /**
+   * keeps track of state for field: _ypos
+   */
+  private boolean _has_ypos;
+
+  /**
+   * Field _fontName.
+   */
+  private java.lang.String _fontName;
+
+  /**
+   * Field _fontSize.
+   */
+  private int _fontSize;
+
+  /**
+   * keeps track of state for field: _fontSize
+   */
+  private boolean _has_fontSize;
+
+  /**
+   * Field _fontStyle.
+   */
+  private int _fontStyle;
+
+  /**
+   * keeps track of state for field: _fontStyle
+   */
+  private boolean _has_fontStyle;
+
+  /**
+   * Field _threshold.
+   */
+  private float _threshold;
+
+  /**
+   * keeps track of state for field: _threshold
+   */
+  private boolean _has_threshold;
+
+  /**
+   * Field _showBootstrap.
+   */
+  private boolean _showBootstrap;
+
+  /**
+   * keeps track of state for field: _showBootstrap
+   */
+  private boolean _has_showBootstrap;
+
+  /**
+   * Field _showDistances.
+   */
+  private boolean _showDistances;
+
+  /**
+   * keeps track of state for field: _showDistances
+   */
+  private boolean _has_showDistances;
+
+  /**
+   * Field _markUnlinked.
+   */
+  private boolean _markUnlinked;
+
+  /**
+   * keeps track of state for field: _markUnlinked
+   */
+  private boolean _has_markUnlinked;
+
+  /**
+   * Field _fitToWindow.
+   */
+  private boolean _fitToWindow;
+
+  /**
+   * keeps track of state for field: _fitToWindow
+   */
+  private boolean _has_fitToWindow;
+
+  /**
+   * Field _currentTree.
+   */
+  private boolean _currentTree;
+
+  /**
+   * keeps track of state for field: _currentTree
+   */
+  private boolean _has_currentTree;
+
+  /**
+   * Field _title.
+   */
+  private java.lang.String _title;
+
+  /**
+   * Field _newick.
+   */
+  private java.lang.String _newick;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Tree()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteCurrentTree()
+  {
+    this._has_currentTree = false;
+  }
+
+  /**
+     */
+  public void deleteFitToWindow()
+  {
+    this._has_fitToWindow = false;
+  }
+
+  /**
+     */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  }
+
+  /**
+     */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  }
+
+  /**
+     */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+     */
+  public void deleteMarkUnlinked()
+  {
+    this._has_markUnlinked = false;
+  }
+
+  /**
+     */
+  public void deleteShowBootstrap()
+  {
+    this._has_showBootstrap = false;
+  }
+
+  /**
+     */
+  public void deleteShowDistances()
+  {
+    this._has_showDistances = false;
+  }
+
+  /**
+     */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  }
+
+  /**
+     */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+     */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+     */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Returns the value of field 'currentTree'.
+   * 
+   * @return the value of field 'CurrentTree'.
+   */
+  public boolean getCurrentTree()
+  {
+    return this._currentTree;
+  }
+
+  /**
+   * Returns the value of field 'fitToWindow'.
+   * 
+   * @return the value of field 'FitToWindow'.
+   */
+  public boolean getFitToWindow()
+  {
+    return this._fitToWindow;
+  }
+
+  /**
+   * Returns the value of field 'fontName'.
+   * 
+   * @return the value of field 'FontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  }
+
+  /**
+   * Returns the value of field 'fontSize'.
+   * 
+   * @return the value of field 'FontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  }
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   * 
+   * @return the value of field 'FontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Returns the value of field 'markUnlinked'.
+   * 
+   * @return the value of field 'MarkUnlinked'.
+   */
+  public boolean getMarkUnlinked()
+  {
+    return this._markUnlinked;
+  }
+
+  /**
+   * Returns the value of field 'newick'.
+   * 
+   * @return the value of field 'Newick'.
+   */
+  public java.lang.String getNewick()
+  {
+    return this._newick;
+  }
+
+  /**
+   * Returns the value of field 'showBootstrap'.
+   * 
+   * @return the value of field 'ShowBootstrap'.
+   */
+  public boolean getShowBootstrap()
+  {
+    return this._showBootstrap;
+  }
+
+  /**
+   * Returns the value of field 'showDistances'.
+   * 
+   * @return the value of field 'ShowDistances'.
+   */
+  public boolean getShowDistances()
+  {
+    return this._showDistances;
+  }
+
+  /**
+   * Returns the value of field 'threshold'.
+   * 
+   * @return the value of field 'Threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasCurrentTree.
+   * 
+   * @return true if at least one CurrentTree has been added
+   */
+  public boolean hasCurrentTree()
+  {
+    return this._has_currentTree;
+  }
+
+  /**
+   * Method hasFitToWindow.
+   * 
+   * @return true if at least one FitToWindow has been added
+   */
+  public boolean hasFitToWindow()
+  {
+    return this._has_fitToWindow;
+  }
+
+  /**
+   * Method hasFontSize.
+   * 
+   * @return true if at least one FontSize has been added
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  }
+
+  /**
+   * Method hasFontStyle.
+   * 
+   * @return true if at least one FontStyle has been added
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasMarkUnlinked.
+   * 
+   * @return true if at least one MarkUnlinked has been added
+   */
+  public boolean hasMarkUnlinked()
+  {
+    return this._has_markUnlinked;
+  }
+
+  /**
+   * Method hasShowBootstrap.
+   * 
+   * @return true if at least one ShowBootstrap has been added
+   */
+  public boolean hasShowBootstrap()
+  {
+    return this._has_showBootstrap;
+  }
+
+  /**
+   * Method hasShowDistances.
+   * 
+   * @return true if at least one ShowDistances has been added
+   */
+  public boolean hasShowDistances()
+  {
+    return this._has_showDistances;
+  }
+
+  /**
+   * Method hasThreshold.
+   * 
+   * @return true if at least one Threshold has been added
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'currentTree'.
+   * 
+   * @return the value of field 'CurrentTree'.
+   */
+  public boolean isCurrentTree()
+  {
+    return this._currentTree;
+  }
+
+  /**
+   * Returns the value of field 'fitToWindow'.
+   * 
+   * @return the value of field 'FitToWindow'.
+   */
+  public boolean isFitToWindow()
+  {
+    return this._fitToWindow;
+  }
+
+  /**
+   * Returns the value of field 'markUnlinked'.
+   * 
+   * @return the value of field 'MarkUnlinked'.
+   */
+  public boolean isMarkUnlinked()
+  {
+    return this._markUnlinked;
+  }
+
+  /**
+   * Returns the value of field 'showBootstrap'.
+   * 
+   * @return the value of field 'ShowBootstrap'.
+   */
+  public boolean isShowBootstrap()
+  {
+    return this._showBootstrap;
+  }
+
+  /**
+   * Returns the value of field 'showDistances'.
+   * 
+   * @return the value of field 'ShowDistances'.
+   */
+  public boolean isShowDistances()
+  {
+    return this._showDistances;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'currentTree'.
+   * 
+   * @param currentTree
+   *          the value of field 'currentTree'.
+   */
+  public void setCurrentTree(final boolean currentTree)
+  {
+    this._currentTree = currentTree;
+    this._has_currentTree = true;
+  }
+
+  /**
+   * Sets the value of field 'fitToWindow'.
+   * 
+   * @param fitToWindow
+   *          the value of field 'fitToWindow'.
+   */
+  public void setFitToWindow(final boolean fitToWindow)
+  {
+    this._fitToWindow = fitToWindow;
+    this._has_fitToWindow = true;
+  }
+
+  /**
+   * Sets the value of field 'fontName'.
+   * 
+   * @param fontName
+   *          the value of field 'fontName'.
+   */
+  public void setFontName(final java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  }
+
+  /**
+   * Sets the value of field 'fontSize'.
+   * 
+   * @param fontSize
+   *          the value of field 'fontSize'.
+   */
+  public void setFontSize(final int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  }
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   * 
+   * @param fontStyle
+   *          the value of field 'fontStyle'.
+   */
+  public void setFontStyle(final int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *          the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * Sets the value of field 'markUnlinked'.
+   * 
+   * @param markUnlinked
+   *          the value of field 'markUnlinked'.
+   */
+  public void setMarkUnlinked(final boolean markUnlinked)
+  {
+    this._markUnlinked = markUnlinked;
+    this._has_markUnlinked = true;
+  }
+
+  /**
+   * Sets the value of field 'newick'.
+   * 
+   * @param newick
+   *          the value of field 'newick'.
+   */
+  public void setNewick(final java.lang.String newick)
+  {
+    this._newick = newick;
+  }
+
+  /**
+   * Sets the value of field 'showBootstrap'.
+   * 
+   * @param showBootstrap
+   *          the value of field 'showBootstrap'.
+   */
+  public void setShowBootstrap(final boolean showBootstrap)
+  {
+    this._showBootstrap = showBootstrap;
+    this._has_showBootstrap = true;
+  }
+
+  /**
+   * Sets the value of field 'showDistances'.
+   * 
+   * @param showDistances
+   *          the value of field 'showDistances'.
+   */
+  public void setShowDistances(final boolean showDistances)
+  {
+    this._showDistances = showDistances;
+    this._has_showDistances = true;
+  }
+
+  /**
+   * Sets the value of field 'threshold'.
+   * 
+   * @param threshold
+   *          the value of field 'threshold'.
+   */
+  public void setThreshold(final float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *          the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *          the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *          the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *          the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Tree
+   */
+  public static jalview.binding.Tree unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Tree) Unmarshaller.unmarshal(
+            jalview.binding.Tree.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java
index 24c97ff..555693c 100644
--- a/src/jalview/binding/UserColourScheme.java
+++ b/src/jalview/binding/UserColourScheme.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,98 +19,107 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColourScheme extends JalviewUserColours 
-implements java.io.Serializable
+public class UserColourScheme extends JalviewUserColours implements
+        java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColourScheme() {
-        super();
-    }
-
+  public UserColourScheme()
+  {
+    super();
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.JalviewUserColours
-     */
-    public static jalview.binding.JalviewUserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.JalviewUserColours
+   */
+  public static jalview.binding.JalviewUserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
+            jalview.binding.UserColourScheme.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java
index bdefe05..6a8d73c 100644
--- a/src/jalview/binding/UserColours.java
+++ b/src/jalview/binding/UserColours.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,151 +19,163 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _userColourScheme.
-     */
-    private jalview.binding.UserColourScheme _userColourScheme;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColours() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'userColourScheme'.
-     * 
-     * @return the value of field 'UserColourScheme'.
-     */
-    public jalview.binding.UserColourScheme getUserColourScheme(
-    ) {
-        return this._userColourScheme;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'userColourScheme'.
-     * 
-     * @param userColourScheme the value of field 'userColourScheme'
-     */
-    public void setUserColourScheme(
-            final jalview.binding.UserColourScheme userColourScheme) {
-        this._userColourScheme = userColourScheme;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.UserColours
-     */
-    public static jalview.binding.UserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class UserColours implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _userColourScheme.
+   */
+  private jalview.binding.UserColourScheme _userColourScheme;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public UserColours()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'userColourScheme'.
+   * 
+   * @return the value of field 'UserColourScheme'.
+   */
+  public jalview.binding.UserColourScheme getUserColourScheme()
+  {
+    return this._userColourScheme;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'userColourScheme'.
+   * 
+   * @param userColourScheme
+   *          the value of field 'userColourScheme'
+   */
+  public void setUserColourScheme(
+          final jalview.binding.UserColourScheme userColourScheme)
+  {
+    this._userColourScheme = userColourScheme;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.UserColours
+   */
+  public static jalview.binding.UserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.UserColours) Unmarshaller.unmarshal(
+            jalview.binding.UserColours.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index 1c92bd3..c06de29 100644
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,563 +19,584 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class VAMSAS implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _alignmentList.
-     */
-    private java.util.Vector _alignmentList;
-
-    /**
-     * Field _treeList.
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _sequenceSetList.
-     */
-    private java.util.Vector _sequenceSetList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VAMSAS() {
-        super();
-        this._alignmentList = new java.util.Vector();
-        this._treeList = new java.util.Vector();
-        this._sequenceSetList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAlignment
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlignment(
-            final Alignment vAlignment)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alignmentList.addElement(vAlignment);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlignment
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlignment(
-            final int index,
-            final Alignment vAlignment)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alignmentList.add(index, vAlignment);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSet(
-            final SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetList.addElement(vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSet(
-            final int index,
-            final SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetList.add(index, vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.addElement(vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final int index,
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.add(index, vTree);
-    }
-
-    /**
-     * Method enumerateAlignment.
-     * 
-     * @return an Enumeration over all Alignment elements
-     */
-    public java.util.Enumeration enumerateAlignment(
-    ) {
-        return this._alignmentList.elements();
-    }
-
-    /**
-     * Method enumerateSequenceSet.
-     * 
-     * @return an Enumeration over all SequenceSet elements
-     */
-    public java.util.Enumeration enumerateSequenceSet(
-    ) {
-        return this._sequenceSetList.elements();
-    }
-
-    /**
-     * Method enumerateTree.
-     * 
-     * @return an Enumeration over all java.lang.String elements
-     */
-    public java.util.Enumeration enumerateTree(
-    ) {
-        return this._treeList.elements();
-    }
-
-    /**
-     * Method getAlignment.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the Alignment at the given index
-     */
-    public Alignment getAlignment(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alignmentList.size()) {
-            throw new IndexOutOfBoundsException("getAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
-        }
-        
-        return (Alignment) _alignmentList.get(index);
-    }
-
-    /**
-     * Method getAlignment.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public Alignment[] getAlignment(
-    ) {
-        Alignment[] array = new Alignment[0];
-        return (Alignment[]) this._alignmentList.toArray(array);
-    }
-
-    /**
-     * Method getAlignmentCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAlignmentCount(
-    ) {
-        return this._alignmentList.size();
-    }
-
-    /**
-     * Method getSequenceSet.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the SequenceSet at the given index
-     */
-    public SequenceSet getSequenceSet(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetList.size()) {
-            throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
-        }
-        
-        return (SequenceSet) _sequenceSetList.get(index);
-    }
-
-    /**
-     * Method getSequenceSet.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public SequenceSet[] getSequenceSet(
-    ) {
-        SequenceSet[] array = new SequenceSet[0];
-        return (SequenceSet[]) this._sequenceSetList.toArray(array);
-    }
-
-    /**
-     * Method getSequenceSetCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceSetCount(
-    ) {
-        return this._sequenceSetList.size();
-    }
-
-    /**
-     * Method getTree.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the java.lang.String at the given index
-     */
-    public java.lang.String getTree(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        return (java.lang.String) _treeList.get(index);
-    }
-
-    /**
-     * Method getTree.Returns the contents of the collection in an
-     * Array.  
Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public java.lang.String[] getTree(
-    ) {
-        java.lang.String[] array = new java.lang.String[0];
-        return (java.lang.String[]) this._treeList.toArray(array);
-    }
-
-    /**
-     * Method getTreeCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getTreeCount(
-    ) {
-        return this._treeList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Method removeAlignment.
-     * 
-     * @param vAlignment
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAlignment(
-            final Alignment vAlignment) {
-        boolean removed = _alignmentList.remove(vAlignment);
-        return removed;
-    }
-
-    /**
-     * Method removeAlignmentAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public Alignment removeAlignmentAt(
-            final int index) {
-        java.lang.Object obj = this._alignmentList.remove(index);
-        return (Alignment) obj;
-    }
-
-    /**
-     */
-    public void removeAllAlignment(
-    ) {
-        this._alignmentList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSequenceSet(
-    ) {
-        this._sequenceSetList.clear();
-    }
-
-    /**
-     */
-    public void removeAllTree(
-    ) {
-        this._treeList.clear();
-    }
-
-    /**
-     * Method removeSequenceSet.
-     * 
-     * @param vSequenceSet
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequenceSet(
-            final SequenceSet vSequenceSet) {
-        boolean removed = _sequenceSetList.remove(vSequenceSet);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceSetAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public SequenceSet removeSequenceSetAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceSetList.remove(index);
-        return (SequenceSet) obj;
-    }
-
-    /**
-     * Method removeTree.
-     * 
-     * @param vTree
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeTree(
-            final java.lang.String vTree) {
-        boolean removed = _treeList.remove(vTree);
-        return removed;
-    }
-
-    /**
-     * Method removeTreeAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public java.lang.String removeTreeAt(
-            final int index) {
-        java.lang.Object obj = this._treeList.remove(index);
-        return (java.lang.String) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlignment
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAlignment(
-            final int index,
-            final Alignment vAlignment)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alignmentList.size()) {
-            throw new IndexOutOfBoundsException("setAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
-        }
-        
-        this._alignmentList.set(index, vAlignment);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAlignmentArray
-     */
-    public void setAlignment(
-            final Alignment[] vAlignmentArray) {
-        //-- copy array
-        _alignmentList.clear();
-        
-        for (int i = 0; i < vAlignmentArray.length; i++) {
-                this._alignmentList.add(vAlignmentArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequenceSet(
-            final int index,
-            final SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetList.size()) {
-            throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
-        }
-        
-        this._sequenceSetList.set(index, vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSetArray
-     */
-    public void setSequenceSet(
-            final SequenceSet[] vSequenceSetArray) {
-        //-- copy array
-        _sequenceSetList.clear();
-        
-        for (int i = 0; i < vSequenceSetArray.length; i++) {
-                this._sequenceSetList.add(vSequenceSetArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setTree(
-            final int index,
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        this._treeList.set(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTreeArray
-     */
-    public void setTree(
-            final java.lang.String[] vTreeArray) {
-        //-- copy array
-        _treeList.clear();
-        
-        for (int i = 0; i < vTreeArray.length; i++) {
-                this._treeList.add(vTreeArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.VAMSAS
-     */
-    public static jalview.binding.VAMSAS unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class VAMSAS implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _alignmentList.
+   */
+  private java.util.Vector _alignmentList;
+
+  /**
+   * Field _treeList.
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _sequenceSetList.
+   */
+  private java.util.Vector _sequenceSetList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public VAMSAS()
+  {
+    super();
+    this._alignmentList = new java.util.Vector();
+    this._treeList = new java.util.Vector();
+    this._sequenceSetList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAlignment
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlignment(final Alignment vAlignment)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alignmentList.addElement(vAlignment);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlignment
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlignment(final int index, final Alignment vAlignment)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alignmentList.add(index, vAlignment);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSet(final SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetList.addElement(vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSet(final int index, final SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetList.add(index, vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.addElement(vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.add(index, vTree);
+  }
+
+  /**
+   * Method enumerateAlignment.
+   * 
+   * @return an Enumeration over all Alignment elements
+   */
+  public java.util.Enumeration enumerateAlignment()
+  {
+    return this._alignmentList.elements();
+  }
+
+  /**
+   * Method enumerateSequenceSet.
+   * 
+   * @return an Enumeration over all SequenceSet elements
+   */
+  public java.util.Enumeration enumerateSequenceSet()
+  {
+    return this._sequenceSetList.elements();
+  }
+
+  /**
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return this._treeList.elements();
+  }
+
+  /**
+   * Method getAlignment.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the Alignment at the given index
+   */
+  public Alignment getAlignment(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alignmentList.size())
+    {
+      throw new IndexOutOfBoundsException("getAlignment: Index value '"
+              + index + "' not in range [0.."
+              + (this._alignmentList.size() - 1) + "]");
+    }
+
+    return (Alignment) _alignmentList.get(index);
+  }
+
+  /**
+   * Method getAlignment.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public Alignment[] getAlignment()
+  {
+    Alignment[] array = new Alignment[0];
+    return (Alignment[]) this._alignmentList.toArray(array);
+  }
+
+  /**
+   * Method getAlignmentCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAlignmentCount()
+  {
+    return this._alignmentList.size();
+  }
+
+  /**
+   * Method getSequenceSet.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the SequenceSet at the given index
+   */
+  public SequenceSet getSequenceSet(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
+    {
+      throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
+    }
+
+    return (SequenceSet) _sequenceSetList.get(index);
+  }
+
+  /**
+   * Method getSequenceSet.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public SequenceSet[] getSequenceSet()
+  {
+    SequenceSet[] array = new SequenceSet[0];
+    return (SequenceSet[]) this._sequenceSetList.toArray(array);
+  }
+
+  /**
+   * Method getSequenceSetCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceSetCount()
+  {
+    return this._sequenceSetList.size();
+  }
+
+  /**
+   * Method getTree.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _treeList.get(index);
+  }
+
+  /**
+   * Method getTree.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getTree()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._treeList.toArray(array);
+  }
+
+  /**
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getTreeCount()
+  {
+    return this._treeList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method removeAlignment.
+   * 
+   * @param vAlignment
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAlignment(final Alignment vAlignment)
+  {
+    boolean removed = _alignmentList.remove(vAlignment);
+    return removed;
+  }
+
+  /**
+   * Method removeAlignmentAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public Alignment removeAlignmentAt(final int index)
+  {
+    java.lang.Object obj = this._alignmentList.remove(index);
+    return (Alignment) obj;
+  }
+
+  /**
+     */
+  public void removeAllAlignment()
+  {
+    this._alignmentList.clear();
+  }
+
+  /**
+     */
+  public void removeAllSequenceSet()
+  {
+    this._sequenceSetList.clear();
+  }
+
+  /**
+     */
+  public void removeAllTree()
+  {
+    this._treeList.clear();
+  }
+
+  /**
+   * Method removeSequenceSet.
+   * 
+   * @param vSequenceSet
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequenceSet(final SequenceSet vSequenceSet)
+  {
+    boolean removed = _sequenceSetList.remove(vSequenceSet);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceSetAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public SequenceSet removeSequenceSetAt(final int index)
+  {
+    java.lang.Object obj = this._sequenceSetList.remove(index);
+    return (SequenceSet) obj;
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final java.lang.String vTree)
+  {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
+
+  /**
+   * Method removeTreeAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeTreeAt(final int index)
+  {
+    java.lang.Object obj = this._treeList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlignment
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAlignment(final int index, final Alignment vAlignment)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alignmentList.size())
+    {
+      throw new IndexOutOfBoundsException("setAlignment: Index value '"
+              + index + "' not in range [0.."
+              + (this._alignmentList.size() - 1) + "]");
+    }
+
+    this._alignmentList.set(index, vAlignment);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlignmentArray
+   */
+  public void setAlignment(final Alignment[] vAlignmentArray)
+  {
+    // -- copy array
+    _alignmentList.clear();
+
+    for (int i = 0; i < vAlignmentArray.length; i++)
+    {
+      this._alignmentList.add(vAlignmentArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSequenceSet(final int index, final SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
+    {
+      throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
+    }
+
+    this._sequenceSetList.set(index, vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSetArray
+   */
+  public void setSequenceSet(final SequenceSet[] vSequenceSetArray)
+  {
+    // -- copy array
+    _sequenceSetList.clear();
+
+    for (int i = 0; i < vSequenceSetArray.length; i++)
+    {
+      this._sequenceSetList.add(vSequenceSetArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    this._treeList.set(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTreeArray
+   */
+  public void setTree(final java.lang.String[] vTreeArray)
+  {
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
+    {
+      this._treeList.add(vTreeArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.VAMSAS
+   */
+  public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
+            jalview.binding.VAMSAS.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java
index 5fda35e..e4c5e0d 100644
--- a/src/jalview/binding/VamsasModel.java
+++ b/src/jalview/binding/VamsasModel.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,98 +19,105 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class VamsasModel extends VAMSAS 
-implements java.io.Serializable
+public class VamsasModel extends VAMSAS implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VamsasModel() {
-        super();
-    }
-
+  public VamsasModel()
+  {
+    super();
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.VAMSAS
-     */
-    public static jalview.binding.VAMSAS unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.VAMSAS
+   */
+  public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
+            jalview.binding.VamsasModel.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java
index 643c323..d144378 100644
--- a/src/jalview/binding/Viewport.java
+++ b/src/jalview/binding/Viewport.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,1414 +19,1445 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Viewport implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _conservationSelected.
-     */
-    private boolean _conservationSelected;
-
-    /**
-     * keeps track of state for field: _conservationSelected
-     */
-    private boolean _has_conservationSelected;
-
-    /**
-     * Field _pidSelected.
-     */
-    private boolean _pidSelected;
-
-    /**
-     * keeps track of state for field: _pidSelected
-     */
-    private boolean _has_pidSelected;
-
-    /**
-     * Field _bgColour.
-     */
-    private java.lang.String _bgColour;
-
-    /**
-     * Field _consThreshold.
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold.
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * Field _showFullId.
-     */
-    private boolean _showFullId;
-
-    /**
-     * keeps track of state for field: _showFullId
-     */
-    private boolean _has_showFullId;
+public class Viewport implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _conservationSelected.
+   */
+  private boolean _conservationSelected;
+
+  /**
+   * keeps track of state for field: _conservationSelected
+   */
+  private boolean _has_conservationSelected;
+
+  /**
+   * Field _pidSelected.
+   */
+  private boolean _pidSelected;
+
+  /**
+   * keeps track of state for field: _pidSelected
+   */
+  private boolean _has_pidSelected;
+
+  /**
+   * Field _bgColour.
+   */
+  private java.lang.String _bgColour;
+
+  /**
+   * Field _consThreshold.
+   */
+  private int _consThreshold;
+
+  /**
+   * keeps track of state for field: _consThreshold
+   */
+  private boolean _has_consThreshold;
+
+  /**
+   * Field _pidThreshold.
+   */
+  private int _pidThreshold;
+
+  /**
+   * keeps track of state for field: _pidThreshold
+   */
+  private boolean _has_pidThreshold;
+
+  /**
+   * Field _title.
+   */
+  private java.lang.String _title;
+
+  /**
+   * Field _showFullId.
+   */
+  private boolean _showFullId;
+
+  /**
+   * keeps track of state for field: _showFullId
+   */
+  private boolean _has_showFullId;
+
+  /**
+   * Field _showText.
+   */
+  private boolean _showText;
+
+  /**
+   * keeps track of state for field: _showText
+   */
+  private boolean _has_showText;
+
+  /**
+   * Field _showColourText.
+   */
+  private boolean _showColourText;
+
+  /**
+   * keeps track of state for field: _showColourText
+   */
+  private boolean _has_showColourText;
+
+  /**
+   * Field _showBoxes.
+   */
+  private boolean _showBoxes;
+
+  /**
+   * keeps track of state for field: _showBoxes
+   */
+  private boolean _has_showBoxes;
+
+  /**
+   * Field _wrapAlignment.
+   */
+  private boolean _wrapAlignment;
+
+  /**
+   * keeps track of state for field: _wrapAlignment
+   */
+  private boolean _has_wrapAlignment;
+
+  /**
+   * Field _renderGaps.
+   */
+  private boolean _renderGaps;
+
+  /**
+   * keeps track of state for field: _renderGaps
+   */
+  private boolean _has_renderGaps;
+
+  /**
+   * Field _showSequenceFeatures.
+   */
+  private boolean _showSequenceFeatures;
+
+  /**
+   * keeps track of state for field: _showSequenceFeatures
+   */
+  private boolean _has_showSequenceFeatures;
+
+  /**
+   * Field _showAnnotation.
+   */
+  private boolean _showAnnotation;
+
+  /**
+   * keeps track of state for field: _showAnnotation
+   */
+  private boolean _has_showAnnotation;
+
+  /**
+   * Field _showConservation.
+   */
+  private boolean _showConservation;
+
+  /**
+   * keeps track of state for field: _showConservation
+   */
+  private boolean _has_showConservation;
+
+  /**
+   * Field _showQuality.
+   */
+  private boolean _showQuality;
+
+  /**
+   * keeps track of state for field: _showQuality
+   */
+  private boolean _has_showQuality;
+
+  /**
+   * Field _showIdentity.
+   */
+  private boolean _showIdentity;
+
+  /**
+   * keeps track of state for field: _showIdentity
+   */
+  private boolean _has_showIdentity;
+
+  /**
+   * Field _xpos.
+   */
+  private int _xpos;
+
+  /**
+   * keeps track of state for field: _xpos
+   */
+  private boolean _has_xpos;
+
+  /**
+   * Field _ypos.
+   */
+  private int _ypos;
+
+  /**
+   * keeps track of state for field: _ypos
+   */
+  private boolean _has_ypos;
+
+  /**
+   * Field _width.
+   */
+  private int _width;
+
+  /**
+   * keeps track of state for field: _width
+   */
+  private boolean _has_width;
+
+  /**
+   * Field _height.
+   */
+  private int _height;
+
+  /**
+   * keeps track of state for field: _height
+   */
+  private boolean _has_height;
+
+  /**
+   * Field _startRes.
+   */
+  private int _startRes;
+
+  /**
+   * keeps track of state for field: _startRes
+   */
+  private boolean _has_startRes;
+
+  /**
+   * Field _startSeq.
+   */
+  private int _startSeq;
+
+  /**
+   * keeps track of state for field: _startSeq
+   */
+  private boolean _has_startSeq;
+
+  /**
+   * Field _fontName.
+   */
+  private java.lang.String _fontName;
+
+  /**
+   * Field _fontSize.
+   */
+  private int _fontSize;
+
+  /**
+   * keeps track of state for field: _fontSize
+   */
+  private boolean _has_fontSize;
+
+  /**
+   * Field _fontStyle.
+   */
+  private int _fontStyle;
+
+  /**
+   * keeps track of state for field: _fontStyle
+   */
+  private boolean _has_fontStyle;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Viewport()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Field _showText.
+  /**
      */
-    private boolean _showText;
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  }
 
-    /**
-     * keeps track of state for field: _showText
+  /**
      */
-    private boolean _has_showText;
+  public void deleteConservationSelected()
+  {
+    this._has_conservationSelected = false;
+  }
 
-    /**
-     * Field _showColourText.
+  /**
      */
-    private boolean _showColourText;
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  }
 
-    /**
-     * keeps track of state for field: _showColourText
+  /**
      */
-    private boolean _has_showColourText;
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  }
 
-    /**
-     * Field _showBoxes.
+  /**
      */
-    private boolean _showBoxes;
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
 
-    /**
-     * keeps track of state for field: _showBoxes
+  /**
      */
-    private boolean _has_showBoxes;
+  public void deletePidSelected()
+  {
+    this._has_pidSelected = false;
+  }
 
-    /**
-     * Field _wrapAlignment.
+  /**
      */
-    private boolean _wrapAlignment;
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  }
 
-    /**
-     * keeps track of state for field: _wrapAlignment
+  /**
      */
-    private boolean _has_wrapAlignment;
+  public void deleteRenderGaps()
+  {
+    this._has_renderGaps = false;
+  }
 
-    /**
-     * Field _renderGaps.
+  /**
      */
-    private boolean _renderGaps;
+  public void deleteShowAnnotation()
+  {
+    this._has_showAnnotation = false;
+  }
 
-    /**
-     * keeps track of state for field: _renderGaps
+  /**
      */
-    private boolean _has_renderGaps;
+  public void deleteShowBoxes()
+  {
+    this._has_showBoxes = false;
+  }
 
-    /**
-     * Field _showSequenceFeatures.
+  /**
      */
-    private boolean _showSequenceFeatures;
+  public void deleteShowColourText()
+  {
+    this._has_showColourText = false;
+  }
 
-    /**
-     * keeps track of state for field: _showSequenceFeatures
+  /**
      */
-    private boolean _has_showSequenceFeatures;
+  public void deleteShowConservation()
+  {
+    this._has_showConservation = false;
+  }
 
-    /**
-     * Field _showAnnotation.
+  /**
      */
-    private boolean _showAnnotation;
+  public void deleteShowFullId()
+  {
+    this._has_showFullId = false;
+  }
 
-    /**
-     * keeps track of state for field: _showAnnotation
+  /**
      */
-    private boolean _has_showAnnotation;
+  public void deleteShowIdentity()
+  {
+    this._has_showIdentity = false;
+  }
 
-    /**
-     * Field _showConservation.
+  /**
      */
-    private boolean _showConservation;
-
-    /**
-     * keeps track of state for field: _showConservation
-     */
-    private boolean _has_showConservation;
-
-    /**
-     * Field _showQuality.
-     */
-    private boolean _showQuality;
-
-    /**
-     * keeps track of state for field: _showQuality
-     */
-    private boolean _has_showQuality;
-
-    /**
-     * Field _showIdentity.
-     */
-    private boolean _showIdentity;
-
-    /**
-     * keeps track of state for field: _showIdentity
-     */
-    private boolean _has_showIdentity;
-
-    /**
-     * Field _xpos.
-     */
-    private int _xpos;
-
-    /**
-     * keeps track of state for field: _xpos
-     */
-    private boolean _has_xpos;
-
-    /**
-     * Field _ypos.
-     */
-    private int _ypos;
-
-    /**
-     * keeps track of state for field: _ypos
-     */
-    private boolean _has_ypos;
-
-    /**
-     * Field _width.
-     */
-    private int _width;
-
-    /**
-     * keeps track of state for field: _width
-     */
-    private boolean _has_width;
-
-    /**
-     * Field _height.
-     */
-    private int _height;
-
-    /**
-     * keeps track of state for field: _height
-     */
-    private boolean _has_height;
-
-    /**
-     * Field _startRes.
-     */
-    private int _startRes;
-
-    /**
-     * keeps track of state for field: _startRes
-     */
-    private boolean _has_startRes;
-
-    /**
-     * Field _startSeq.
-     */
-    private int _startSeq;
-
-    /**
-     * keeps track of state for field: _startSeq
-     */
-    private boolean _has_startSeq;
-
-    /**
-     * Field _fontName.
-     */
-    private java.lang.String _fontName;
-
-    /**
-     * Field _fontSize.
-     */
-    private int _fontSize;
-
-    /**
-     * keeps track of state for field: _fontSize
-     */
-    private boolean _has_fontSize;
-
-    /**
-     * Field _fontStyle.
-     */
-    private int _fontStyle;
-
-    /**
-     * keeps track of state for field: _fontStyle
-     */
-    private boolean _has_fontStyle;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Viewport() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteConsThreshold(
-    ) {
-        this._has_consThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteConservationSelected(
-    ) {
-        this._has_conservationSelected= false;
-    }
-
-    /**
-     */
-    public void deleteFontSize(
-    ) {
-        this._has_fontSize= false;
-    }
-
-    /**
-     */
-    public void deleteFontStyle(
-    ) {
-        this._has_fontStyle= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deletePidSelected(
-    ) {
-        this._has_pidSelected= false;
-    }
-
-    /**
-     */
-    public void deletePidThreshold(
-    ) {
-        this._has_pidThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteRenderGaps(
-    ) {
-        this._has_renderGaps= false;
-    }
-
-    /**
-     */
-    public void deleteShowAnnotation(
-    ) {
-        this._has_showAnnotation= false;
-    }
-
-    /**
-     */
-    public void deleteShowBoxes(
-    ) {
-        this._has_showBoxes= false;
-    }
-
-    /**
-     */
-    public void deleteShowColourText(
-    ) {
-        this._has_showColourText= false;
-    }
-
-    /**
-     */
-    public void deleteShowConservation(
-    ) {
-        this._has_showConservation= false;
-    }
-
-    /**
-     */
-    public void deleteShowFullId(
-    ) {
-        this._has_showFullId= false;
-    }
-
-    /**
-     */
-    public void deleteShowIdentity(
-    ) {
-        this._has_showIdentity= false;
-    }
-
-    /**
-     */
-    public void deleteShowQuality(
-    ) {
-        this._has_showQuality= false;
-    }
-
-    /**
-     */
-    public void deleteShowSequenceFeatures(
-    ) {
-        this._has_showSequenceFeatures= false;
-    }
-
-    /**
-     */
-    public void deleteShowText(
-    ) {
-        this._has_showText= false;
-    }
-
-    /**
-     */
-    public void deleteStartRes(
-    ) {
-        this._has_startRes= false;
-    }
-
-    /**
-     */
-    public void deleteStartSeq(
-    ) {
-        this._has_startSeq= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteWrapAlignment(
-    ) {
-        this._has_wrapAlignment= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Returns the value of field 'bgColour'.
-     * 
-     * @return the value of field 'BgColour'.
-     */
-    public java.lang.String getBgColour(
-    ) {
-        return this._bgColour;
-    }
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return the value of field 'ConsThreshold'.
-     */
-    public int getConsThreshold(
-    ) {
-        return this._consThreshold;
-    }
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return the value of field 'ConservationSelected'.
-     */
-    public boolean getConservationSelected(
-    ) {
-        return this._conservationSelected;
-    }
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return the value of field 'FontName'.
-     */
-    public java.lang.String getFontName(
-    ) {
-        return this._fontName;
-    }
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return the value of field 'FontSize'.
-     */
-    public int getFontSize(
-    ) {
-        return this._fontSize;
-    }
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return the value of field 'FontStyle'.
-     */
-    public int getFontStyle(
-    ) {
-        return this._fontStyle;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return the value of field 'PidSelected'.
-     */
-    public boolean getPidSelected(
-    ) {
-        return this._pidSelected;
-    }
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return the value of field 'PidThreshold'.
-     */
-    public int getPidThreshold(
-    ) {
-        return this._pidThreshold;
-    }
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return the value of field 'RenderGaps'.
-     */
-    public boolean getRenderGaps(
-    ) {
-        return this._renderGaps;
-    }
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return the value of field 'ShowAnnotation'.
-     */
-    public boolean getShowAnnotation(
-    ) {
-        return this._showAnnotation;
-    }
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return the value of field 'ShowBoxes'.
-     */
-    public boolean getShowBoxes(
-    ) {
-        return this._showBoxes;
-    }
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return the value of field 'ShowColourText'.
-     */
-    public boolean getShowColourText(
-    ) {
-        return this._showColourText;
-    }
-
-    /**
-     * Returns the value of field 'showConservation'.
-     * 
-     * @return the value of field 'ShowConservation'.
-     */
-    public boolean getShowConservation(
-    ) {
-        return this._showConservation;
-    }
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return the value of field 'ShowFullId'.
-     */
-    public boolean getShowFullId(
-    ) {
-        return this._showFullId;
-    }
-
-    /**
-     * Returns the value of field 'showIdentity'.
-     * 
-     * @return the value of field 'ShowIdentity'.
-     */
-    public boolean getShowIdentity(
-    ) {
-        return this._showIdentity;
-    }
-
-    /**
-     * Returns the value of field 'showQuality'.
-     * 
-     * @return the value of field 'ShowQuality'.
-     */
-    public boolean getShowQuality(
-    ) {
-        return this._showQuality;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return the value of field 'ShowSequenceFeatures'.
-     */
-    public boolean getShowSequenceFeatures(
-    ) {
-        return this._showSequenceFeatures;
-    }
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return the value of field 'ShowText'.
-     */
-    public boolean getShowText(
-    ) {
-        return this._showText;
-    }
-
-    /**
-     * Returns the value of field 'startRes'.
-     * 
-     * @return the value of field 'StartRes'.
-     */
-    public int getStartRes(
-    ) {
-        return this._startRes;
-    }
-
-    /**
-     * Returns the value of field 'startSeq'.
-     * 
-     * @return the value of field 'StartSeq'.
-     */
-    public int getStartSeq(
-    ) {
-        return this._startSeq;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return the value of field 'WrapAlignment'.
-     */
-    public boolean getWrapAlignment(
-    ) {
-        return this._wrapAlignment;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasConsThreshold.
-     * 
-     * @return true if at least one ConsThreshold has been added
-     */
-    public boolean hasConsThreshold(
-    ) {
-        return this._has_consThreshold;
-    }
-
-    /**
-     * Method hasConservationSelected.
-     * 
-     * @return true if at least one ConservationSelected has been
-     * added
-     */
-    public boolean hasConservationSelected(
-    ) {
-        return this._has_conservationSelected;
-    }
-
-    /**
-     * Method hasFontSize.
-     * 
-     * @return true if at least one FontSize has been added
-     */
-    public boolean hasFontSize(
-    ) {
-        return this._has_fontSize;
-    }
-
-    /**
-     * Method hasFontStyle.
-     * 
-     * @return true if at least one FontStyle has been added
-     */
-    public boolean hasFontStyle(
-    ) {
-        return this._has_fontStyle;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasPidSelected.
-     * 
-     * @return true if at least one PidSelected has been added
-     */
-    public boolean hasPidSelected(
-    ) {
-        return this._has_pidSelected;
-    }
-
-    /**
-     * Method hasPidThreshold.
-     * 
-     * @return true if at least one PidThreshold has been added
-     */
-    public boolean hasPidThreshold(
-    ) {
-        return this._has_pidThreshold;
-    }
-
-    /**
-     * Method hasRenderGaps.
-     * 
-     * @return true if at least one RenderGaps has been added
-     */
-    public boolean hasRenderGaps(
-    ) {
-        return this._has_renderGaps;
-    }
-
-    /**
-     * Method hasShowAnnotation.
-     * 
-     * @return true if at least one ShowAnnotation has been added
-     */
-    public boolean hasShowAnnotation(
-    ) {
-        return this._has_showAnnotation;
-    }
-
-    /**
-     * Method hasShowBoxes.
-     * 
-     * @return true if at least one ShowBoxes has been added
-     */
-    public boolean hasShowBoxes(
-    ) {
-        return this._has_showBoxes;
-    }
-
-    /**
-     * Method hasShowColourText.
-     * 
-     * @return true if at least one ShowColourText has been added
-     */
-    public boolean hasShowColourText(
-    ) {
-        return this._has_showColourText;
-    }
-
-    /**
-     * Method hasShowConservation.
-     * 
-     * @return true if at least one ShowConservation has been added
-     */
-    public boolean hasShowConservation(
-    ) {
-        return this._has_showConservation;
-    }
-
-    /**
-     * Method hasShowFullId.
-     * 
-     * @return true if at least one ShowFullId has been added
-     */
-    public boolean hasShowFullId(
-    ) {
-        return this._has_showFullId;
-    }
-
-    /**
-     * Method hasShowIdentity.
-     * 
-     * @return true if at least one ShowIdentity has been added
-     */
-    public boolean hasShowIdentity(
-    ) {
-        return this._has_showIdentity;
-    }
-
-    /**
-     * Method hasShowQuality.
-     * 
-     * @return true if at least one ShowQuality has been added
-     */
-    public boolean hasShowQuality(
-    ) {
-        return this._has_showQuality;
-    }
-
-    /**
-     * Method hasShowSequenceFeatures.
-     * 
-     * @return true if at least one ShowSequenceFeatures has been
-     * added
-     */
-    public boolean hasShowSequenceFeatures(
-    ) {
-        return this._has_showSequenceFeatures;
-    }
-
-    /**
-     * Method hasShowText.
-     * 
-     * @return true if at least one ShowText has been added
-     */
-    public boolean hasShowText(
-    ) {
-        return this._has_showText;
-    }
-
-    /**
-     * Method hasStartRes.
-     * 
-     * @return true if at least one StartRes has been added
-     */
-    public boolean hasStartRes(
-    ) {
-        return this._has_startRes;
-    }
-
-    /**
-     * Method hasStartSeq.
-     * 
-     * @return true if at least one StartSeq has been added
-     */
-    public boolean hasStartSeq(
-    ) {
-        return this._has_startSeq;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasWrapAlignment.
-     * 
-     * @return true if at least one WrapAlignment has been added
-     */
-    public boolean hasWrapAlignment(
-    ) {
-        return this._has_wrapAlignment;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return the value of field 'ConservationSelected'.
-     */
-    public boolean isConservationSelected(
-    ) {
-        return this._conservationSelected;
-    }
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return the value of field 'PidSelected'.
-     */
-    public boolean isPidSelected(
-    ) {
-        return this._pidSelected;
-    }
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return the value of field 'RenderGaps'.
-     */
-    public boolean isRenderGaps(
-    ) {
-        return this._renderGaps;
-    }
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return the value of field 'ShowAnnotation'.
-     */
-    public boolean isShowAnnotation(
-    ) {
-        return this._showAnnotation;
-    }
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return the value of field 'ShowBoxes'.
-     */
-    public boolean isShowBoxes(
-    ) {
-        return this._showBoxes;
-    }
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return the value of field 'ShowColourText'.
-     */
-    public boolean isShowColourText(
-    ) {
-        return this._showColourText;
-    }
-
-    /**
-     * Returns the value of field 'showConservation'.
-     * 
-     * @return the value of field 'ShowConservation'.
-     */
-    public boolean isShowConservation(
-    ) {
-        return this._showConservation;
-    }
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return the value of field 'ShowFullId'.
-     */
-    public boolean isShowFullId(
-    ) {
-        return this._showFullId;
-    }
-
-    /**
-     * Returns the value of field 'showIdentity'.
-     * 
-     * @return the value of field 'ShowIdentity'.
-     */
-    public boolean isShowIdentity(
-    ) {
-        return this._showIdentity;
-    }
-
-    /**
-     * Returns the value of field 'showQuality'.
-     * 
-     * @return the value of field 'ShowQuality'.
-     */
-    public boolean isShowQuality(
-    ) {
-        return this._showQuality;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return the value of field 'ShowSequenceFeatures'.
-     */
-    public boolean isShowSequenceFeatures(
-    ) {
-        return this._showSequenceFeatures;
-    }
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return the value of field 'ShowText'.
-     */
-    public boolean isShowText(
-    ) {
-        return this._showText;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return the value of field 'WrapAlignment'.
-     */
-    public boolean isWrapAlignment(
-    ) {
-        return this._wrapAlignment;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'bgColour'.
-     * 
-     * @param bgColour the value of field 'bgColour'.
-     */
-    public void setBgColour(
-            final java.lang.String bgColour) {
-        this._bgColour = bgColour;
-    }
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(
-            final int consThreshold) {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'conservationSelected'.
-     * 
-     * @param conservationSelected the value of field
-     * 'conservationSelected'.
-     */
-    public void setConservationSelected(
-            final boolean conservationSelected) {
-        this._conservationSelected = conservationSelected;
-        this._has_conservationSelected = true;
-    }
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(
-            final java.lang.String fontName) {
-        this._fontName = fontName;
-    }
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(
-            final int fontSize) {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    }
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(
-            final int fontStyle) {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * Sets the value of field 'pidSelected'.
-     * 
-     * @param pidSelected the value of field 'pidSelected'.
-     */
-    public void setPidSelected(
-            final boolean pidSelected) {
-        this._pidSelected = pidSelected;
-        this._has_pidSelected = true;
-    }
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(
-            final int pidThreshold) {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'renderGaps'.
-     * 
-     * @param renderGaps the value of field 'renderGaps'.
-     */
-    public void setRenderGaps(
-            final boolean renderGaps) {
-        this._renderGaps = renderGaps;
-        this._has_renderGaps = true;
-    }
-
-    /**
-     * Sets the value of field 'showAnnotation'.
-     * 
-     * @param showAnnotation the value of field 'showAnnotation'.
-     */
-    public void setShowAnnotation(
-            final boolean showAnnotation) {
-        this._showAnnotation = showAnnotation;
-        this._has_showAnnotation = true;
-    }
-
-    /**
-     * Sets the value of field 'showBoxes'.
-     * 
-     * @param showBoxes the value of field 'showBoxes'.
-     */
-    public void setShowBoxes(
-            final boolean showBoxes) {
-        this._showBoxes = showBoxes;
-        this._has_showBoxes = true;
-    }
-
-    /**
-     * Sets the value of field 'showColourText'.
-     * 
-     * @param showColourText the value of field 'showColourText'.
-     */
-    public void setShowColourText(
-            final boolean showColourText) {
-        this._showColourText = showColourText;
-        this._has_showColourText = true;
-    }
-
-    /**
-     * Sets the value of field 'showConservation'.
-     * 
-     * @param showConservation the value of field 'showConservation'
-     */
-    public void setShowConservation(
-            final boolean showConservation) {
-        this._showConservation = showConservation;
-        this._has_showConservation = true;
-    }
-
-    /**
-     * Sets the value of field 'showFullId'.
-     * 
-     * @param showFullId the value of field 'showFullId'.
-     */
-    public void setShowFullId(
-            final boolean showFullId) {
-        this._showFullId = showFullId;
-        this._has_showFullId = true;
-    }
-
-    /**
-     * Sets the value of field 'showIdentity'.
-     * 
-     * @param showIdentity the value of field 'showIdentity'.
-     */
-    public void setShowIdentity(
-            final boolean showIdentity) {
-        this._showIdentity = showIdentity;
-        this._has_showIdentity = true;
-    }
-
-    /**
-     * Sets the value of field 'showQuality'.
-     * 
-     * @param showQuality the value of field 'showQuality'.
-     */
-    public void setShowQuality(
-            final boolean showQuality) {
-        this._showQuality = showQuality;
-        this._has_showQuality = true;
-    }
-
-    /**
-     * Sets the value of field 'showSequenceFeatures'.
-     * 
-     * @param showSequenceFeatures the value of field
-     * 'showSequenceFeatures'.
-     */
-    public void setShowSequenceFeatures(
-            final boolean showSequenceFeatures) {
-        this._showSequenceFeatures = showSequenceFeatures;
-        this._has_showSequenceFeatures = true;
-    }
-
-    /**
-     * Sets the value of field 'showText'.
-     * 
-     * @param showText the value of field 'showText'.
-     */
-    public void setShowText(
-            final boolean showText) {
-        this._showText = showText;
-        this._has_showText = true;
-    }
-
-    /**
-     * Sets the value of field 'startRes'.
-     * 
-     * @param startRes the value of field 'startRes'.
-     */
-    public void setStartRes(
-            final int startRes) {
-        this._startRes = startRes;
-        this._has_startRes = true;
-    }
-
-    /**
-     * Sets the value of field 'startSeq'.
-     * 
-     * @param startSeq the value of field 'startSeq'.
-     */
-    public void setStartSeq(
-            final int startSeq) {
-        this._startSeq = startSeq;
-        this._has_startSeq = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'wrapAlignment'.
-     * 
-     * @param wrapAlignment the value of field 'wrapAlignment'.
-     */
-    public void setWrapAlignment(
-            final boolean wrapAlignment) {
-        this._wrapAlignment = wrapAlignment;
-        this._has_wrapAlignment = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.binding.Viewport
-     */
-    public static jalview.binding.Viewport unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  public void deleteShowQuality()
+  {
+    this._has_showQuality = false;
+  }
+
+  /**
+     */
+  public void deleteShowSequenceFeatures()
+  {
+    this._has_showSequenceFeatures = false;
+  }
+
+  /**
+     */
+  public void deleteShowText()
+  {
+    this._has_showText = false;
+  }
+
+  /**
+     */
+  public void deleteStartRes()
+  {
+    this._has_startRes = false;
+  }
+
+  /**
+     */
+  public void deleteStartSeq()
+  {
+    this._has_startSeq = false;
+  }
+
+  /**
+     */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+     */
+  public void deleteWrapAlignment()
+  {
+    this._has_wrapAlignment = false;
+  }
+
+  /**
+     */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+     */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Returns the value of field 'bgColour'.
+   * 
+   * @return the value of field 'BgColour'.
+   */
+  public java.lang.String getBgColour()
+  {
+    return this._bgColour;
+  }
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   * 
+   * @return the value of field 'ConsThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  }
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   * 
+   * @return the value of field 'ConservationSelected'.
+   */
+  public boolean getConservationSelected()
+  {
+    return this._conservationSelected;
+  }
+
+  /**
+   * Returns the value of field 'fontName'.
+   * 
+   * @return the value of field 'FontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  }
+
+  /**
+   * Returns the value of field 'fontSize'.
+   * 
+   * @return the value of field 'FontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  }
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   * 
+   * @return the value of field 'FontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   * 
+   * @return the value of field 'PidSelected'.
+   */
+  public boolean getPidSelected()
+  {
+    return this._pidSelected;
+  }
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   * 
+   * @return the value of field 'PidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  }
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   * 
+   * @return the value of field 'RenderGaps'.
+   */
+  public boolean getRenderGaps()
+  {
+    return this._renderGaps;
+  }
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   * 
+   * @return the value of field 'ShowAnnotation'.
+   */
+  public boolean getShowAnnotation()
+  {
+    return this._showAnnotation;
+  }
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   * 
+   * @return the value of field 'ShowBoxes'.
+   */
+  public boolean getShowBoxes()
+  {
+    return this._showBoxes;
+  }
+
+  /**
+   * Returns the value of field 'showColourText'.
+   * 
+   * @return the value of field 'ShowColourText'.
+   */
+  public boolean getShowColourText()
+  {
+    return this._showColourText;
+  }
+
+  /**
+   * Returns the value of field 'showConservation'.
+   * 
+   * @return the value of field 'ShowConservation'.
+   */
+  public boolean getShowConservation()
+  {
+    return this._showConservation;
+  }
+
+  /**
+   * Returns the value of field 'showFullId'.
+   * 
+   * @return the value of field 'ShowFullId'.
+   */
+  public boolean getShowFullId()
+  {
+    return this._showFullId;
+  }
+
+  /**
+   * Returns the value of field 'showIdentity'.
+   * 
+   * @return the value of field 'ShowIdentity'.
+   */
+  public boolean getShowIdentity()
+  {
+    return this._showIdentity;
+  }
+
+  /**
+   * Returns the value of field 'showQuality'.
+   * 
+   * @return the value of field 'ShowQuality'.
+   */
+  public boolean getShowQuality()
+  {
+    return this._showQuality;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   * 
+   * @return the value of field 'ShowSequenceFeatures'.
+   */
+  public boolean getShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  }
+
+  /**
+   * Returns the value of field 'showText'.
+   * 
+   * @return the value of field 'ShowText'.
+   */
+  public boolean getShowText()
+  {
+    return this._showText;
+  }
+
+  /**
+   * Returns the value of field 'startRes'.
+   * 
+   * @return the value of field 'StartRes'.
+   */
+  public int getStartRes()
+  {
+    return this._startRes;
+  }
+
+  /**
+   * Returns the value of field 'startSeq'.
+   * 
+   * @return the value of field 'StartSeq'.
+   */
+  public int getStartSeq()
+  {
+    return this._startSeq;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   * 
+   * @return the value of field 'WrapAlignment'.
+   */
+  public boolean getWrapAlignment()
+  {
+    return this._wrapAlignment;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasConsThreshold.
+   * 
+   * @return true if at least one ConsThreshold has been added
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  }
+
+  /**
+   * Method hasConservationSelected.
+   * 
+   * @return true if at least one ConservationSelected has been added
+   */
+  public boolean hasConservationSelected()
+  {
+    return this._has_conservationSelected;
+  }
+
+  /**
+   * Method hasFontSize.
+   * 
+   * @return true if at least one FontSize has been added
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  }
+
+  /**
+   * Method hasFontStyle.
+   * 
+   * @return true if at least one FontStyle has been added
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasPidSelected.
+   * 
+   * @return true if at least one PidSelected has been added
+   */
+  public boolean hasPidSelected()
+  {
+    return this._has_pidSelected;
+  }
+
+  /**
+   * Method hasPidThreshold.
+   * 
+   * @return true if at least one PidThreshold has been added
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  }
+
+  /**
+   * Method hasRenderGaps.
+   * 
+   * @return true if at least one RenderGaps has been added
+   */
+  public boolean hasRenderGaps()
+  {
+    return this._has_renderGaps;
+  }
+
+  /**
+   * Method hasShowAnnotation.
+   * 
+   * @return true if at least one ShowAnnotation has been added
+   */
+  public boolean hasShowAnnotation()
+  {
+    return this._has_showAnnotation;
+  }
+
+  /**
+   * Method hasShowBoxes.
+   * 
+   * @return true if at least one ShowBoxes has been added
+   */
+  public boolean hasShowBoxes()
+  {
+    return this._has_showBoxes;
+  }
+
+  /**
+   * Method hasShowColourText.
+   * 
+   * @return true if at least one ShowColourText has been added
+   */
+  public boolean hasShowColourText()
+  {
+    return this._has_showColourText;
+  }
+
+  /**
+   * Method hasShowConservation.
+   * 
+   * @return true if at least one ShowConservation has been added
+   */
+  public boolean hasShowConservation()
+  {
+    return this._has_showConservation;
+  }
+
+  /**
+   * Method hasShowFullId.
+   * 
+   * @return true if at least one ShowFullId has been added
+   */
+  public boolean hasShowFullId()
+  {
+    return this._has_showFullId;
+  }
+
+  /**
+   * Method hasShowIdentity.
+   * 
+   * @return true if at least one ShowIdentity has been added
+   */
+  public boolean hasShowIdentity()
+  {
+    return this._has_showIdentity;
+  }
+
+  /**
+   * Method hasShowQuality.
+   * 
+   * @return true if at least one ShowQuality has been added
+   */
+  public boolean hasShowQuality()
+  {
+    return this._has_showQuality;
+  }
+
+  /**
+   * Method hasShowSequenceFeatures.
+   * 
+   * @return true if at least one ShowSequenceFeatures has been added
+   */
+  public boolean hasShowSequenceFeatures()
+  {
+    return this._has_showSequenceFeatures;
+  }
+
+  /**
+   * Method hasShowText.
+   * 
+   * @return true if at least one ShowText has been added
+   */
+  public boolean hasShowText()
+  {
+    return this._has_showText;
+  }
+
+  /**
+   * Method hasStartRes.
+   * 
+   * @return true if at least one StartRes has been added
+   */
+  public boolean hasStartRes()
+  {
+    return this._has_startRes;
+  }
+
+  /**
+   * Method hasStartSeq.
+   * 
+   * @return true if at least one StartSeq has been added
+   */
+  public boolean hasStartSeq()
+  {
+    return this._has_startSeq;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasWrapAlignment.
+   * 
+   * @return true if at least one WrapAlignment has been added
+   */
+  public boolean hasWrapAlignment()
+  {
+    return this._has_wrapAlignment;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   * 
+   * @return the value of field 'ConservationSelected'.
+   */
+  public boolean isConservationSelected()
+  {
+    return this._conservationSelected;
+  }
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   * 
+   * @return the value of field 'PidSelected'.
+   */
+  public boolean isPidSelected()
+  {
+    return this._pidSelected;
+  }
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   * 
+   * @return the value of field 'RenderGaps'.
+   */
+  public boolean isRenderGaps()
+  {
+    return this._renderGaps;
+  }
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   * 
+   * @return the value of field 'ShowAnnotation'.
+   */
+  public boolean isShowAnnotation()
+  {
+    return this._showAnnotation;
+  }
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   * 
+   * @return the value of field 'ShowBoxes'.
+   */
+  public boolean isShowBoxes()
+  {
+    return this._showBoxes;
+  }
+
+  /**
+   * Returns the value of field 'showColourText'.
+   * 
+   * @return the value of field 'ShowColourText'.
+   */
+  public boolean isShowColourText()
+  {
+    return this._showColourText;
+  }
+
+  /**
+   * Returns the value of field 'showConservation'.
+   * 
+   * @return the value of field 'ShowConservation'.
+   */
+  public boolean isShowConservation()
+  {
+    return this._showConservation;
+  }
+
+  /**
+   * Returns the value of field 'showFullId'.
+   * 
+   * @return the value of field 'ShowFullId'.
+   */
+  public boolean isShowFullId()
+  {
+    return this._showFullId;
+  }
+
+  /**
+   * Returns the value of field 'showIdentity'.
+   * 
+   * @return the value of field 'ShowIdentity'.
+   */
+  public boolean isShowIdentity()
+  {
+    return this._showIdentity;
+  }
+
+  /**
+   * Returns the value of field 'showQuality'.
+   * 
+   * @return the value of field 'ShowQuality'.
+   */
+  public boolean isShowQuality()
+  {
+    return this._showQuality;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   * 
+   * @return the value of field 'ShowSequenceFeatures'.
+   */
+  public boolean isShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  }
+
+  /**
+   * Returns the value of field 'showText'.
+   * 
+   * @return the value of field 'ShowText'.
+   */
+  public boolean isShowText()
+  {
+    return this._showText;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   * 
+   * @return the value of field 'WrapAlignment'.
+   */
+  public boolean isWrapAlignment()
+  {
+    return this._wrapAlignment;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'bgColour'.
+   * 
+   * @param bgColour
+   *          the value of field 'bgColour'.
+   */
+  public void setBgColour(final java.lang.String bgColour)
+  {
+    this._bgColour = bgColour;
+  }
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   * 
+   * @param consThreshold
+   *          the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(final int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'conservationSelected'.
+   * 
+   * @param conservationSelected
+   *          the value of field 'conservationSelected'.
+   */
+  public void setConservationSelected(final boolean conservationSelected)
+  {
+    this._conservationSelected = conservationSelected;
+    this._has_conservationSelected = true;
+  }
+
+  /**
+   * Sets the value of field 'fontName'.
+   * 
+   * @param fontName
+   *          the value of field 'fontName'.
+   */
+  public void setFontName(final java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  }
+
+  /**
+   * Sets the value of field 'fontSize'.
+   * 
+   * @param fontSize
+   *          the value of field 'fontSize'.
+   */
+  public void setFontSize(final int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  }
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   * 
+   * @param fontStyle
+   *          the value of field 'fontStyle'.
+   */
+  public void setFontStyle(final int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *          the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * Sets the value of field 'pidSelected'.
+   * 
+   * @param pidSelected
+   *          the value of field 'pidSelected'.
+   */
+  public void setPidSelected(final boolean pidSelected)
+  {
+    this._pidSelected = pidSelected;
+    this._has_pidSelected = true;
+  }
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   * 
+   * @param pidThreshold
+   *          the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(final int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'renderGaps'.
+   * 
+   * @param renderGaps
+   *          the value of field 'renderGaps'.
+   */
+  public void setRenderGaps(final boolean renderGaps)
+  {
+    this._renderGaps = renderGaps;
+    this._has_renderGaps = true;
+  }
+
+  /**
+   * Sets the value of field 'showAnnotation'.
+   * 
+   * @param showAnnotation
+   *          the value of field 'showAnnotation'.
+   */
+  public void setShowAnnotation(final boolean showAnnotation)
+  {
+    this._showAnnotation = showAnnotation;
+    this._has_showAnnotation = true;
+  }
+
+  /**
+   * Sets the value of field 'showBoxes'.
+   * 
+   * @param showBoxes
+   *          the value of field 'showBoxes'.
+   */
+  public void setShowBoxes(final boolean showBoxes)
+  {
+    this._showBoxes = showBoxes;
+    this._has_showBoxes = true;
+  }
+
+  /**
+   * Sets the value of field 'showColourText'.
+   * 
+   * @param showColourText
+   *          the value of field 'showColourText'.
+   */
+  public void setShowColourText(final boolean showColourText)
+  {
+    this._showColourText = showColourText;
+    this._has_showColourText = true;
+  }
+
+  /**
+   * Sets the value of field 'showConservation'.
+   * 
+   * @param showConservation
+   *          the value of field 'showConservation'
+   */
+  public void setShowConservation(final boolean showConservation)
+  {
+    this._showConservation = showConservation;
+    this._has_showConservation = true;
+  }
+
+  /**
+   * Sets the value of field 'showFullId'.
+   * 
+   * @param showFullId
+   *          the value of field 'showFullId'.
+   */
+  public void setShowFullId(final boolean showFullId)
+  {
+    this._showFullId = showFullId;
+    this._has_showFullId = true;
+  }
+
+  /**
+   * Sets the value of field 'showIdentity'.
+   * 
+   * @param showIdentity
+   *          the value of field 'showIdentity'.
+   */
+  public void setShowIdentity(final boolean showIdentity)
+  {
+    this._showIdentity = showIdentity;
+    this._has_showIdentity = true;
+  }
+
+  /**
+   * Sets the value of field 'showQuality'.
+   * 
+   * @param showQuality
+   *          the value of field 'showQuality'.
+   */
+  public void setShowQuality(final boolean showQuality)
+  {
+    this._showQuality = showQuality;
+    this._has_showQuality = true;
+  }
+
+  /**
+   * Sets the value of field 'showSequenceFeatures'.
+   * 
+   * @param showSequenceFeatures
+   *          the value of field 'showSequenceFeatures'.
+   */
+  public void setShowSequenceFeatures(final boolean showSequenceFeatures)
+  {
+    this._showSequenceFeatures = showSequenceFeatures;
+    this._has_showSequenceFeatures = true;
+  }
+
+  /**
+   * Sets the value of field 'showText'.
+   * 
+   * @param showText
+   *          the value of field 'showText'.
+   */
+  public void setShowText(final boolean showText)
+  {
+    this._showText = showText;
+    this._has_showText = true;
+  }
+
+  /**
+   * Sets the value of field 'startRes'.
+   * 
+   * @param startRes
+   *          the value of field 'startRes'.
+   */
+  public void setStartRes(final int startRes)
+  {
+    this._startRes = startRes;
+    this._has_startRes = true;
+  }
+
+  /**
+   * Sets the value of field 'startSeq'.
+   * 
+   * @param startSeq
+   *          the value of field 'startSeq'.
+   */
+  public void setStartSeq(final int startSeq)
+  {
+    this._startSeq = startSeq;
+    this._has_startSeq = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *          the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *          the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'wrapAlignment'.
+   * 
+   * @param wrapAlignment
+   *          the value of field 'wrapAlignment'.
+   */
+  public void setWrapAlignment(final boolean wrapAlignment)
+  {
+    this._wrapAlignment = wrapAlignment;
+    this._has_wrapAlignment = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *          the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *          the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Viewport
+   */
+  public static jalview.binding.Viewport unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Viewport) Unmarshaller.unmarshal(
+            jalview.binding.Viewport.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 2d3a8d8..4b21137 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -307,8 +307,7 @@ public class EditCommand implements CommandI
    * @param performEdit
    */
   final public void appendEdit(Action command, SequenceI[] seqs,
-          int position,
-          int number, AlignmentI al, boolean performEdit)
+          int position, int number, AlignmentI al, boolean performEdit)
   {
     appendEdit(command, seqs, position, number, al, performEdit, null);
   }
@@ -326,8 +325,8 @@ public class EditCommand implements CommandI
    * @param views
    */
   final public void appendEdit(Action command, SequenceI[] seqs,
-          int position,
-          int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
+          int position, int number, AlignmentI al, boolean performEdit,
+          AlignmentI[] views)
   {
     Edit edit = new Edit(command, seqs, position, number,
             al.getGapCharacter());
@@ -432,7 +431,7 @@ public class EditCommand implements CommandI
    */
   @Override
   final public void undoCommand(AlignmentI[] views)
-  { 
+  {
     ListIterator iterator = edits.listIterator(edits.size());
     while (iterator.hasPrevious())
     {
@@ -474,8 +473,8 @@ public class EditCommand implements CommandI
 
     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);
       // System.out.println("pos: "+command.position+" number: "+command.number);
     }
 
@@ -560,8 +559,8 @@ public class EditCommand implements CommandI
                     command,
                     i,
                     sequence.findPosition(command.position),
-                    sequence.findPosition(command.position
-                            + command.number), false);
+                    sequence.findPosition(command.position + command.number),
+                    false);
           }
         }
       }
@@ -1045,7 +1044,7 @@ public class EditCommand implements CommandI
           int copylen = Math.min(command.position,
                   annotations[a].annotations.length);
           if (copylen > 0)
-           {
+          {
             System.arraycopy(annotations[a].annotations, 0, temp, 0,
                     copylen); // command.position);
           }
@@ -1117,8 +1116,7 @@ public class EditCommand implements CommandI
       if (command.editedFeatures != null
               && command.editedFeatures.containsKey(seq))
       {
-        sequence.setSequenceFeatures(command.editedFeatures
-                .get(seq));
+        sequence.setSequenceFeatures(command.editedFeatures.get(seq));
       }
 
       return;
@@ -1265,8 +1263,7 @@ public class EditCommand implements CommandI
           if (action == Action.DELETE_GAP)
           {
             preEdit.setSequence(new String(StringUtils.insertCharAt(
-                    preEdit.getSequence(), position,
-                    number, gap)));
+                    preEdit.getSequence(), position, number, gap)));
           }
           else if (action == Action.INSERT_GAP)
           {
diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index 490dc4a..3266874 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -88,8 +88,7 @@ public class RemoveGapColCommand extends EditCommand
       if (!delete && startCol > -1)
       {
         this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
-                endCol
-                - startCol, al, false, null);
+                endCol - startCol, al, false, null);
 
         columnsDeleted += (endCol - startCol);
         startCol = -1;
@@ -103,8 +102,7 @@ public class RemoveGapColCommand extends EditCommand
       // end of the alignment
 
       this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
-              end
-              - startCol + 1, al, false, null);
+              end - startCol + 1, al, false, null);
 
       columnsDeleted += (end - startCol + 1);
     }
diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index db1725b..c8dadfa 100644
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -109,9 +109,9 @@ public class RemoveGapsCommand extends EditCommand
 
         if (!delete && startCol > -1)
         {
-          this.appendEdit(Action.DELETE_GAP, new SequenceI[]
-          { seqs[s] }, start + startCol - deletedCols, endCol - startCol,
-                  al, false, null);
+          this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
+                  start + startCol - deletedCols, endCol - startCol, al,
+                  false, null);
 
           deletedCols += (endCol - startCol);
           startCol = -1;
@@ -120,8 +120,8 @@ public class RemoveGapsCommand extends EditCommand
       }
       if (delete && startCol > -1)
       {
-        this.appendEdit(Action.DELETE_GAP, new SequenceI[]
-        { seqs[s] }, start + startCol - deletedCols, jSize - startCol, al,
+        this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
+                start + startCol - deletedCols, jSize - startCol, al,
                 false, null);
       }
 
diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 3be32bb..a39dc80 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -86,20 +86,23 @@ public class AlignViewController implements AlignViewControllerI
     if (sg != null
             && (cs == null || cs.getSelected() == null || cs.size() == 0))
     {
-      gps = jalview.analysis.Grouping.makeGroupsFrom(
-              viewport.getSequenceSelection(),
-              viewport.getAlignmentView(true).getSequenceStrings(
-                      viewport.getGapCharacter()), viewport.getAlignment()
-                      .getGroups());
-    } else {
-      if (cs!=null) {
+      gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
+              .getSequenceSelection(), viewport.getAlignmentView(true)
+              .getSequenceStrings(viewport.getGapCharacter()), viewport
+              .getAlignment().getGroups());
+    }
+    else
+    {
+      if (cs != null)
+      {
         gps = jalview.analysis.Grouping.makeGroupsFromCols(
                 (sg == null) ? viewport.getAlignment().getSequencesArray()
                         : sg.getSequences().toArray(new SequenceI[0]), cs,
                 viewport.getAlignment().getGroups());
       }
     }
-    if (gps!=null) {
+    if (gps != null)
+    {
       viewport.getAlignment().deleteAllGroups();
       viewport.clearSequenceColours();
       viewport.setSelectionGroup(null);
@@ -289,17 +292,22 @@ public class AlignViewController implements AlignViewControllerI
       }
       viewport.setColumnSelection(cs);
       alignPanel.paintAlignment(true);
-      avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
-    		  new String[]{
-    	  			(toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
-    	  			(invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
-    	  			featureType, Integer.valueOf(nseq).toString()
-      		 	}));
+      avcg.setStatus(MessageManager.formatMessage(
+              "label.view_controller_toggled_marked",
+              new String[] {
+                  (toggle ? MessageManager.getString("label.toggled")
+                          : MessageManager.getString("label.marked")),
+                  (invert ? (Integer.valueOf((alw - alStart)
+                          - bs.cardinality()).toString()) : (Integer
+                          .valueOf(bs.cardinality()).toString())),
+                  featureType, Integer.valueOf(nseq).toString() }));
       return true;
     }
     else
     {
-      avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
+      avcg.setStatus(MessageManager.formatMessage(
+              "label.no_feature_of_type_found",
+              new String[] { featureType }));
       if (!extendCurrent && cs != null)
       {
         cs.clear();
@@ -309,8 +317,6 @@ public class AlignViewController implements AlignViewControllerI
     }
   }
 
-
-
   @Override
   public void sortAlignmentByFeatureDensity(String[] typ)
   {
@@ -322,10 +328,10 @@ public class AlignViewController implements AlignViewControllerI
     FeatureRenderer fr = alignPanel.getFeatureRenderer();
     if (typ == null)
     {
-      typ = fr==null ? null : fr.getDisplayedFeatureTypes();
+      typ = fr == null ? null : fr.getDisplayedFeatureTypes();
     }
     String gps[] = null;
-    gps = fr==null ? null : fr.getDisplayedFeatureGroups();
+    gps = fr == null ? null : fr.getDisplayedFeatureGroups();
     if (typ != null)
     {
       ArrayList types = new ArrayList();
diff --git a/src/jalview/controller/FeatureSettingsController.java b/src/jalview/controller/FeatureSettingsController.java
index 7dd1399..68d717b 100644
--- a/src/jalview/controller/FeatureSettingsController.java
+++ b/src/jalview/controller/FeatureSettingsController.java
@@ -4,10 +4,12 @@ import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsModelI;
 
 public class FeatureSettingsController // implements
-                                       // jalview.api.FeatureSettingsControllerI
+// jalview.api.FeatureSettingsControllerI
 {
   FeatureSettingsControllerGuiI settingUI;
+
   FeatureRenderer fr;
+
   FeatureSettingsModelI fsettings;
-  
+
 }
diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index eb977bc..627f0a6 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -20,12 +20,12 @@
  */
 package jalview.datamodel;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Stores mapping between the columns of a protein alignment and a DNA alignment
  * and a list of individual codon to amino acid mappings between sequences.
@@ -373,7 +373,8 @@ public class AlignedCodonFrame
       if (dnaSeqs[mi] == targetDs && dnaToProt[mi].to == sourceDs)
       {
         int[] codon = dnaToProt[mi].map.locateInFrom(pos, pos);
-        if (codon != null) {
+        if (codon != null)
+        {
           return codon;
         }
       }
@@ -422,8 +423,7 @@ public class AlignedCodonFrame
      * Read off the mapped nucleotides (converting to position base 0)
      */
     codonPos = MappingUtils.flattenRanges(codonPos);
-    return new char[]
-    { dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
+    return new char[] { dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
         dnaSeq[codonPos[2] - 1] };
   }
 
@@ -444,7 +444,7 @@ public class AlignedCodonFrame
     List related = new ArrayList();
     SequenceI seqDs = seq.getDatasetSequence();
     seqDs = seqDs != null ? seqDs : seq;
-  
+
     for (int ds = 0; ds < dnaSeqs.length; ds++)
     {
       final Mapping mapping = dnaToProt[ds];
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 5d1fc60..7ea9985 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -147,7 +147,9 @@ public class Alignment implements AlignmentI
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
-    throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
+    throw new Error(
+            MessageManager
+                    .getString("error.alignment_cigararray_not_implemented"));
     // this(compactAlignment.refCigars);
   }
 
@@ -236,8 +238,7 @@ public class Alignment implements AlignmentI
     }
     if (sequences == null)
     {
-      initAlignment(new SequenceI[]
-      { snew });
+      initAlignment(new SequenceI[] { snew });
     }
     else
     {
@@ -1588,38 +1589,37 @@ public class Alignment implements AlignmentI
     }
   }
 
+  private SequenceI seqrep = null;
 
- private SequenceI seqrep=null;
-
- /**
-  * 
-  * @return the representative sequence for this group
-  */
- public SequenceI getSeqrep()
- {
-   return seqrep;
- }
+  /**
+   * 
+   * @return the representative sequence for this group
+   */
+  public SequenceI getSeqrep()
+  {
+    return seqrep;
+  }
 
- /**
-  * set the representative sequence for this group. Note - this affects the
-  * interpretation of the Hidereps attribute.
-  * 
-  * @param seqrep
-  *          the seqrep to set (null means no sequence representative)
-  */
- public void setSeqrep(SequenceI seqrep)
- {
-   this.seqrep = seqrep;
- }
+  /**
+   * set the representative sequence for this group. Note - this affects the
+   * interpretation of the Hidereps attribute.
+   * 
+   * @param seqrep
+   *          the seqrep to set (null means no sequence representative)
+   */
+  public void setSeqrep(SequenceI seqrep)
+  {
+    this.seqrep = seqrep;
+  }
 
- /**
-  * 
-  * @return true if group has a sequence representative
-  */
- public boolean hasSeqrep()
- {
-   return seqrep != null;
- }
+  /**
+   * 
+   * @return true if group has a sequence representative
+   */
+  public boolean hasSeqrep()
+  {
+    return seqrep != null;
+  }
 
   @Override
   public int getEndRes()
@@ -1678,7 +1678,7 @@ public class Alignment implements AlignmentI
    * @param preserveUnmappedGaps
    *          if true, gaps within and between unmapped codons are preserved
    */
-//  @Override
+  // @Override
   public int alignAs(AlignmentI al, boolean preserveMappedGaps,
           boolean preserveUnmappedGaps)
   {
@@ -1693,9 +1693,8 @@ public class Alignment implements AlignmentI
 
     char thisGapChar = this.getGapCharacter();
     String gap = thisIsNucleotide && thatIsProtein ? String
-            .valueOf(new char[]
-            { thisGapChar, thisGapChar, thisGapChar }) : String
-            .valueOf(thisGapChar);
+            .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
+            : String.valueOf(thisGapChar);
 
     // TODO handle intron regions? Needs a 'holistic' alignment of dna,
     // not just sequence by sequence. But how to 'gap' intron regions?
@@ -1705,8 +1704,8 @@ public class Alignment implements AlignmentI
      */
     for (SequenceI alignTo : getSequences())
     {
-      count += AlignmentUtils.alignSequenceAs(alignTo, al, gap, preserveMappedGaps,
-              preserveUnmappedGaps) ? 1 : 0;
+      count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
+              preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
     }
     return count;
   }
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 322fd54..bb45b67 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,6 +20,10 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -28,10 +32,6 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 /**
  * DOCUMENT ME!
  * 
@@ -164,6 +164,7 @@ public class AlignmentAnnotation
     }
     setScore(mxval);
   }
+
   /**
    * map of positions in the associated annotation
    */
@@ -692,10 +693,10 @@ public class AlignmentAnnotation
     this.scaleColLabel = annotation.scaleColLabel;
     this.showAllColLabels = annotation.showAllColLabels;
     this.calcId = annotation.calcId;
-    if (annotation.properties!=null)
+    if (annotation.properties != null)
     {
-      properties = new HashMap();
-      for (Map.Entry val:annotation.properties.entrySet())
+      properties = new HashMap();
+      for (Map.Entry val : annotation.properties.entrySet())
       {
         properties.put(val.getKey(), val.getValue());
       }
@@ -1042,7 +1043,8 @@ public class AlignmentAnnotation
     {
       if (sequenceRef != null)
       {
-        boolean rIsDs=sequenceRef.getDatasetSequence()==null,tIsDs=sequenceI.getDatasetSequence()==null;
+        boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI
+                .getDatasetSequence() == null;
         if (sequenceRef != sequenceI
                 && (rIsDs && !tIsDs && sequenceRef != sequenceI
                         .getDatasetSequence())
@@ -1238,8 +1240,10 @@ public class AlignmentAnnotation
   {
     if (sp2sq.getMappedWidth() != sp2sq.getWidth())
     {
-      // TODO: employ getWord/MappedWord to transfer annotation between cDNA and Protein reference frames
-      throw new Error("liftOver currently not implemented for transfer of annotation between different types of seqeunce");
+      // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
+      // Protein reference frames
+      throw new Error(
+              "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
     }
     boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
             .getTo() == sq.getDatasetSequence()) : false;
@@ -1354,9 +1358,9 @@ public class AlignmentAnnotation
 
   public void setProperty(String property, String value)
   {
-    if (properties==null)
+    if (properties == null)
     {
-      properties = new HashMap();
+      properties = new HashMap();
     }
     properties.put(property, value);
   }
diff --git a/src/jalview/datamodel/AlignmentExportData.java b/src/jalview/datamodel/AlignmentExportData.java
index ff550ea..35a8c61 100644
--- a/src/jalview/datamodel/AlignmentExportData.java
+++ b/src/jalview/datamodel/AlignmentExportData.java
@@ -2,7 +2,6 @@ package jalview.datamodel;
 
 import jalview.api.AlignExportSettingI;
 
-
 public class AlignmentExportData
 {
   private AlignmentI alignment;
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 8194bf0..de79488 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -473,9 +473,8 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * @return existing annotation matching the given attributes
    */
-  AlignmentAnnotation findOrCreateAnnotation(String name,
-          String calcId, boolean autoCalc, SequenceI seqRef,
-          SequenceGroup groupRef);
+  AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
+          boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
 
   /**
    * move the given group up or down in the alignment by the given number of
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index e089a11..756a116 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -47,7 +47,7 @@ public class AlignmentView
    * one or more ScGroup objects, which are referenced by each seqCigar's group
    * membership
    */
-  private List scGroups=null;
+  private List scGroups = null;
 
   private boolean isNa = false;
 
@@ -133,7 +133,7 @@ public class AlignmentView
       selseqs = alignment.getSequencesArray();
     }
 
-    List> seqsets=new ArrayList>();
+    List> seqsets = new ArrayList>();
     // get the alignment's group list and make a copy
     List grps = new ArrayList();
     List gg = alignment.getGroups();
@@ -241,7 +241,9 @@ public class AlignmentView
   {
     if (!seqcigararray.isSeqCigarArray())
     {
-      throw new Error(MessageManager.getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
     }
     // contigs = seqcigararray.applyDeletions();
     contigs = seqcigararray.getDeletedRegions();
@@ -298,8 +300,7 @@ public class AlignmentView
   {
     ColumnSelection colsel = new ColumnSelection();
 
-    return new Object[]
-    {
+    return new Object[] {
         SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
                 contigs), colsel };
   }
@@ -663,7 +664,9 @@ public class AlignmentView
   {
     if (sequences == null || width <= 0)
     {
-      throw new Error(MessageManager.getString("error.empty_view_cannot_be_updated"));
+      throw new Error(
+              MessageManager
+                      .getString("error.empty_view_cannot_be_updated"));
     }
     if (nvismsa == null)
     {
@@ -693,7 +696,17 @@ public class AlignmentView
               j++;
               if (mseq.length != sequences.length)
               {
-                throw new Error(MessageManager.formatMessage("error.mismatch_between_number_of_sequences_in_block", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(mseq.length).toString(),Integer.valueOf(sequences.length).toString() }));
+                throw new Error(
+                        MessageManager
+                                .formatMessage(
+                                        "error.mismatch_between_number_of_sequences_in_block",
+                                        new String[] {
+                                            Integer.valueOf(j).toString(),
+                                            Integer.valueOf(mseq.length)
+                                                    .toString(),
+                                            Integer.valueOf(
+                                                    sequences.length)
+                                                    .toString() }));
               }
               swidth = mseq[0].getLength(); // JBPNote: could ensure padded
               // here.
@@ -846,25 +859,30 @@ public class AlignmentView
               else
               {
                 // place gaps.
-                throw new Error(MessageManager.getString("error.padding_not_yet_implemented"));
+                throw new Error(
+                        MessageManager
+                                .getString("error.padding_not_yet_implemented"));
               }
             }
           }
         }
       }
-      return new Object[]
-      { alignment, columnselection };
+      return new Object[] { alignment, columnselection };
     }
     else
     {
       if (nvismsa.length != 1)
       {
-        throw new Error(MessageManager.formatMessage("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", new String[]{Integer.valueOf(nvismsa.length).toString()}));
+        throw new Error(
+                MessageManager
+                        .formatMessage(
+                                "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",
+                                new String[] { Integer.valueOf(
+                                        nvismsa.length).toString() }));
       }
       if (nvismsa[0] != null)
       {
-        return new Object[]
-        { nvismsa[0], new ColumnSelection() };
+        return new Object[] { nvismsa[0], new ColumnSelection() };
       }
       else
       {
@@ -925,8 +943,7 @@ public class AlignmentView
     }
     else
     {
-      return new int[]
-      { 0, width };
+      return new int[] { 0, width };
     }
   }
 
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index baec986..ed57dce 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -20,7 +20,8 @@
  */
 package jalview.datamodel;
 
-import jalview.schemes.*;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.ScoreMatrix;
 
 /**
  * Encode a sequence as a numeric vector using either classic residue binary
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index ebc7cd1..f6e5862 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -97,8 +97,7 @@ public class CigarArray extends CigarBase
   private static int[] _calcStartEndBounds(AlignmentI alignment,
           SequenceGroup selectionGroup)
   {
-    int[] startend = new int[]
-    { 0, 0, 0 };
+    int[] startend = new int[] { 0, 0, 0 };
     if (selectionGroup != null)
     {
       startend[0] = selectionGroup.getSize();
@@ -343,8 +342,11 @@ public class CigarArray extends CigarBase
           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
+        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);
diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index 1506cee..bcf8596 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -22,7 +22,7 @@ package jalview.datamodel;
 
 import jalview.util.MessageManager;
 
-import java.util.*;
+import java.util.Vector;
 
 public abstract class CigarBase
 {
@@ -101,8 +101,7 @@ public abstract class CigarBase
       case D:
         if (!consecutive_del)
         {
-          deletions[++delcount] = new int[]
-          { cursor, 0, alcursor };
+          deletions[++delcount] = new int[] { cursor, 0, alcursor };
         }
         cursor += range[i];
         deletions[delcount][1] = cursor - 1;
@@ -146,7 +145,9 @@ public abstract class CigarBase
         endpos = alcursor;
         break;
       default:
-        throw new Error(MessageManager.formatMessage("error.unknown_seq_cigar_operation", new String[]{new StringBuffer(operation[i]).toString()}));
+        throw new Error(MessageManager.formatMessage(
+                "error.unknown_seq_cigar_operation",
+                new String[] { new StringBuffer(operation[i]).toString() }));
       }
     }
     if (++delcount > 0)
@@ -155,9 +156,8 @@ public abstract class CigarBase
       System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
     }
     deletions = null;
-    return new Object[]
-    { ((reference != null) ? sq.toString() : null), new int[]
-    { start, startpos, end, endpos }, trunc_deletions };
+    return new Object[] { ((reference != null) ? sq.toString() : null),
+        new int[] { start, startpos, end, endpos }, trunc_deletions };
   }
 
   protected void compact_operations()
@@ -225,7 +225,9 @@ public abstract class CigarBase
       } while (c >= '0' && c <= '9' && j < l);
       if (j >= l && c >= '0' && c <= '9')
       {
-        throw new Exception(MessageManager.getString("exception.unterminated_cigar_string"));
+        throw new Exception(
+                MessageManager
+                        .getString("exception.unterminated_cigar_string"));
       }
       try
       {
@@ -234,7 +236,9 @@ public abstract class CigarBase
         i = j;
       } catch (Exception e)
       {
-        throw new Error(MessageManager.getString("error.implementation_bug_parse_cigar_string"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_bug_parse_cigar_string"));
       }
       if (c >= 'a' && c <= 'z')
       {
@@ -246,15 +250,13 @@ public abstract class CigarBase
       }
       else
       {
-        throw new Exception(MessageManager.formatMessage("exception.unexpected_operation_cigar_string_pos", new String[]{
-        		new StringBuffer(c).toString(),
-        		Integer.valueOf(i).toString(),
-        		cigarString
-        }));
+        throw new Exception(MessageManager.formatMessage(
+                "exception.unexpected_operation_cigar_string_pos",
+                new String[] { new StringBuffer(c).toString(),
+                    Integer.valueOf(i).toString(), cigarString }));
       }
     }
-    return new Object[]
-    { operation, range };
+    return new Object[] { operation, range };
   }
 
   /**
@@ -273,7 +275,9 @@ public abstract class CigarBase
     }
     if (op != M && op != D && op != I)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_invalid_operation_string"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_invalid_operation_string"));
     }
     if (range == 0)
     {
@@ -281,7 +285,8 @@ public abstract class CigarBase
     }
     if (range < 0)
     {
-      throw new Error(MessageManager.getString("error.invalid_range_string"));
+      throw new Error(
+              MessageManager.getString("error.invalid_range_string"));
     }
     int lngth = 0;
     if (operation == null)
@@ -393,7 +398,9 @@ public abstract class CigarBase
     }
     if (start < 0 || start > end)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_delete_range_out_of_bounds"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_delete_range_out_of_bounds"));
     }
     // find beginning
     int cursor = 0; // mark the position for the current operation being edited.
@@ -465,9 +472,13 @@ public abstract class CigarBase
           }
           break;
         case D:
-          throw new Error(MessageManager.getString("error.implementation_error")); // do nothing;
+          throw new Error(
+                  MessageManager.getString("error.implementation_error")); // do
+                                                                           // nothing;
         default:
-          throw new Error(MessageManager.formatMessage("error.implementation_error_unknown_operation", new String[]{new StringBuffer(oldops[o]).toString()}));
+          throw new Error(MessageManager.formatMessage(
+                  "error.implementation_error_unknown_operation",
+                  new String[] { new StringBuffer(oldops[o]).toString() }));
         }
         rlength -= remain;
         remain = oldrange[++o]; // number of op characters left to edit
@@ -526,8 +537,7 @@ public abstract class CigarBase
         vcursor += range[i];
         break;
       case D:
-        dr.addElement(new int[]
-        { vcursor, cursor, range[i] });
+        dr.addElement(new int[] { vcursor, cursor, range[i] });
         cursor += range[i];
       }
     }
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 3916b7d..57db830 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -486,6 +486,7 @@ public class ColumnSelection
 
   /**
    * This Method is used to return all the HiddenColumn regions
+   * 
    * @return empty list or List of hidden column intervals
    */
   public List getHiddenColumns()
@@ -666,8 +667,7 @@ public class ColumnSelection
       }
       else if (end < region[0] && start < region[0])
       {
-        hiddenColumns.insertElementAt(new int[]
-        { start, end }, i);
+        hiddenColumns.insertElementAt(new int[] { start, end }, i);
         added = true;
         break;
       }
@@ -679,8 +679,7 @@ public class ColumnSelection
     }
     else if (!added)
     {
-      hiddenColumns.addElement(new int[]
-      { start, end });
+      hiddenColumns.addElement(new int[] { start, end });
     }
 
   }
@@ -909,16 +908,14 @@ public class ColumnSelection
         }
         if (hideStart > vstart)
         {
-          visiblecontigs.add(new int[]
-          { vstart, hideStart - 1 });
+          visiblecontigs.add(new int[] { vstart, hideStart - 1 });
         }
         vstart = hideEnd + 1;
       }
 
       if (vstart < end)
       {
-        visiblecontigs.add(new int[]
-        { vstart, end - 1 });
+        visiblecontigs.add(new int[] { vstart, end - 1 });
       }
       int[] vcontigs = new int[visiblecontigs.size() * 2];
       for (int i = 0, j = visiblecontigs.size(); i < j; i++)
@@ -933,8 +930,7 @@ public class ColumnSelection
     }
     else
     {
-      return new int[]
-      { start, end - 1 };
+      return new int[] { start, end - 1 };
     }
   }
 
@@ -975,7 +971,7 @@ public class ColumnSelection
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       // then mangle the alignmentAnnotation annotation array
-      Vector annels = new Vector();
+      Vector annels = new Vector();
       Annotation[] els = null;
       List regions = getHiddenColumns();
       int blockStart = start, blockEnd = end;
@@ -1035,7 +1031,7 @@ public class ColumnSelection
       alignmentAnnotation.annotations = new Annotation[w];
       w = 0;
 
-        for (Annotation [] chnk : annels)
+      for (Annotation[] chnk : annels)
       {
         System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
                 chnk.length);
@@ -1284,7 +1280,7 @@ public class ColumnSelection
   {
     return hiddenColumns != null && hiddenColumns.size() > 0;
   }
-  
+
   /**
    * 
    * @return true if there are more than one set of columns hidden
@@ -1308,7 +1304,7 @@ public class ColumnSelection
       hideColumns(r[0], r[1]);
     }
   }
-  
+
   public boolean filterAnnotations(Annotation[] annotations,
           AnnotationFilterParameter filterParams)
   {
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 6982594..6a676cf 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -44,7 +44,7 @@ public class DBRefSource
    * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
    */
   public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
-  
+
   public static final String EMBLCDSProduct = "EMBLCDSProtein"
           .toUpperCase();
 
@@ -81,23 +81,19 @@ public class DBRefSource
   /**
    * List of databases whose sequences might have coding regions annotated
    */
-  public static final String[] DNACODINGDBS =
-  { EMBL, EMBLCDS, GENEDB };
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB };
 
-  public static final String[] CODINGDBS =
-  { EMBLCDS, GENEDB };
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB };
 
-  public static final String[] PROTEINDBS =
-  { UNIPROT, PDB, UNIPROTKB, EMBLCDSProduct };
+  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+      EMBLCDSProduct };
 
-  public static final String[] PROTEINSEQ =
-  { UNIPROT, UNIPROTKB, EMBLCDSProduct };
+  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
+      EMBLCDSProduct };
 
-  public static final String[] PROTEINSTR =
-  { PDB };
+  public static final String[] PROTEINSTR = { PDB };
 
-  public static final String[] DOMAINDBS =
-  { PFAM, RFAM };
+  public static final String[] DOMAINDBS = { PFAM, RFAM };
 
   /**
    * set of unique DBRefSource property constants. These could be used to
diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index d7b7eb9..1272538 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -20,12 +20,12 @@
  */
 package jalview.datamodel;
 
+import jalview.util.MapList;
+
 import java.util.Iterator;
 import java.util.NoSuchElementException;
 import java.util.Vector;
 
-import jalview.util.MapList;
-
 public class Mapping
 {
   /**
@@ -163,7 +163,8 @@ public class Mapping
     {
       // TODO should ideally handle toRatio other than 1 as well...
       // i.e. code like getNextCodon()
-      if (toPosition <= currentToRange[1]) {
+      if (toPosition <= currentToRange[1])
+      {
         char pep = Mapping.this.to.getSequence()[toPosition - 1];
         toPosition++;
         return String.valueOf(pep);
@@ -466,8 +467,7 @@ public class Mapping
       int[] mp = map.shiftFrom(pos);
       if (mp != null)
       {
-        return new int[]
-        { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
+        return new int[] { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
       }
     }
     return null;
@@ -528,8 +528,7 @@ public class Mapping
       }
     }
     // give up and just return the feature.
-    return new SequenceFeature[]
-    { f };
+    return new SequenceFeature[] { f };
   }
 
   /**
@@ -565,8 +564,7 @@ public class Mapping
       }
       return map.locateInFrom(from, to);
     }
-    return new int[]
-    { from, to };
+    return new int[] { from, to };
   }
 
   /**
@@ -602,8 +600,7 @@ public class Mapping
       }
       return map.locateInTo(from, to);
     }
-    return new int[]
-    { from, to };
+    return new int[] { from, to };
   }
 
   /**
@@ -631,13 +628,11 @@ public class Mapping
         {
           for (int m = 0; m < mpr.length; m += 2)
           {
-            toRange.addElement(new int[]
-            { mpr[m], mpr[m + 1] });
+            toRange.addElement(new int[] { mpr[m], mpr[m + 1] });
             int[] xpos = locateRange(mpr[m], mpr[m + 1]);
             for (int x = 0; x < xpos.length; x += 2)
             {
-              fromRange.addElement(new int[]
-              { xpos[x], xpos[x + 1] });
+              fromRange.addElement(new int[] { xpos[x], xpos[x + 1] });
             }
           }
         }
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index d0cef5d..589bc7b 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -36,6 +36,7 @@ public class PDBEntry
   {
     PDB, FILE
   }
+
   Hashtable properties;
 
   /*
@@ -55,9 +56,8 @@ public class PDBEntry
       return true;
     }
     PDBEntry o = (PDBEntry) obj;
-    return
-    (type == o.type || (type != null && o.type != null && o.type
-                    .equals(type)))
+    return (type == o.type || (type != null && o.type != null && o.type
+            .equals(type)))
             && (id == o.id || (id != null && o.id != null && o.id
                     .equalsIgnoreCase(id)))
             && (chainCode == o.chainCode || (chainCode != null
@@ -66,7 +66,7 @@ public class PDBEntry
             && (properties == o.properties || (properties != null
                     && o.properties != null && properties
                       .equals(o.properties)));
-    
+
   }
 
   /**
@@ -86,7 +86,7 @@ public class PDBEntry
   // this.file = filePath;
   // this.id = pdbId;
   // }
-  
+
   public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
           String filePath)
   {
@@ -127,6 +127,7 @@ public class PDBEntry
   {
     this.type = t;
   }
+
   public void setType(PDBEntry.Type type)
   {
     this.type = type == null ? null : type.toString();
diff --git a/src/jalview/datamodel/Provenance.java b/src/jalview/datamodel/Provenance.java
index 54842d0..a1a821e 100755
--- a/src/jalview/datamodel/Provenance.java
+++ b/src/jalview/datamodel/Provenance.java
@@ -20,7 +20,7 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.Vector;
 
 public class Provenance
 {
diff --git a/src/jalview/datamodel/RnaViewerModel.java b/src/jalview/datamodel/RnaViewerModel.java
index 33783ec..e6ec786 100644
--- a/src/jalview/datamodel/RnaViewerModel.java
+++ b/src/jalview/datamodel/RnaViewerModel.java
@@ -1,6 +1,5 @@
 package jalview.datamodel;
 
-
 /**
  * A data bean class to hold properties of an RNA viewer
  */
@@ -32,8 +31,7 @@ public class RnaViewerModel
    * @param dividerLocation
    */
   public RnaViewerModel(String viewId, String title, int xpos, int ypos,
-          int width,
- int height, int dividerLocation)
+          int width, int height, int dividerLocation)
   {
     this.viewId = viewId;
     this.title = title;
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 3329431..ad0e472 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -232,8 +232,7 @@ public class SearchResults
 
           if (result == null)
           {
-            result = new int[]
-            { matchStart, matchEnd };
+            result = new int[] { matchStart, matchEnd };
           }
           else
           {
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 09b2e89..d279a26 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -20,14 +20,14 @@
  */
 package jalview.datamodel;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
-
 import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
 import jalview.util.MessageManager;
 import jalview.util.ShiftList;
 
+import java.util.Enumeration;
+import java.util.Hashtable;
+
 public class SeqCigar extends CigarSimple
 {
   /**
@@ -95,7 +95,9 @@ public class SeqCigar extends CigarSimple
             refseq.getSequenceAsString(start, end), GapChar);
     if (edit_result == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
     }
     int bounds[] = (int[]) edit_result[1];
     seq = new Sequence(refseq.getName(), (String) edit_result[0],
@@ -143,11 +145,15 @@ public class SeqCigar extends CigarSimple
     boolean hasgaps = false;
     if (seq == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_set_seq_null"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_set_seq_null"));
     }
     if (_s < 0)
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_s", new String[]{Integer.valueOf(_s).toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_s", new String[] { Integer
+                      .valueOf(_s).toString() }));
     }
     String seq_string = seq.getSequenceAsString();
     if (_e == 0 || _e < _s || _e > seq_string.length())
@@ -213,7 +219,9 @@ public class SeqCigar extends CigarSimple
     // Check offsets
     if (end > ds.getLength())
     {
-      throw new Error(MessageManager.getString("error.implementation_error_seqcigar_possible"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_seqcigar_possible"));
       // end = ds.getLength();
     }
 
@@ -237,11 +245,14 @@ public class SeqCigar extends CigarSimple
     super();
     if (seq == null)
     {
-      throw new Error(MessageManager.getString("error.implmentation_bug_seq_null"));
+      throw new Error(
+              MessageManager.getString("error.implmentation_bug_seq_null"));
     }
     if (operation.length != range.length)
     {
-      throw new Error(MessageManager.getString("error.implementation_bug_cigar_operation_list_range_list"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_bug_cigar_operation_list_range_list"));
     }
 
     if (operation != null)
@@ -251,14 +262,22 @@ public class SeqCigar extends CigarSimple
 
       if (_setSeq(seq, false, 0, 0))
       {
-        throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+        throw new Error(
+                MessageManager
+                        .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
       }
       for (int i = this.length, j = 0; j < operation.length; i++, j++)
       {
         char op = operation[j];
         if (op != M && op != I && op != D)
         {
-          throw new Error(MessageManager.formatMessage("error.implementation_bug_cigar_operation", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(op).toString(),Integer.valueOf(M).toString(),Integer.valueOf(I).toString(),Integer.valueOf(D).toString()}));
+          throw new Error(MessageManager.formatMessage(
+                  "error.implementation_bug_cigar_operation", new String[] {
+                      Integer.valueOf(j).toString(),
+                      Integer.valueOf(op).toString(),
+                      Integer.valueOf(M).toString(),
+                      Integer.valueOf(I).toString(),
+                      Integer.valueOf(D).toString() }));
         }
         this.operation[i] = op;
         this.range[i] = range[j];
@@ -272,7 +291,9 @@ public class SeqCigar extends CigarSimple
       this.length = 0;
       if (_setSeq(seq, false, 0, 0))
       {
-        throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+        throw new Error(
+                MessageManager
+                        .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
       }
     }
   }
@@ -379,7 +400,9 @@ public class SeqCigar extends CigarSimple
     super();
     if (seq == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_for_new_cigar"));
     }
     _setSeq(seq, false, 0, 0);
     // there is still work to do
@@ -401,7 +424,9 @@ public class SeqCigar extends CigarSimple
     super();
     if (seq == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_for_new_cigar"));
     }
     _setSeq(seq, false, start, end + 1);
     // there is still work to do
@@ -456,7 +481,9 @@ public class SeqCigar extends CigarSimple
       // endcol}, hidden regions {{start, end, col}})
       if (gs_regions[i] == null)
       {
-        throw new Error(MessageManager.formatMessage("error.implementation_error_cigar_seq_no_operations", new String[]{Integer.valueOf(i).toString()}));
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cigar_seq_no_operations",
+                new String[] { Integer.valueOf(i).toString() }));
       }
       g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
       // visible
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 19ad30f..c7581d8 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -59,7 +59,6 @@ public class Sequence extends ASequence implements SequenceI
 
   RNA rna;
 
-
   /**
    * This annotation is displayed below the alignment but the positions are tied
    * to the residues of this sequence
@@ -748,8 +747,7 @@ public class Sequence extends ASequence implements SequenceI
       {
         if (lastj != -1)
         {
-          map.add(new int[]
-          { lastj, j - 1 });
+          map.add(new int[] { lastj, j - 1 });
           lastj = -1;
         }
       }
@@ -757,8 +755,7 @@ public class Sequence extends ASequence implements SequenceI
     }
     if (lastj != -1)
     {
-      map.add(new int[]
-      { lastj, j - 1 });
+      map.add(new int[] { lastj, j - 1 });
       lastj = -1;
     }
     return map;
@@ -956,7 +953,6 @@ public class Sequence extends ASequence implements SequenceI
             .toArray(new AlignmentAnnotation[annotation.size()]);
   }
 
-
   @Override
   public boolean hasAnnotation(AlignmentAnnotation ann)
   {
@@ -1208,8 +1204,7 @@ public class Sequence extends ASequence implements SequenceI
       for (int si = 0; si < sfs.length; si++)
       {
         SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
-                : new SequenceFeature[]
-                { new SequenceFeature(sfs[si]) };
+                : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
         if (sf != null && sf.length > 0)
         {
           for (int sfi = 0; sfi < sf.length; sfi++)
diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 7777dce..aca79c8 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -29,20 +29,26 @@ public interface SequenceCollectionI
 
   List getSequences(
           Map hiddenReps);
+
   int getWidth();
+
   /**
    * 
    * @return true if getSeqrep doesn't return null
    */
   boolean hasSeqrep();
+
   /**
    * get the reference or representative sequence within this collection
+   * 
    * @return null or the current reference sequence
    */
   SequenceI getSeqrep();
+
   /**
-   * set the reference or representative sequence for this collection. 
-   * Reference is assumed to be present within the collection.
+   * set the reference or representative sequence for this collection. Reference
+   * is assumed to be present within the collection.
+   * 
    * @return
    */
   void setSeqrep(SequenceI refseq);
diff --git a/src/jalview/datamodel/SequenceDummy.java b/src/jalview/datamodel/SequenceDummy.java
index 4a8c3ee..f472a71 100644
--- a/src/jalview/datamodel/SequenceDummy.java
+++ b/src/jalview/datamodel/SequenceDummy.java
@@ -8,6 +8,7 @@ public class SequenceDummy extends Sequence implements SequenceI
   }
 
   private boolean dummy = true;
+
   /**
    * become a proxy for mseq, merging any existing annotation on this sequence
    * 
@@ -16,7 +17,7 @@ public class SequenceDummy extends Sequence implements SequenceI
   public void become(SequenceI mseq)
   {
     initSeqFrom(mseq, null);
-    dummy=false;
+    dummy = false;
   }
 
   /**
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 3439248..cc70e25 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -20,6 +20,11 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -27,11 +32,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import jalview.analysis.AAFrequency;
-import jalview.analysis.Conservation;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-
 /**
  * Collects a set contiguous ranges on a set of sequences
  * 
@@ -613,13 +613,13 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
-    if (sequences.contains(s))
-    {
-      deleteSequence(s, recalc);
-    }
-    else
-    {
-      addSequence(s, recalc);
+      if (sequences.contains(s))
+      {
+        deleteSequence(s, recalc);
+      }
+      else
+      {
+        addSequence(s, recalc);
       }
     }
   }
@@ -775,8 +775,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     synchronized (sequences)
     {
       // MC This needs to get reset when characters are inserted and deleted
-      boolean first=true;
-      for (SequenceI seq:sequences) {
+      boolean first = true;
+      for (SequenceI seq : sequences)
+      {
         if (first || seq.getLength() > width)
         {
           width = seq.getLength();
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 2ff619b..0e649c0 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -239,6 +239,7 @@ public interface SequenceI extends ASequenceI
 
   /**
    * DOCUMENT ME!
+   * 
    * @param position
    *          DOCUMENT ME!
    * @param ch
@@ -382,8 +383,8 @@ public interface SequenceI extends ASequenceI
   /**
    * Transfer any database references or annotation from entry under a sequence
    * mapping. 

-   * Note: DOES NOT transfer sequence associated alignment
-   * annotation 

+   * Note: DOES NOT transfer sequence associated alignment annotation
+   * 

    * 
    * @param entry
    * @param mp
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 6f6aeb7..b2f054c 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -20,7 +20,7 @@
  */
 package jalview.datamodel;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/datamodel/StructureViewerModel.java b/src/jalview/datamodel/StructureViewerModel.java
index 8bc745a..affaa84 100644
--- a/src/jalview/datamodel/StructureViewerModel.java
+++ b/src/jalview/datamodel/StructureViewerModel.java
@@ -41,6 +41,7 @@ public class StructureViewerModel
     private String pdbId;
 
     private List seqList;
+
     // TODO and possibly a list of chains?
 
     /**
diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 9c9447e..87e2789 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -408,9 +408,9 @@ public class EmblEntry
       dna.addDBRef(retrievedref);
       // add map to indicate the sequence is a valid coordinate frame for the
       // dbref
-      retrievedref.setMap(new Mapping(null, new int[]
-      { 1, dna.getLength() }, new int[]
-      { 1, dna.getLength() }, 1, 1));
+      retrievedref.setMap(new Mapping(null,
+              new int[] { 1, dna.getLength() }, new int[] { 1,
+                  dna.getLength() }, 1, 1));
       // TODO: transform EMBL Database refs to canonical form
       if (dbRefs != null)
       {
@@ -422,7 +422,7 @@ public class EmblEntry
     }
     try
     {
-      for (EmblFeature feature: features)
+      for (EmblFeature feature : features)
       {
         if (!noNa)
         {
@@ -599,19 +599,18 @@ public class EmblEntry
                   .println("Not allowing for additional stop codon at end of cDNA fragment... !");
           // this might occur for CDS sequences where no features are
           // marked.
-          exon = new int[]
-          { dna.getStart() + (prstart - 1), dna.getEnd() };
-          map = new jalview.datamodel.Mapping(product, exon, new int[]
-          { 1, prseq.length() }, 3, 1);
+          exon = new int[] { dna.getStart() + (prstart - 1), dna.getEnd() };
+          map = new jalview.datamodel.Mapping(product, exon, new int[] { 1,
+              prseq.length() }, 3, 1);
         }
         if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
         {
           System.err
                   .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
-          exon = new int[]
-          { dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
-          map = new jalview.datamodel.Mapping(product, exon, new int[]
-          { 1, prseq.length() }, 3, 1);
+          exon = new int[] { dna.getStart() + (prstart - 1),
+              dna.getEnd() - 3 };
+          map = new jalview.datamodel.Mapping(product, exon, new int[] { 1,
+              prseq.length() }, 3, 1);
         }
       }
       else
@@ -632,8 +631,8 @@ public class EmblEntry
           // final product length trunctation check
 
           map = new jalview.datamodel.Mapping(product,
-                  adjustForProteinLength(prseq.length(), exon), new int[]
-                  { 1, prseq.length() }, 3, 1);
+                  adjustForProteinLength(prseq.length(), exon), new int[] {
+                      1, prseq.length() }, 3, 1);
           // reconstruct the EMBLCDS entry
           // TODO: this is only necessary when there codon annotation is
           // complete (I think JBPNote)
@@ -641,9 +640,9 @@ public class EmblEntry
           pcdnaref.setAccessionId(prid);
           pcdnaref.setSource(DBRefSource.EMBLCDS);
           pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
-          jalview.util.MapList mp = new jalview.util.MapList(new int[]
-          { 1, prseq.length() }, new int[]
-          { 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
+          jalview.util.MapList mp = new jalview.util.MapList(new int[] { 1,
+              prseq.length() }, new int[] { 1 + (prstart - 1),
+              (prstart - 1) + 3 * prseq.length() }, 1, 3);
           // { 1 + (prstart - 1) * 3,
           // 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[]
           // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeature.java b/src/jalview/datamodel/xdb/embl/EmblFeature.java
index 7f53eb3..7e503c9 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeature.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeature.java
@@ -20,10 +20,10 @@
  */
 package jalview.datamodel.xdb.embl;
 
-import java.util.Vector;
-
 import jalview.datamodel.DBRefEntry;
 
+import java.util.Vector;
+
 /**
  * Data model for a <feature> element returned from an EMBL query reply
  * 
diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index 2129054..e0b5ede 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -116,9 +116,8 @@ public class EmblFile
       try
       {
         // uncomment to DEBUG EMBLFile reading
-        if (jalview.bin.Cache.getDefault(
-                jalview.bin.Cache.CASTORLOGLEVEL, "debug")
-                .equalsIgnoreCase("DEBUG"))
+        if (jalview.bin.Cache.getDefault(jalview.bin.Cache.CASTORLOGLEVEL,
+                "debug").equalsIgnoreCase("DEBUG"))
         {
           unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
         }
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 729780c..b464c94 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -231,10 +231,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void superposeStructures(AlignmentI alignment, int refStructure,
           ColumnSelection hiddenCols)
   {
-    superposeStructures(new AlignmentI[]
-    { alignment }, new int[]
-    { refStructure }, new ColumnSelection[]
-    { hiddenCols });
+    superposeStructures(new AlignmentI[] { alignment },
+            new int[] { refStructure },
+            new ColumnSelection[] { hiddenCols });
   }
 
   /**
@@ -458,8 +457,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
                 + selectioncom.toString() + "); cartoons; ");
         // selcom.append("; ribbons; ");
         String cmdString = command.toString();
-        System.out
-.println("Superimpose command(s):\n" + cmdString);
+        System.out.println("Superimpose command(s):\n" + cmdString);
 
         evalStateCommand(cmdString);
       }
@@ -516,7 +514,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     AlignmentI alignment = alignmentv.getAlignment();
 
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+            files, sr, fr, alignment))
     {
       for (String cbyseq : cpdbbyseq.commands)
       {
@@ -536,10 +535,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
   {
-    return JmolCommands
-            .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
-                    fr,
-                    alignment);
+    return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+            getSequence(), sr, fr, alignment);
   }
 
   /**
@@ -592,8 +589,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     // TODO: verify atomIndex is selecting correct model.
     // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
-    int colour = viewer.ms.at[atomIndex]
-            .atomPropertyInt(T.color);
+    int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
     return new Color(colour);
   }
 
@@ -891,8 +887,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         pdbfilename = modelFileNames[_mp];
         if (pdbfilename == null)
         {
-          pdbfilename = new File(
-                  viewer.ms.getModelFileName(mnumber))
+          pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
                   .getAbsolutePath();
         }
 
@@ -1135,8 +1130,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
                 + ".0", "PDB");
       }
-        // search pdbentries and sequences to find correct pdbentry for this
-        // model
+      // search pdbentries and sequences to find correct pdbentry for this
+      // model
       for (int pe = 0; pe < getPdbCount(); pe++)
       {
         boolean matches = false;
@@ -1460,4 +1455,3 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     showConsole(false);
   }
 }
-
diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index ddfa1b0..8d76afc 100644
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -86,8 +86,9 @@ public class PDBFileWithJmol extends AlignFile implements
                 null, "-x -o -n", this);
       } catch (ClassCastException x)
       {
-        throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
-                x);
+        throw new Error(MessageManager.formatMessage(
+                "error.jmol_version_not_compatible_with_jalview_version",
+                new String[] { JmolViewer.getJmolVersion() }), x);
       }
     }
     return viewer;
@@ -236,7 +237,8 @@ public class PDBFileWithJmol extends AlignFile implements
                * equivalent (e.g. MSE with MET->M) to maximise sequence matching
                */
               String threeLetterCode = group.getGroup3();
-              String canonical = ResidueProperties.getCanonicalAminoAcid(threeLetterCode);
+              String canonical = ResidueProperties
+                      .getCanonicalAminoAcid(threeLetterCode);
               if (canonical != null
                       && !canonical.equalsIgnoreCase(threeLetterCode))
               {
diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index 55c3c1d..85c84ab 100644
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -137,7 +137,8 @@ public class Annotate3D
     // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
     // vals));
     ArrayList readers = new ArrayList();
-    final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
+    final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(
+            twoDtoolsURL, vals, 0, 0);
     readers.add(postResponse);
     return readers.iterator();
 
@@ -190,14 +191,16 @@ public class Annotate3D
         @Override
         public void remove()
         {
-          throw new Error(MessageManager.getString("error.not_implemented_remove"));
+          throw new Error(
+                  MessageManager.getString("error.not_implemented_remove"));
 
         }
 
         @Override
         protected Object clone() throws CloneNotSupportedException
         {
-          throw new CloneNotSupportedException(MessageManager.getString("error.not_implemented_clone"));
+          throw new CloneNotSupportedException(
+                  MessageManager.getString("error.not_implemented_clone"));
         }
 
         @Override
@@ -218,7 +221,10 @@ public class Annotate3D
       };
     } catch (Exception foo)
     {
-      throw new Exception(MessageManager.getString("exception.couldnt_parse_responde_from_annotated3d_server"), foo);
+      throw new Exception(
+              MessageManager
+                      .getString("exception.couldnt_parse_responde_from_annotated3d_server"),
+              foo);
     }
 
   }
diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 148f252..5342dc8 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -20,13 +20,6 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
@@ -37,6 +30,13 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
 /**
  * Routines for generating Chimera commands for Jalview/Chimera binding
  * 
@@ -67,8 +67,7 @@ public class ChimeraCommands
             ChimeraCommands.class, null,
             colourCommands.toArray(new String[0]));
 
-    return new StructureMappingcommandSet[]
-    { cs };
+    return new StructureMappingcommandSet[] { cs };
   }
 
   /**
@@ -79,7 +78,7 @@ public class ChimeraCommands
    * 
 color colorname #modelnumber:range.chain e.g. color #00ff00
    * #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
    * 
-   * @see http
+   * @see http 
    *      ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
    *      .html 
    * 
@@ -107,7 +106,8 @@ public class ChimeraCommands
       sb.append("color ").append(colourCode).append(" ");
       firstColour = false;
       boolean firstModelForColour = true;
-      final Map>> colourData = colourMap.get(colour);
+      final Map>> colourData = colourMap
+              .get(colour);
       for (Integer model : colourData.keySet())
       {
         boolean firstPositionForModel = true;
@@ -287,8 +287,7 @@ public class ChimeraCommands
     /*
      * Add the start/end positions
      */
-    chainData.add(new int[]
-    { startPos, endPos });
+    chainData.add(new int[] { startPos, endPos });
   }
 
 }
diff --git a/src/jalview/ext/rbvi/chimera/ChimeraListener.java b/src/jalview/ext/rbvi/chimera/ChimeraListener.java
index 2882cb5..ead51b3 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraListener.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraListener.java
@@ -1,13 +1,13 @@
 package jalview.ext.rbvi.chimera;
 
+import jalview.httpserver.AbstractRequestHandler;
+import jalview.structure.SelectionSource;
+
 import java.net.BindException;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import jalview.httpserver.AbstractRequestHandler;
-import jalview.structure.SelectionSource;
-
 /**
  * This is a simple Http handler that can listen for selections in Chimera.
  * 

diff --git a/src/jalview/gui/AlignExportSettings.java b/src/jalview/gui/AlignExportSettings.java
index 0856365..41dc101 100644
--- a/src/jalview/gui/AlignExportSettings.java
+++ b/src/jalview/gui/AlignExportSettings.java
@@ -28,8 +28,7 @@ public class AlignExportSettings extends GAlignExportSettings implements
     {
 
       JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
-              JOptionPane.DEFAULT_OPTION, null, new Object[]
-              { this });
+              JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
       dialog = pane.createDialog(Desktop.desktop,
               MessageManager.getString("label.export_settings"));
       dialog.addWindowListener(new WindowAdapter()
@@ -47,7 +46,6 @@ public class AlignExportSettings extends GAlignExportSettings implements
     }
   }
 
-
   public void ok_actionPerformed(ActionEvent e)
   {
     cancelled = false;
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fbcecbe..500dfdb 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -241,7 +241,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     this(al, hiddenColumns, width, height, null);
   }
 
-
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
@@ -286,7 +285,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     alignPanel = new AlignmentPanel(this, viewport);
 
-
     addAlignmentPanel(alignPanel, true);
     init();
   }
@@ -312,7 +310,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     init();
   }
 
-
   /**
    * Make a new AlignFrame from existing alignmentPanels
    * 
@@ -374,7 +371,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
     buildTreeMenu();
-    
+
     if (viewport.getWrapAlignment())
     {
       wrapMenuItem_actionPerformed(null);
@@ -558,8 +555,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_SPACE:
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
-                    || evt.isShiftDown() || evt.isAltDown());
+            alignPanel.getSeqPanel().insertGapAtCursor(
+                    evt.isControlDown() || evt.isShiftDown()
+                            || evt.isAltDown());
           }
           break;
 
@@ -582,8 +580,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
-                    || evt.isShiftDown() || evt.isAltDown());
+            alignPanel.getSeqPanel().deleteGapAtCursor(
+                    evt.isControlDown() || evt.isShiftDown()
+                            || evt.isAltDown());
           }
 
           break;
@@ -631,8 +630,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_F2:
           viewport.cursorMode = !viewport.cursorMode;
           statusBar.setText(MessageManager.formatMessage(
-                  "label.keyboard_editing_mode", new String[]
-                  { (viewport.cursorMode ? "on" : "off") }));
+                  "label.keyboard_editing_mode",
+                  new String[] { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
@@ -1077,7 +1076,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             currentFileFormat, false);
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_alignment_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -1135,8 +1135,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       success = new Jalview2XML().saveAlignment(this, file, shortName);
 
       statusBar.setText(MessageManager.formatMessage(
-              "label.successfully_saved_to_file_in_format", new Object[]
-              { fileName, format }));
+              "label.successfully_saved_to_file_in_format", new Object[] {
+                  fileName, format }));
 
     }
     else
@@ -1160,7 +1160,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       FormatAdapter f = new FormatAdapter(alignPanel,
               exportData.getSettings());
-      String output = f.formatSequences(format,
+      String output = f.formatSequences(
+              format,
               exportData.getAlignment(), // class cast exceptions will
               // occur in the distant future
               exportData.getOmitHidden(), exportData.getStartEndPostions(),
@@ -1183,8 +1184,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
                   "label.successfully_saved_to_file_in_format",
-                  new Object[]
-                  { fileName, format }));
+                  new Object[] { fileName, format }));
         } catch (Exception ex)
         {
           success = false;
@@ -1196,8 +1196,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (!success)
     {
       JOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.couldnt_save_file", new Object[]
-              { fileName }), MessageManager
+              .formatMessage("label.couldnt_save_file",
+                      new Object[] { fileName }), MessageManager
               .getString("label.error_saving_file"),
               JOptionPane.WARNING_MESSAGE);
     }
@@ -1205,7 +1205,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return success;
   }
 
-
   private void warningMessage(String warning, String title)
   {
     if (new jalview.util.Platform().isHeadless())
@@ -1242,14 +1241,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     try
     {
       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
-              .formatSequences(
-              e.getActionCommand(),
- exportData.getAlignment(),
-              exportData.getOmitHidden(), exportData.getStartEndPostions(),
-              viewport.getColumnSelection()));
+              .formatSequences(e.getActionCommand(),
+                      exportData.getAlignment(),
+                      exportData.getOmitHidden(),
+                      exportData.getStartEndPostions(),
+                      viewport.getColumnSelection()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.alignment_output_command", new Object[]
-              { e.getActionCommand() }), 600, 500);
+              "label.alignment_output_command",
+              new Object[] { e.getActionCommand() }), 600, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
@@ -1258,8 +1257,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
-  public static AlignmentExportData getAlignmentForExport(String exportFormat,
- AlignViewportI viewport,
+  public static AlignmentExportData getAlignmentForExport(
+          String exportFormat, AlignViewportI viewport,
           AlignExportSettingI exportSettings)
   {
     AlignmentI alignmentToExport = null;
@@ -1270,16 +1269,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     HiddenSequences hiddenSeqs = viewport.getAlignment()
             .getHiddenSequences();
 
-
     alignmentToExport = viewport.getAlignment();
-    alignmentStartEnd = new int[]
-    { 0, alignmentToExport.getWidth() - 1 };
+    alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
 
     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
     if (settings == null)
     {
       settings = new AlignExportSettings(hasHiddenSeqs,
-            viewport.hasHiddenColumns(), exportFormat);
+              viewport.hasHiddenColumns(), exportFormat);
     }
     // settings.isExportAnnotations();
 
@@ -1298,8 +1295,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
               .getColumnSelection().getHiddenColumns());
     }
-    AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd,
-            settings);
+    AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+            omitHidden, alignmentStartEnd, settings);
     return ed;
   }
 
@@ -1340,26 +1337,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     // System.out.println("Export range : " + minPos + " - " + maxPos);
-    return new int[]
-    { startPos, endPos };
+    return new int[] { startPos, endPos };
   }
 
   public static void main(String[] args)
   {
     ArrayList hiddenCols = new ArrayList();
-    hiddenCols.add(new int[]
-    { 0, 4 });
-    hiddenCols.add(new int[]
-    { 6, 9 });
-    hiddenCols.add(new int[]
-    { 11, 12 });
-    hiddenCols.add(new int[]
-    { 33, 33 });
-    hiddenCols.add(new int[]
-    { 45, 50 });
-
-    int[] x = getStartEnd(new int[]
-    { 0, 50 }, hiddenCols);
+    hiddenCols.add(new int[] { 0, 4 });
+    hiddenCols.add(new int[] { 6, 9 });
+    hiddenCols.add(new int[] { 11, 12 });
+    hiddenCols.add(new int[] { 33, 33 });
+    hiddenCols.add(new int[] { 45, 50 });
+
+    int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
     // System.out.println("Export range : " + x[0] + " - " + x[1]);
   }
 
@@ -1381,6 +1371,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
   }
+
   public void createImageMap(File file, String image)
   {
     alignPanel.makePNGImageMap(file, image);
@@ -1414,6 +1405,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     alignPanel.makeSVG(f);
   }
+
   @Override
   public void pageSetup_actionPerformed(ActionEvent e)
   {
@@ -1557,8 +1549,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       undoMenuItem.setEnabled(true);
       CommandI command = viewport.getHistoryList().peek();
       undoMenuItem.setText(MessageManager.formatMessage(
-              "label.undo_command", new Object[]
-              { command.getDescription() }));
+              "label.undo_command",
+              new Object[] { command.getDescription() }));
     }
     else
     {
@@ -1572,8 +1564,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       CommandI command = viewport.getRedoList().peek();
       redoMenuItem.setText(MessageManager.formatMessage(
-              "label.redo_command", new Object[]
-              { command.getDescription() }));
+              "label.redo_command",
+              new Object[] { command.getDescription() }));
     }
     else
     {
@@ -1615,8 +1607,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     if (viewport != null)
     {
-      return new AlignmentI[]
-      { viewport.getAlignment() };
+      return new AlignmentI[] { viewport.getAlignment() };
     }
     return null;
   }
@@ -1850,8 +1841,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     boolean appendHistoryItem = false;
     Deque historyList = viewport.getHistoryList();
     boolean inSplitFrame = getSplitViewContainer() != null;
-    if (!inSplitFrame && historyList != null
-            && historyList.size() > 0
+    if (!inSplitFrame && historyList != null && historyList.size() > 0
             && historyList.peek() instanceof SlideSequencesCommand)
     {
       appendHistoryItem = ssc
@@ -1922,17 +1912,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
         {
-          hiddenColumns.add(new int[]
-          { region[0] - hiddenOffset, region[1] - hiddenOffset });
+          hiddenColumns.add(new int[] { region[0] - hiddenOffset,
+              region[1] - hiddenOffset });
         }
       }
     }
 
-    Desktop.jalviewClipboard = new Object[]
-    { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
+    Desktop.jalviewClipboard = new Object[] { seqs,
+        viewport.getAlignment().getDataset(), hiddenColumns };
     statusBar.setText(MessageManager.formatMessage(
-            "label.copied_sequences_to_clipboard", new Object[]
-            { Integer.valueOf(seqs.length).toString() }));
+            "label.copied_sequences_to_clipboard", new Object[] { Integer
+                    .valueOf(seqs.length).toString() }));
   }
 
   /**
@@ -2141,8 +2131,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         //
         addHistoryItem(new EditCommand(
                 MessageManager.getString("label.add_sequences"),
-                Action.PASTE,
-                sequences, 0, alignment.getWidth(), alignment));
+                Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
       }
       // Add any annotations attached to sequences
       for (int i = 0; i < sequences.length; i++)
@@ -2260,7 +2249,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // found!!<<<
         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
                 .transferSettings(
-                        alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+                        alignPanel.getSeqPanel().seqCanvas
+                                .getFeatureRenderer());
 
         // TODO: maintain provenance of an alignment, rather than just make the
         // title a concatenation of operations.
@@ -2319,7 +2309,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // found!!<<<
       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
               .transferSettings(
-                      alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+                      alignPanel.getSeqPanel().seqCanvas
+                              .getFeatureRenderer());
 
       // TODO: maintain provenance of an alignment, rather than just make the
       // title a concatenation of operations.
@@ -2589,8 +2580,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       statusBar.setText(MessageManager.formatMessage(
-              "label.removed_columns", new String[]
-              { Integer.valueOf(trimRegion.getSize()).toString() }));
+              "label.removed_columns",
+              new String[] { Integer.valueOf(trimRegion.getSize())
+                      .toString() }));
 
       addHistoryItem(trimRegion);
 
@@ -2639,8 +2631,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     addHistoryItem(removeGapCols);
 
     statusBar.setText(MessageManager.formatMessage(
-            "label.removed_empty_columns", new Object[]
-            { Integer.valueOf(removeGapCols.getSize()).toString() }));
+            "label.removed_empty_columns",
+            new Object[] { Integer.valueOf(removeGapCols.getSize())
+                    .toString() }));
 
     // This is to maintain viewport position on first residue
     // of first sequence
@@ -2890,8 +2883,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowJVSuffix(seqLimits.isSelected());
 
-    alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
-            .calculateIdWidth());
+    alignPanel.getIdPanel().getIdCanvas()
+            .setPreferredSize(alignPanel.calculateIdWidth());
     alignPanel.paintAlignment(true);
   }
 
@@ -2976,7 +2969,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
-//    alignPanel.paintAlignment(true);
+    // alignPanel.paintAlignment(true);
   }
 
   /**
@@ -3281,14 +3274,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
             .formatAsHtml();
     editPane.setText(MessageManager.formatMessage("label.html_content",
-            new Object[]
-            { contents.toString() }));
+            new Object[] { contents.toString() }));
     JInternalFrame frame = new JInternalFrame();
     frame.getContentPane().add(new JScrollPane(editPane));
 
     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
-            "label.alignment_properties", new Object[]
-            { getTitle() }), 500, 400);
+            "label.alignment_properties", new Object[] { getTitle() }),
+            500, 400);
   }
 
   /**
@@ -3309,8 +3301,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
-            "label.overview_params", new Object[]
-            { this.getTitle() }), frame.getWidth(), frame.getHeight());
+            "label.overview_params", new Object[] { this.getTitle() }),
+            frame.getWidth(), frame.getHeight());
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
@@ -4030,7 +4022,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void addSortByOrderMenuItem(String title,
           final AlignmentOrder order)
   {
-    final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
+    final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
+            "action.by_title_param", new Object[] { title }));
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
@@ -4149,8 +4142,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     calculateTree.removeAll();
     // build the calculate menu
 
-    for (final String type : new String[]
-    { "NJ", "AV" })
+    for (final String type : new String[] { "NJ", "AV" })
     {
       String treecalcnm = MessageManager.getString("label.tree_calc_"
               + type.toLowerCase());
@@ -4299,8 +4291,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
     if (!viewport.getAlignment().isAligned(false))
     {
-      seqs.setSequences(new SeqCigar[]
-      { seqs.getSequences()[0] });
+      seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
       // TODO: if seqs.getSequences().length>1 then should really have warned
       // user!
 
@@ -4747,8 +4738,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         final long sttime = System.currentTimeMillis();
         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
-                "status.searching_for_sequences_from", new Object[]
-                { source }), sttime);
+                "status.searching_for_sequences_from",
+                new Object[] { source }), sttime);
         try
         {
           // update our local dataset reference
@@ -4855,9 +4846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
                 "status.finished_searching_for_sequences_from",
-                new Object[]
-                { source }),
-                sttime);
+                new Object[] { source }), sttime);
       }
 
     };
@@ -4922,8 +4911,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
       af.setFileFormat(this.currentFileFormat);
       final String newTitle = MessageManager.formatMessage(
-              "label.translation_of_params", new Object[]
-              { this.getTitle() });
+              "label.translation_of_params",
+              new Object[] { this.getTitle() });
       af.setTitle(newTitle);
       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
       {
@@ -4961,7 +4950,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     return avc.parseFeaturesFile(file, type,
             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
-    
+
   }
 
   @Override
@@ -4976,8 +4965,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showSeqFeatures.setSelected(true);
     }
 
-
   }
+
   @Override
   public void dragEnter(DropTargetDragEvent evt)
   {
@@ -5108,8 +5097,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 if (type.equalsIgnoreCase("PDB"))
                 {
-                  filesmatched.add(new Object[]
-                  { file, protocol, mtch });
+                  filesmatched.add(new Object[] { file, protocol, mtch });
                   continue;
                 }
               }
@@ -5128,10 +5116,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                   MessageManager
                                           .formatMessage(
                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
-                                                  new Object[]
-                                                  { Integer.valueOf(
-                                                          filesmatched
-                                                                  .size())
+                                                  new Object[] { Integer
+                                                          .valueOf(
+                                                                  filesmatched
+                                                                          .size())
                                                           .toString() }),
                                   MessageManager
                                           .getString("label.automatically_associate_pdb_files_by_name"),
@@ -5168,14 +5156,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
                           .showConfirmDialog(
                                   this,
-                                  ""+MessageManager
-                                          .formatMessage(
-                                                  "label.ignore_unmatched_dropped_files_info",
-                                                  new Object[]
-                                                  { Integer.valueOf(
-                                                          filesnotmatched
-                                                                  .size())
-                                                          .toString() })+"",
+                                  ""
+                                          + MessageManager
+                                                  .formatMessage(
+                                                          "label.ignore_unmatched_dropped_files_info",
+                                                          new Object[] { Integer
+                                                                  .valueOf(
+                                                                          filesnotmatched
+                                                                                  .size())
+                                                                  .toString() })
+                                          + "",
                                   MessageManager
                                           .getString("label.ignore_unmatched_dropped_files"),
                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
@@ -5218,8 +5208,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // try to parse as annotation.
       boolean isAnnotation = (format == null || format
               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
-              .annotateAlignmentView(viewport, file, protocol)
-              : false;
+              .annotateAlignmentView(viewport, file, protocol) : false;
 
       if (!isAnnotation)
       {
@@ -5612,7 +5601,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
 
                 });
-                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
+                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                        MessageManager.formatMessage(
+                                "label.fetch_retrieve_from",
+                                new Object[] { src.getDbName() })));
                 dfetch.add(fetchr);
                 comp++;
               }
@@ -5623,8 +5615,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 // fetch all entry
                 DbSourceProxy src = otherdb.get(0);
                 fetchr = new JMenuItem(MessageManager.formatMessage(
-                        "label.fetch_all_param", new Object[]
-                        { src.getDbSource() }));
+                        "label.fetch_all_param",
+                        new Object[] { src.getDbSource() }));
                 fetchr.addActionListener(new ActionListener()
                 {
                   @Override
@@ -5645,11 +5637,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
                 });
 
-                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
+                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                        MessageManager.formatMessage(
+                                "label.fetch_retrieve_from_all_sources",
+                                new Object[] {
+                                    Integer.valueOf(otherdb.size())
+                                            .toString(), src.getDbSource(),
+                                    src.getDbName() })));
                 dfetch.add(fetchr);
                 comp++;
                 // and then build the rest of the individual menus
-                ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
+                ifetch = new JMenu(MessageManager.formatMessage(
+                        "label.source_from_db_source",
+                        new Object[] { src.getDbSource() }));
                 icomp = 0;
                 String imname = null;
                 int i = 0;
@@ -5662,11 +5662,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           0, 10) + "..." : dbname;
                   if (imname == null)
                   {
-                    imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
+                    imname = MessageManager.formatMessage(
+                            "label.from_msname", new Object[] { sname });
                   }
                   fetchr = new JMenuItem(msname);
-                  final DbSourceProxy[] dassrc =
-                  { sproxy };
+                  final DbSourceProxy[] dassrc = { sproxy };
                   fetchr.addActionListener(new ActionListener()
                   {
 
@@ -5689,7 +5689,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
                   });
                   fetchr.setToolTipText(""
-                          + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
+                          + MessageManager.formatMessage(
+                                  "label.fetch_retrieve_from", new Object[]
+                                  { dbname }));
                   ifetch.add(fetchr);
                   ++i;
                   if (++icomp >= mcomp || i == (otherdb.size()))
@@ -5853,10 +5855,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       alignPanel.paintAlignment(true);
     }
   }
+
   public void clearAlignmentSeqRep()
   {
     // TODO refactor alignmentseqrep to controller
-    if (viewport.getAlignment().hasSeqrep()) {
+    if (viewport.getAlignment().hasSeqrep())
+    {
       viewport.getAlignment().setSeqrep(null);
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
@@ -5892,7 +5896,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (!viewport.getSequenceSetId().equals(
             alignmentPanel.av.getSequenceSetId()))
     {
-      throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_cannot_show_view_alignment_frame"));
     }
     if (tabbedPane != null
             && tabbedPane.getTabCount() > 0
@@ -5955,8 +5961,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public List getAlignPanels()
   {
-    return alignPanels == null ? Arrays.asList(alignPanel)
-            : alignPanels;
+    return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
   }
 
   /**
@@ -5973,8 +5978,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
     List cdnaSeqs = new ArrayList();
-    for (SequenceI aaSeq : alignment.getSequences()) {
-      for (AlignedCodonFrame acf : mappings) {
+    for (SequenceI aaSeq : alignment.getSequences())
+    {
+      for (AlignedCodonFrame acf : mappings)
+      {
         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
         if (dnaSeq != null)
         {
@@ -6002,8 +6009,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
             + this.title;
     Desktop.addInternalFrame(alignFrame, newtitle,
-            AlignFrame.DEFAULT_WIDTH,
-            AlignFrame.DEFAULT_HEIGHT);
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
   }
 
   /**
@@ -6016,7 +6022,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showComplement_actionPerformed(boolean show)
   {
     SplitContainerI sf = getSplitViewContainer();
-    if (sf != null) {
+    if (sf != null)
+    {
       sf.setComplementVisible(this, show);
     }
   }
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 579b476..8378f30 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -109,6 +109,7 @@ public class AlignViewport extends AlignmentViewport implements
   private boolean gatherViewsHere = false;
 
   private AnnotationColumnChooser annotationColumnSelectionState;
+
   /**
    * Creates a new AlignViewport object.
    * 
@@ -399,6 +400,7 @@ public class AlignViewport extends AlignmentViewport implements
             viewStyle.getFontSize()), false);
 
   }
+
   /**
    * DOCUMENT ME!
    * 
@@ -565,11 +567,9 @@ public class AlignViewport extends AlignmentViewport implements
     // TODO: JAL-1126
     if (historyList == null || redoList == null)
     {
-      return new long[]
-      { -1, -1 };
+      return new long[] { -1, -1 };
     }
-    return new long[]
-    { historyList.hashCode(), this.redoList.hashCode() };
+    return new long[] { historyList.hashCode(), this.redoList.hashCode() };
   }
 
   /**
@@ -714,8 +714,7 @@ public class AlignViewport extends AlignmentViewport implements
       List seqs = new ArrayList();
       for (SequenceI sq : alignment.getSequences())
       {
-        Vector pdbs = sq
-                .getDatasetSequence().getAllPDBEntries();
+        Vector pdbs = sq.getDatasetSequence().getAllPDBEntries();
         if (pdbs == null)
         {
           continue;
@@ -893,8 +892,8 @@ public class AlignViewport extends AlignmentViewport implements
    */
   protected boolean openLinkedAlignment(AlignmentI al, String title)
   {
-    String[] options = new String[]
-    { MessageManager.getString("action.no"),
+    String[] options = new String[] {
+        MessageManager.getString("action.no"),
         MessageManager.getString("label.split_window"),
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
@@ -937,8 +936,7 @@ public class AlignViewport extends AlignmentViewport implements
             AlignFrame.DEFAULT_HEIGHT);
     newAlignFrame.setTitle(title);
     newAlignFrame.statusBar.setText(MessageManager.formatMessage(
-            "label.successfully_loaded_file", new Object[]
-            { title }));
+            "label.successfully_loaded_file", new Object[] { title }));
 
     // TODO if we want this (e.g. to enable reload of the alignment from file),
     // we will need to add parameters to the stack.
@@ -950,15 +948,13 @@ public class AlignViewport extends AlignmentViewport implements
     if (openInNewWindow)
     {
       Desktop.addInternalFrame(newAlignFrame, title,
-              AlignFrame.DEFAULT_WIDTH,
-              AlignFrame.DEFAULT_HEIGHT);
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
     }
 
     try
     {
       newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
-              "SHOW_FULLSCREEN",
-              false));
+              "SHOW_FULLSCREEN", false));
     } catch (java.beans.PropertyVetoException ex)
     {
     }
@@ -987,7 +983,8 @@ public class AlignViewport extends AlignmentViewport implements
   {
     /*
      * Make a new frame with a copy of the alignment we are adding to. If this
-     * is protein, the mappings to cDNA will be registered with StructureSelectionManager as a side-effect.
+     * is protein, the mappings to cDNA will be registered with
+     * StructureSelectionManager as a side-effect.
      */
     AlignFrame copyMe = new AlignFrame(complement,
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -996,8 +993,7 @@ public class AlignViewport extends AlignmentViewport implements
     AlignmentI al = newAlignFrame.viewport.getAlignment();
     final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
             : newAlignFrame;
-    final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
-            : copyMe;
+    final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
     cdnaFrame.setVisible(true);
     proteinFrame.setVisible(true);
     String linkedTitle = MessageManager
@@ -1074,7 +1070,8 @@ public class AlignViewport extends AlignmentViewport implements
     if (!sr.isEmpty())
     {
       // TODO would like next line without cast but needs more refactoring...
-      final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
+      final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+              .getAlignPanel();
       complementPanel.setFollowingComplementScroll(true);
       complementPanel.scrollToCentre(sr, verticalOffset);
     }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 1b93f10..ec83a5d 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -76,6 +76,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   private IdPanel idPanel;
 
   private boolean headless;
+
   IdwidthAdjuster idwidthAdjuster;
 
   /** DOCUMENT ME!! */
@@ -155,6 +156,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return av;
   }
+
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -177,8 +179,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
             + fm.getDescent()));
     idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
-            .getCharHeight()
-            + fm.getDescent()));
+            .getCharHeight() + fm.getDescent()));
 
     getIdPanel().getIdCanvas().gg = null;
     getSeqPanel().seqCanvas.img = null;
@@ -317,7 +318,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param redrawOverview
    * @return
    */
-  public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
+  public boolean scrollToPosition(SearchResults searchResults,
+          boolean redrawOverview)
   {
     return scrollToPosition(searchResults, 0, redrawOverview, false);
   }
@@ -337,8 +339,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return false if results were not found
    */
   public boolean scrollToPosition(SearchResults results,
-          int verticalOffset,
-          boolean redrawOverview, boolean centre)
+          int verticalOffset, boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
     // TODO: properly locate search results in view when large numbers of hidden
@@ -363,8 +364,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       int start = r[0];
       int end = r[1];
       // DEBUG
-//       System.err.println(this.av.viewName + " Seq : " + seqIndex
-//       + " Scroll to " + start + "," + end);
+      // System.err.println(this.av.viewName + " Seq : " + seqIndex
+      // + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -747,7 +748,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+              .getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -844,8 +846,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
-    sorter.sort(getAlignment()
-            .getAlignmentAnnotation(),
+    sorter.sort(getAlignment().getAlignmentAnnotation(),
             av.getSortAnnotationsBy());
     repaint();
 
@@ -1063,9 +1064,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 - 4;
       }
 
-      pg.drawString(
-              seq.getDisplayId(av.getShowJVSuffix()),
-              xPos,
+      pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
               (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
@@ -1074,7 +1073,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     // draw main sequence panel
     pg.translate(idWidth, 0);
-    getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+    getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq,
+            endSeq, 0);
 
     if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
     {
@@ -1176,12 +1176,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       if (labels != null)
       {
-        pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.getCharHeight()));
+        pg.translate(-3,
+                ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
-        pg.translate(+3, -ypos
+        pg.translate(
+                +3,
+                -ypos
                         - (av.getAlignment().getHeight() * av
                                 .getCharHeight()));
       }
@@ -1191,8 +1193,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pg.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
-            0);
+    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+            totalHeight, 0);
 
     if ((pi * pheight) < totalHeight)
     {
@@ -1250,8 +1252,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (alignFrame != null && !headless)
     {
       alignFrame.setProgressBar(MessageManager.formatMessage(
-              "status.saving_file", new Object[]
-              { type.getLabel() }), progress);
+              "status.saving_file", new Object[] { type.getLabel() }),
+              progress);
     }
     try
     {
@@ -1312,7 +1314,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       if (alignFrame != null && !headless)
       {
-        alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
+        alignFrame.setProgressBar(
+                MessageManager.getString("status.export_complete"),
+                progress);
       }
     }
   }
@@ -1377,6 +1381,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
   }
+
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
     // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
@@ -1414,8 +1419,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
             if (av.getAlignment().isNucleotide())
             {
               triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(res)
-                      + "");
+                      .getCharAt(res) + "");
             }
             else
             {
@@ -1437,8 +1441,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append(" selectedTypes = new HashMap();
-  
+
   /**
    * Constructor.
    * 
@@ -388,7 +388,7 @@ public class AnnotationChooser extends JPanel
     final boolean wholeAlignment = this.sg == null;
     JPanel applyToOptions = new JPanel(new FlowLayout(FlowLayout.LEFT));
     CheckboxGroup actingOn = new CheckboxGroup();
-    
+
     String forAll = MessageManager.getString("label.all_sequences");
     final Checkbox allSequences = new Checkbox(forAll, actingOn,
             wholeAlignment);
@@ -397,7 +397,8 @@ public class AnnotationChooser extends JPanel
       @Override
       public void itemStateChanged(ItemEvent evt)
       {
-        if (evt.getStateChange() == ItemEvent.SELECTED) {
+        if (evt.getStateChange() == ItemEvent.SELECTED)
+        {
           AnnotationChooser.this.setApplyToSelectedSequences(true);
           AnnotationChooser.this.setApplyToUnselectedSequences(true);
           AnnotationChooser.this.changeApplyTo_actionPerformed();
@@ -405,7 +406,7 @@ public class AnnotationChooser extends JPanel
       }
     });
     applyToOptions.add(allSequences);
-    
+
     String forSelected = MessageManager
             .getString("label.selected_sequences");
     final Checkbox selectedSequences = new Checkbox(forSelected, actingOn,
@@ -425,10 +426,11 @@ public class AnnotationChooser extends JPanel
       }
     });
     applyToOptions.add(selectedSequences);
-    
+
     String exceptSelected = MessageManager
             .getString("label.except_selected_sequences");
-    final Checkbox unselectedSequences = new Checkbox(exceptSelected, actingOn, false);
+    final Checkbox unselectedSequences = new Checkbox(exceptSelected,
+            actingOn, false);
     unselectedSequences.setEnabled(!wholeAlignment);
     unselectedSequences.addItemListener(new ItemListener()
     {
@@ -444,7 +446,7 @@ public class AnnotationChooser extends JPanel
       }
     });
     applyToOptions.add(unselectedSequences);
-    
+
     // set member variables to match the initial selection state
     this.applyToSelectedSequences = selectedSequences.getState()
             || allSequences.getState();
@@ -476,7 +478,8 @@ public class AnnotationChooser extends JPanel
       @Override
       public void itemStateChanged(ItemEvent evt)
       {
-        if (evt.getStateChange() == ItemEvent.SELECTED) {
+        if (evt.getStateChange() == ItemEvent.SELECTED)
+        {
           AnnotationChooser.this.setShowSelected(true);
           AnnotationChooser.this.changeShowHide_actionPerformed();
         }
@@ -521,7 +524,7 @@ public class AnnotationChooser extends JPanel
   {
     JPanel jp = new JPanel();
     final Font labelFont = JvSwingUtils.getLabelFont();
-    
+
     JButton ok = new JButton(MessageManager.getString("action.ok"));
     ok.setFont(labelFont);
     ok.addActionListener(new ActionListener()
@@ -533,7 +536,7 @@ public class AnnotationChooser extends JPanel
       }
     });
     jp.add(ok);
-    
+
     JButton cancel = new JButton(MessageManager.getString("action.cancel"));
     cancel.setFont(labelFont);
     cancel.addActionListener(new ActionListener()
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index c8dd889..19eed27 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -63,7 +63,6 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
   JButton defColours = new JButton();
 
-
   JPanel jPanel1 = new JPanel();
 
   JPanel jPanel2 = new JPanel();
@@ -140,7 +139,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         getThreshold().setSelectedIndex(2);
         break;
       default:
-        throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_dont_know_about_thereshold_setting"));
       }
       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
       thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -348,7 +349,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
   public void minColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
+            MessageManager.getString("label.select_colour_minimum_value"),
+            minColour.getBackground());
     if (col != null)
     {
       minColour.setBackground(col);
@@ -360,7 +362,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
   public void maxColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
+            MessageManager.getString("label.select_colour_maximum_value"),
+            maxColour.getBackground());
     if (col != null)
     {
       maxColour.setBackground(col);
@@ -449,9 +452,10 @@ public class AnnotationColourChooser extends AnnotationRowFilter
             && getCurrentAnnotation().threshold == null)
     {
       getCurrentAnnotation()
-              .setThreshold(new jalview.datamodel.GraphLine(
-                      (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
-                      "Threshold", Color.black));
+              .setThreshold(
+                      new jalview.datamodel.GraphLine(
+                              (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+                              "Threshold", Color.black));
     }
 
     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index e87be35..c0d7084 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -66,6 +66,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
           .getLayout());
+
   private JPanel noGraphFilterView = new JPanel();
 
   private JPanel graphFilterView = new JPanel();
@@ -294,6 +295,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       slider.setToolTipText(defaultTtip);
     }
   }
+
   public void reset()
   {
     if (this.getOldColumnSelection() != null)
@@ -585,7 +587,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     updateView();
   }
 
-
   public class FurtherActionPanel extends JPanel
   {
     private AnnotationColumnChooser aColChooser;
@@ -646,8 +647,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
       {
-        this.optionsGroup.setSelected(this.hideOption.getModel(),
-                true);
+        this.optionsGroup.setSelected(this.hideOption.getModel(), true);
       }
       else
       {
@@ -816,27 +816,26 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       JvSwingUtils.jvInitComponent(searchBox);
       searchBox.setToolTipText(MessageManager
               .getString("info.enter_search_text_here"));
-      searchBox.getDocument().addDocumentListener(
-              new DocumentListener()
-              {
-                @Override
-                public void insertUpdate(DocumentEvent e)
-                {
-                  searchStringAction();
-                }
-
-                @Override
-                public void removeUpdate(DocumentEvent e)
-                {
-                  searchStringAction();
-                }
-
-                @Override
-                public void changedUpdate(DocumentEvent e)
-                {
-                  searchStringAction();
-                }
-              });
+      searchBox.getDocument().addDocumentListener(new DocumentListener()
+      {
+        @Override
+        public void insertUpdate(DocumentEvent e)
+        {
+          searchStringAction();
+        }
+
+        @Override
+        public void removeUpdate(DocumentEvent e)
+        {
+          searchStringAction();
+        }
+
+        @Override
+        public void changedUpdate(DocumentEvent e)
+        {
+          searchStringAction();
+        }
+      });
 
       JvSwingUtils.jvInitComponent(displayName, "label.label");
       displayName.setEnabled(false);
@@ -905,15 +904,14 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       String defaultTtip = MessageManager
               .getString("info.enter_search_text_to_enable");
-      String labelTtip = MessageManager
-.formatMessage(
+      String labelTtip = MessageManager.formatMessage(
               "info.search_in_annotation_label", annotations
                       .getSelectedItem().toString());
-      String descTtip = MessageManager
-.formatMessage(
+      String descTtip = MessageManager.formatMessage(
               "info.search_in_annotation_description", annotations
                       .getSelectedItem().toString());
-      displayName.setToolTipText(displayName.isEnabled() ? labelTtip : defaultTtip);
+      displayName.setToolTipText(displayName.isEnabled() ? labelTtip
+              : defaultTtip);
       description.setToolTipText(description.isEnabled() ? descTtip
               : defaultTtip);
     }
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 9b25388..643d8a0 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -120,8 +120,9 @@ public class AnnotationExporter extends JPanel
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(features ? MessageManager.getString("label.save_features_to_file")
-            : MessageManager.getString("label.save_annotation_to_file"));
+    chooser.setDialogTitle(features ? MessageManager
+            .getString("label.save_features_to_file") : MessageManager
+            .getString("label.save_annotation_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -186,6 +187,7 @@ public class AnnotationExporter extends JPanel
     }
     return text;
   }
+
   public void toTextbox_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
@@ -197,23 +199,26 @@ public class AnnotationExporter extends JPanel
       Desktop.addInternalFrame(
               cap,
               (features ? MessageManager.formatMessage(
-                      "label.features_for_params", new String[]
-                      { ap.alignFrame.getTitle() }) : MessageManager
-                      .formatMessage("label.annotations_for_params",
-                              new String[]
-                              { ap.alignFrame.getTitle() })), 600, 500);
+                      "label.features_for_params",
+                      new String[] { ap.alignFrame.getTitle() })
+                      : MessageManager.formatMessage(
+                              "label.annotations_for_params",
+                              new String[] { ap.alignFrame.getTitle() })),
+              600, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning((features ? MessageManager.formatMessage(
-              "label.generating_features_for_params", new String[]
-              { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
-              "label.generating_annotations_for_params", new String[]
-              { ap.alignFrame.getTitle() })), oom);
+              "label.generating_features_for_params",
+              new String[] { ap.alignFrame.getTitle() })
+              : MessageManager.formatMessage(
+                      "label.generating_annotations_for_params",
+                      new String[] { ap.alignFrame.getTitle() })), oom);
       cap.dispose();
     }
 
     close_actionPerformed(null);
   }
+
   public void close_actionPerformed(ActionEvent e)
   {
     try
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4e625e1..d4300e4 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -70,13 +70,16 @@ import javax.swing.ToolTipManager;
 public class AnnotationLabels extends JPanel implements MouseListener,
         MouseMotionListener, ActionListener
 {
-  private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+  private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+          .compile("<");
 
-  String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
+  String TOGGLE_LABELSCALE = MessageManager
+          .getString("label.scale_label_to_column");
 
   String ADDNEW = MessageManager.getString("label.add_new_row");
 
-  String EDITNAME = MessageManager.getString("label.edit_label_description");
+  String EDITNAME = MessageManager
+          .getString("label.edit_label_description");
 
   String HIDE = MessageManager.getString("label.hide_row");
 
@@ -86,7 +89,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
   String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
 
-  String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
+  String COPYCONS_SEQ = MessageManager
+          .getString("label.copy_consensus_sequence");
 
   boolean resizePanel = false;
 
@@ -253,8 +257,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
       new AnnotationExporter().exportAnnotations(ap,
-              new AlignmentAnnotation[]
-      { aa[selectedRow] });
+              new AlignmentAnnotation[] { aa[selectedRow] });
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
@@ -547,9 +550,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           }
           else
           {
-            ap.getSeqPanel().ap.getIdPanel()
-                    .highlightSearchResults(aa[selectedRow].groupRef
-                            .getSequences(null));
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
+                    aa[selectedRow].groupRef.getSequences(null));
           }
           return;
         }
@@ -557,36 +559,45 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {
           if (evt.getClickCount() == 1)
           {
-            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays
-                    .asList(new SequenceI[]
-                    { aa[selectedRow].sequenceRef }));
+            ap.getSeqPanel().ap
+                    .getIdPanel()
+                    .highlightSearchResults(
+                            Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
           }
           else if (evt.getClickCount() >= 2)
           {
             ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
             SequenceGroup sg = ap.av.getSelectionGroup();
-            if (sg!=null)
+            if (sg != null)
             {
-              // we make a copy rather than edit the current selection if no modifiers pressed
+              // we make a copy rather than edit the current selection if no
+              // modifiers pressed
               // see Enhancement JAL-1557
               if (!(evt.isControlDown() || evt.isShiftDown()))
               {
                 sg = new SequenceGroup(sg);
                 sg.clear();
                 sg.addSequence(aa[selectedRow].sequenceRef, false);
-              } else {
+              }
+              else
+              {
                 if (evt.isControlDown())
                 {
                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
-                } else {
-                  // notionally, we should also add intermediate sequences from last added sequence ?
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
                   sg.addSequence(aa[selectedRow].sequenceRef, true);
                 }
               }
-            } else {
+            }
+            else
+            {
               sg = new SequenceGroup();
               sg.setStartRes(0);
-              sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+              sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
               sg.addSequence(aa[selectedRow].sequenceRef, false);
             }
             ap.av.setSelectionGroup(sg);
@@ -632,7 +643,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       {
         final String label = aa[selectedRow].label;
         JMenuItem hideType = new JMenuItem();
-        String text = MessageManager.getString("label.hide_all") + " " + label;
+        String text = MessageManager.getString("label.hide_all") + " "
+                + label;
         hideType.setText(text);
         hideType.addActionListener(new ActionListener()
         {
@@ -692,7 +704,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         pop.addSeparator();
         // av and sequencegroup need to implement same interface for
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-                        MessageManager.getString("label.ignore_gaps_consensus"),
+                MessageManager.getString("label.ignore_gaps_consensus"),
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
                         .getIgnoreGapsConsensus() : ap.av
                         .isIgnoreGapsConsensus());
@@ -705,7 +717,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               // TODO: pass on reference to ap so the view can be updated.
               aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
-              ap.getAnnotationPanel().paint(ap.getAnnotationPanel().getGraphics());
+              ap.getAnnotationPanel().paint(
+                      ap.getAnnotationPanel().getGraphics());
             }
             else
             {
@@ -718,7 +731,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aaa.groupRef != null)
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_group_histogram"),
+                  MessageManager.getString("label.show_group_histogram"),
                   aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
@@ -737,7 +750,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_group_logo"),
+                  MessageManager.getString("label.show_group_logo"),
                   aa[selectedRow].groupRef.isShowSequenceLogo());
           cprofl.addActionListener(new ActionListener()
           {
@@ -756,7 +769,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprofl);
           final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.normalise_group_logo"),
+                  MessageManager.getString("label.normalise_group_logo"),
                   aa[selectedRow].groupRef.isNormaliseSequenceLogo());
           cproflnorm.addActionListener(new ActionListener()
           {
@@ -781,7 +794,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         else
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+                  MessageManager.getString("label.show_histogram"),
+                  av.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -800,7 +814,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+                  MessageManager.getString("label.show_logo"),
+                  av.isShowSequenceLogo());
           cprof.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -819,7 +834,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprof);
           final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+                  MessageManager.getString("label.normalise_logo"),
+                  av.isNormaliseSequenceLogo());
           cprofnorm.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -855,11 +871,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   protected void copy_annotseqtoclipboard(SequenceI sq)
   {
-    SequenceI[] seqs = new SequenceI[]
-    { sq };
+    SequenceI[] seqs = new SequenceI[] { sq };
     String[] omitHidden = null;
-    SequenceI[] dseqs = new SequenceI[]
-    { sq.getDatasetSequence() };
+    SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() };
     if (dseqs[0] == null)
     {
       dseqs[0] = new Sequence(sq);
@@ -875,8 +889,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               sq.getLength(), seqs);
     }
 
-    int[] alignmentStartEnd = new int[]
-    { 0, ds.getWidth() - 1 };
+    int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
     List hiddenCols = av.getColumnSelection().getHiddenColumns();
     if (hiddenCols != null)
     {
@@ -895,13 +908,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       hiddenColumns = new ArrayList();
       for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        hiddenColumns.add(new int[]
-        { region[0], region[1] });
+        hiddenColumns.add(new int[] { region[0], region[1] });
       }
     }
 
-    Desktop.jalviewClipboard = new Object[]
-    { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+    Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
+                                                        // of a consensus
+                                                        // sequence ? need to
+                                                        // flag
         // sequence as special.
         hiddenColumns };
   }
@@ -990,8 +1004,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     int ofontH = fontHeight;
     int sOffset = 0;
     int visHeight = 0;
-    int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel()
-            .getVisibleVRange() : null;
+    int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
+            .getAnnotationPanel().getVisibleVRange() : null;
     if (clip && visr != null)
     {
       sOffset = visr[0];
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 97752f2..77d6b51 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -335,7 +335,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (evt.getActionCommand().equals(COLOUR))
     {
       Color col = JColorChooser.showDialog(this,
-              MessageManager.getString("label.select_foreground_colour"), Color.black);
+              MessageManager.getString("label.select_foreground_colour"),
+              Color.black);
 
       for (int i = 0; i < av.getColumnSelection().size(); i++)
       {
@@ -412,7 +413,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           anot[index] = new Annotation(label, "", type, 0);
         }
 
-        
         anot[index].secondaryStructure = type != 'S' ? type : label
                 .length() == 0 ? ' ' : label.charAt(0);
         anot[index].displayCharacter = label;
@@ -709,8 +709,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               && aa[row].annotations[res].description != null
               && aa[row].annotations[res].description.length() > 0)
       {
-        this.setToolTipText(JvSwingUtils
-                        .wrapTooltip(true, aa[row].annotations[res].description));
+        this.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                aa[row].annotations[res].description));
       }
       else
       {
@@ -809,8 +809,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       try
       {
-        image = new BufferedImage(imgWidth, ap.getAnnotationPanel().getHeight(),
-                BufferedImage.TYPE_INT_RGB);
+        image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
+                .getHeight(), BufferedImage.TYPE_INT_RGB);
       } catch (OutOfMemoryError oom)
       {
         try
diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index ac767cf..7b2fb36 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -111,7 +111,6 @@ public abstract class AnnotationRowFilter extends JPanel
     });
   }
 
-
   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
   {
     this.av = av;
@@ -363,7 +362,6 @@ public abstract class AnnotationRowFilter extends JPanel
     return false;
   }
 
-
   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
   {
     return currentAnnotation;
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index fdc47fc..d876755 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -174,7 +174,8 @@ public class AppJmol extends StructureViewerBase
       _alignwith = new Vector();
     }
 
-    seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
+    seqColourBy = new ViewSelectionMenu(
+            MessageManager.getString("label.colour_by"), this, _colourwith,
             new ItemListener()
             {
 
@@ -194,7 +195,8 @@ public class AppJmol extends StructureViewerBase
             });
     viewMenu.add(seqColourBy);
     final ItemListener handler;
-    JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
+    JMenu alpanels = new ViewSelectionMenu(
+            MessageManager.getString("label.superpose_with"), this,
             _alignwith, handler = new ItemListener()
             {
 
@@ -205,8 +207,8 @@ public class AppJmol extends StructureViewerBase
                 alignStructs.setToolTipText(MessageManager
                         .formatMessage(
                                 "label.align_structures_using_linked_alignment_views",
-                                new String[]
-                                { new Integer(_alignwith.size()).toString() }));
+                                new String[] { new Integer(_alignwith
+                                        .size()).toString() }));
               }
             });
     handler.itemStateChanged(null);
@@ -488,7 +490,8 @@ public class AppJmol extends StructureViewerBase
           long hdl = pdbid.hashCode() - System.currentTimeMillis();
           if (progressBar != null)
           {
-            progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
+            progressBar.setProgressBar(MessageManager.formatMessage(
+                    "status.fetching_pdb", new String[] { pdbid }), hdl);
           }
           try
           {
@@ -503,7 +506,8 @@ public class AppJmol extends StructureViewerBase
           }
           if (progressBar != null)
           {
-            progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
+            progressBar.setProgressBar(
+                    MessageManager.getString("label.state_completed"), hdl);
           }
           if (pdbseq != null)
           {
@@ -554,9 +558,8 @@ public class AppJmol extends StructureViewerBase
 
       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.pdb_entries_couldnt_be_retrieved",
-                      new String[]
-                      { errormsgs.toString() }), MessageManager
-              .getString("label.couldnt_load_file"),
+                      new String[] { errormsgs.toString() }),
+              MessageManager.getString("label.couldnt_load_file"),
               JOptionPane.ERROR_MESSAGE);
 
     }
@@ -674,8 +677,7 @@ public class AppJmol extends StructureViewerBase
       try
       {
         // TODO: cope with multiple PDB files in view
-        in = new BufferedReader(new FileReader(
-                jmb.getPdbFile()[0]));
+        in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
         File outFile = chooser.getSelectedFile();
 
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -749,15 +751,14 @@ public class AppJmol extends StructureViewerBase
     if (type == jalview.util.ImageMaker.TYPE.PNG)
     {
       im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.PNG,
-              "Make PNG image from view", width, height, null, null);
+              jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+              width, height, null, null);
     }
     else if (type == jalview.util.ImageMaker.TYPE.EPS)
     {
       im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.EPS,
-              "Make EPS file from view", width, height, null,
-              this.getTitle());
+              jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+              width, height, null, this.getTitle());
     }
     else
     {
@@ -889,8 +890,9 @@ public class AppJmol extends StructureViewerBase
   @Override
   public void backGround_actionPerformed(ActionEvent actionEvent)
   {
-    java.awt.Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_backgroud_colour"), null);
+    java.awt.Color col = JColorChooser
+            .showDialog(this, MessageManager
+                    .getString("label.select_backgroud_colour"), null);
     if (col != null)
     {
       jmb.setBackgroundColour(col);
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 5c4346e..1c54a5e 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -49,11 +49,10 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
-            : (AlignmentPanel) alignment;
+    AlignmentPanel ap = (alignment == null) ? appJmolWindow
+            .getAlignmentPanel() : (AlignmentPanel) alignment;
     if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
@@ -70,8 +69,7 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment)
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 99bcff4..f4a4f4d 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -64,8 +64,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
         SecondaryStructureListener, InterfaceVARNASelectionListener,
         VamsasSource
 {
-  private static final byte[] PAIRS = new byte[]
-  { '(', ')', '[', ']', '{', '}', '<', '>' };
+  private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
+      '}', '<', '>' };
 
   private AppVarnaBinding vab;
 
@@ -181,8 +181,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     String theTitle = sname
             + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
     theTitle = MessageManager.formatMessage("label.varna_params",
-            new String[]
-            { theTitle });
+            new String[] { theTitle });
     setTitle(theTitle);
 
     String gappedTitle = sname + " (with gaps)";
@@ -195,7 +194,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     vab.setSelectedIndex(0);
   }
 
-
   /**
    * Constructor that links the viewer to a parent panel (but has no structures
    * yet - use addModel to add them)
@@ -677,7 +675,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     vab.setSelectedIndex(selectedIndex);
   }
 
-
   /**
    * Add a model with associated Varna session file
    * 
@@ -716,7 +713,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     }
   }
 
-
   /**
    * Replace everything except RNA secondary structure characters with a period
    * 
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 25af7d1..521bb3e 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -113,7 +113,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
     _sideList.addMouseListener(new MouseAdapter()
     {
       @Override
-      public void mouseClicked(MouseEvent e) {
+      public void mouseClicked(MouseEvent e)
+      {
         AppVarnaBinding.this.mouseClicked(e);
       }
     });
@@ -150,7 +151,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
     _listPanel.add(j, BorderLayout.NORTH);
     _listPanel.add(listScroller, BorderLayout.CENTER);
 
-    new DropTarget(vp, new DropTargetAdapter() {
+    new DropTarget(vp, new DropTargetAdapter()
+    {
       @Override
       public void drop(DropTargetDropEvent dtde)
       {
@@ -198,8 +200,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
 
   public String[][] getParameterInfo()
   {
-    String[][] info =
-    {
+    String[][] info = {
         // Parameter Name Kind of Value Description,
         { "sequenceDBN", "String", "A raw RNA sequence" },
         { "structureDBN", "String",
@@ -287,7 +288,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
                       {
                         name += " (Model " + mn++ + ")";
                       }
-                      _rnaList.add(varnaPanel.getConfig().clone(), r, name, true);
+                      _rnaList.add(varnaPanel.getConfig().clone(), r, name,
+                              true);
                     }
                   }
                 }
@@ -482,7 +484,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
        * restore the previous display
        */
       vp.showRNA(sel.rna, sel.config);
-      
+
       return filePath;
     } catch (IOException e)
     {
@@ -500,7 +502,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
    * 
    * @param evt
    */
-  protected void changeSelectedStructure_actionPerformed(ListSelectionEvent evt)
+  protected void changeSelectedStructure_actionPerformed(
+          ListSelectionEvent evt)
   {
     if (!evt.getValueIsAdjusting())
     {
diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 7e646e2..861fe56 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -50,8 +50,8 @@ public class AssociatePdbFileWithSeq
     PDBEntry entry = new PDBEntry();
     MCview.PDBfile pdbfile = null;
     pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
-            .setMapping(false, new SequenceI[]
-            { sequence }, null, choice, protocol);
+            .setMapping(false, new SequenceI[] { sequence }, null, choice,
+                    protocol);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index a3e695a..2e72e17 100644
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -331,7 +331,8 @@ public class BlogReader extends JPanel
         {
           createDialog();
           bounds = new Rectangle(5, 5, 550, 350);
-          jd.initDialogFrame(me, false, false, MessageManager.getString("label.news_from_jalview"),
+          jd.initDialogFrame(me, false, false,
+                  MessageManager.getString("label.news_from_jalview"),
                   bounds.width, bounds.height);
           jd.frame.setModalExclusionType(ModalExclusionType.NO_EXCLUDE);
           Cache.log.debug("Displaying news.");
@@ -440,7 +441,9 @@ public class BlogReader extends JPanel
     topBottomSplitPane.setBottomComponent(bottomPanel);
     JScrollPane spTextDescription = new JScrollPane(textDescription);
     textDescription.setText("");
-    statusBar.setText(new StringBuffer("[").append(MessageManager.getString("label.status")).append("]").toString());
+    statusBar.setText(new StringBuffer("[")
+            .append(MessageManager.getString("label.status")).append("]")
+            .toString());
     buttonRefresh.addActionListener(new ActionListener()
     {
 
@@ -819,8 +822,7 @@ class ChannelsRenderer extends DefaultListCellRenderer
       component
               .setText(MessageManager.formatMessage(
                       "label.channel_title_item_count",
-                      new String[]
-                      {
+                      new String[] {
                           channel.getTitle(),
                           Integer.valueOf(channel.getUnreadItemCount())
                                   .toString() }));
@@ -848,8 +850,7 @@ class ItemsRenderer extends DefaultListCellRenderer
       {
         component.setText(MessageManager.formatMessage(
                 "label.blog_item_published_on_date",
-                new String[]
-                {
+                new String[] {
                     DateFormat
                             .getDateInstance(DateFormat.LONG,
                                     MessageManager.getLocale())
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 967d93f..09451dc 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -156,8 +156,8 @@ public class ChimeraViewFrame extends StructureViewerBase
                 alignStructs.setToolTipText(MessageManager
                         .formatMessage(
                                 "label.align_structures_using_linked_alignment_views",
-                                new Object[]
-                                { new Integer(_alignwith.size()).toString() }));
+                                new Object[] { new Integer(_alignwith
+                                        .size()).toString() }));
               }
             });
     handler.itemStateChanged(null);
@@ -298,7 +298,8 @@ public class ChimeraViewFrame extends StructureViewerBase
         String chain = null;
         if (seq.getDatasetSequence() != null)
         {
-          Vector pdbrefs = seq.getDatasetSequence().getAllPDBEntries();
+          Vector pdbrefs = seq.getDatasetSequence()
+                  .getAllPDBEntries();
           if (pdbrefs != null && pdbrefs.size() > 0)
           {
             chain = pdbrefs.get(0).getChainCode();
@@ -323,8 +324,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @param newViewId
    */
   public ChimeraViewFrame(String chimeraSessionFile,
-          AlignmentPanel alignPanel,
-          PDBEntry[] pdbArray,
+          AlignmentPanel alignPanel, PDBEntry[] pdbArray,
           SequenceI[][] seqsArray, boolean colourByChimera,
           boolean colourBySequence, String newViewId)
   {
@@ -414,14 +414,13 @@ public class ChimeraViewFrame extends StructureViewerBase
   void initChimera()
   {
     jmb.setFinishedInit(false);
-    jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
-            getBounds().width, getBounds().height);
+    jalview.gui.Desktop.addInternalFrame(this,
+            jmb.getViewerTitle("Chimera", true), getBounds().width,
+            getBounds().height);
 
     if (!jmb.launchChimera())
     {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
+      JOptionPane.showMessageDialog(Desktop.desktop,
               MessageManager.getString("label.chimera_failed"),
               MessageManager.getString("label.error_loading_file"),
               JOptionPane.ERROR_MESSAGE);
@@ -531,8 +530,8 @@ public class ChimeraViewFrame extends StructureViewerBase
       if (!closeChimera)
       {
         String prompt = MessageManager.formatMessage(
-                "label.confirm_close_chimera", new Object[]
-                { jmb.getViewerTitle("Chimera", false) });
+                "label.confirm_close_chimera",
+                new Object[] { jmb.getViewerTitle("Chimera", false) });
         prompt = JvSwingUtils.wrapTooltip(true, prompt);
         int confirm = JOptionPane.showConfirmDialog(this, prompt,
                 MessageManager.getString("label.close_viewer"),
@@ -625,9 +624,8 @@ public class ChimeraViewFrame extends StructureViewerBase
 
       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.pdb_entries_couldnt_be_retrieved",
-                      new Object[]
-                      { errormsgs.toString() }), MessageManager
-              .getString("label.couldnt_load_file"),
+                      new Object[] { errormsgs.toString() }),
+              MessageManager.getString("label.couldnt_load_file"),
               JOptionPane.ERROR_MESSAGE);
     }
 
@@ -672,9 +670,7 @@ public class ChimeraViewFrame extends StructureViewerBase
             }
             // Explicitly map to the filename used by Chimera ;
             jmb.getSsm().setMapping(jmb.getSequence()[pos],
-                    jmb.getChains()[pos],
-                    pe.getFile(),
-                    protocol);
+                    jmb.getChains()[pos], pe.getFile(), protocol);
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning(
@@ -737,8 +733,7 @@ public class ChimeraViewFrame extends StructureViewerBase
      * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
      */
     String msg = MessageManager.formatMessage("status.fetching_pdb",
-            new Object[]
-            { pdbid });
+            new Object[] { pdbid });
     getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
     // long hdl = startProgressBar(MessageManager.formatMessage(
     // "status.fetching_pdb", new Object[]
@@ -751,8 +746,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
     } finally
     {
-      msg = pdbid + " "
-              + MessageManager.getString("label.state_completed");
+      msg = pdbid + " " + MessageManager.getString("label.state_completed");
       getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
       // stopProgressBar(msg, hdl);
     }
diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java
index 4ab7586..280b4c0 100644
--- a/src/jalview/gui/Console.java
+++ b/src/jalview/gui/Console.java
@@ -22,10 +22,25 @@ package jalview.gui;
 
 import jalview.util.MessageManager;
 
-import java.io.*;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GraphicsEnvironment;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.io.IOException;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
+import java.io.PrintStream;
+
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
 
 import org.apache.log4j.SimpleLayout;
 
@@ -501,7 +516,8 @@ public class Console extends WindowAdapter implements WindowListener,
       } catch (InterruptedException ie)
       {
       }
-      throw new NullPointerException(MessageManager.getString("exception.application_test_npe"));
+      throw new NullPointerException(
+              MessageManager.getString("exception.application_test_npe"));
     }
   }
 
diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index ea5c75e..7d5d8d7 100644
--- a/src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java
@@ -20,20 +20,28 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteHtmlTransfer;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
 import java.io.StringWriter;
 
-import javax.swing.*;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
 import javax.swing.event.HyperlinkEvent;
-import javax.swing.event.HyperlinkListener;
 import javax.swing.event.HyperlinkEvent.EventType;
-
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
+import javax.swing.event.HyperlinkListener;
 
 /**
  * Cut'n'paste files into the desktop See JAL-1105
@@ -142,7 +150,8 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer
 
     chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_text_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index cd5c792..f5a8e1c 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -66,6 +66,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   AlignViewportI viewport;
 
   FileParse source = null;
+
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -129,7 +130,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_text_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -233,8 +235,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.formatMessage(
-                        "label.couldnt_read_pasted_text", new String[]
-                        { ex.toString() }), MessageManager
+                        "label.couldnt_read_pasted_text",
+                        new String[] { ex.toString() }), MessageManager
                         .getString("label.error_parsing_text"),
                 JOptionPane.WARNING_MESSAGE);
       }
@@ -243,8 +245,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     if (al != null && al.hasValidSequence())
     {
       String title = MessageManager.formatMessage(
-              "label.input_cut_paste_params", new String[]
-              { format });
+              "label.input_cut_paste_params", new String[] { format });
       if (viewport != null)
       {
         ((AlignViewport) viewport).addAlignment(al, title);
@@ -265,8 +266,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
           FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                   .getDisplayedFeatures();
           af = new AlignFrame(al, hiddenSeqs, colSel,
-                  AlignFrame.DEFAULT_WIDTH,
-                  AlignFrame.DEFAULT_HEIGHT);
+                  AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.getViewport().setFeaturesDisplayed(fd);
           af.changeColour(cs);
@@ -306,7 +306,6 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
   }
 
-
   /**
    * DOCUMENT ME!
    * 
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index fab4cb3..53e3c8d 100644
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -20,6 +20,12 @@
  */
 package jalview.gui;
 
+import jalview.jbgui.GDasSourceBrowser;
+import jalview.util.MessageManager;
+import jalview.util.TableSorter;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+
 import java.awt.BorderLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
@@ -46,12 +52,6 @@ import org.biodas.jdas.schema.sources.COORDINATES;
 import org.biodas.jdas.schema.sources.PROP;
 import org.biodas.jdas.schema.sources.VERSION;
 
-import jalview.jbgui.GDasSourceBrowser;
-import jalview.util.MessageManager;
-import jalview.util.TableSorter;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-
 public class DasSourceBrowser extends GDasSourceBrowser implements
         Runnable, ListSelectionListener
 {
@@ -535,8 +535,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
       return;
     }
 
-    Object[] options =
-    { "Edit", "Remove", "Cancel" };
+    Object[] options = { "Edit", "Remove", "Cancel" };
     int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
             "Do you want to edit or remove " + nickname + "?",
             "Edit / Remove Local DAS Source",
@@ -601,8 +600,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
     // 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" };
     List srcs = sourceRegistry.getSources();
     for (jalviewSourceI ds : srcs)
     {
@@ -632,8 +630,8 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
 
       for (int j = 0; j < coords.size(); j++)
       {
-        if (selectedInList(filter1.getSelectedValues(), new String[]
-        { coords.get(j).getAuthority() })
+        if (selectedInList(filter1.getSelectedValues(),
+                new String[] { coords.get(j).getAuthority() })
                 && selectedInList(filter2.getSelectedValues(), new String[]
                 { coords.get(j).getSource() }))
         {
@@ -739,8 +737,9 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
       this.data = data;
     }
 
-    private String[] columnNames = new String[]
-    { MessageManager.getString("label.nickname"), MessageManager.getString("label.use_source") };
+    private String[] columnNames = new String[] {
+        MessageManager.getString("label.nickname"),
+        MessageManager.getString("label.use_source") };
 
     private Object[][] data;
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 2a360cc..270805a 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1106,8 +1106,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.formatMessage("label.couldnt_locate",
-                        new Object[]
-                        { url }), MessageManager
+                        new Object[] { url }), MessageManager
                         .getString("label.url_not_found"),
                 JOptionPane.WARNING_MESSAGE);
 
@@ -1495,9 +1494,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void saveState_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "jvp" }, new String[]
-            { "Jalview Project" }, "Jalview Project");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "jvp" }, new String[] { "Jalview Project" },
+            "Jalview Project");
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_state"));
@@ -1516,8 +1515,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           // TODO: refactor to Jalview desktop session controller action.
           setProgressBar(MessageManager.formatMessage(
-                  "label.saving_jalview_project", new Object[]
-                  { choice.getName() }), choice.hashCode());
+                  "label.saving_jalview_project",
+                  new Object[] { choice.getName() }), choice.hashCode());
           jalview.bin.Cache.setProperty("LAST_DIRECTORY",
                   choice.getParent());
           // TODO catch and handle errors for savestate
@@ -1536,8 +1535,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                     ex);
             JOptionPane.showMessageDialog(me, MessageManager.formatMessage(
                     "label.error_whilst_saving_current_state_to",
-                    new Object[]
-                    { choice.getName() }), MessageManager
+                    new Object[] { choice.getName() }), MessageManager
                     .getString("label.couldnt_save_project"),
                     JOptionPane.WARNING_MESSAGE);
           }
@@ -1567,10 +1565,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void loadState_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "jvp", "jar" }, new String[]
-            { "Jalview Project", "Jalview Project (old)" },
-            "Jalview Project");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
+                "jvp", "jar" }, new String[] { "Jalview Project",
+                "Jalview Project (old)" }, "Jalview Project");
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
 
@@ -1587,9 +1584,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         public void run()
         {
-          setProgressBar(MessageManager.formatMessage(
-                  "label.loading_jalview_project", new Object[]
-                  { choice }), choice.hashCode());
+          setProgressBar(
+                  MessageManager.formatMessage(
+                          "label.loading_jalview_project",
+                          new Object[] { choice }), choice.hashCode());
           try
           {
             new Jalview2XML().loadJalviewAlign(choice);
@@ -1603,8 +1601,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
                     .formatMessage(
                             "label.error_whilst_loading_project_from",
-                            new Object[]
-                            { choice }), MessageManager
+                            new Object[] { choice }), MessageManager
                     .getString("label.couldnt_load_project"),
                     JOptionPane.WARNING_MESSAGE);
           }
@@ -1629,8 +1626,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (fileLoadingCount == 0)
     {
       fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage(
-              "label.loading_file", new Object[]
-              { fileName })));
+              "label.loading_file", new Object[] { fileName })));
     }
     fileLoadingCount++;
   }
@@ -1724,7 +1720,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       for (AlignmentPanel ap : af.alignPanels)
       {
-        if (alignmentId==null || alignmentId.equals(ap.av.getSequenceSetId()))
+        if (alignmentId == null
+                || alignmentId.equals(ap.av.getSequenceSetId()))
         {
           aps.add(ap);
         }
@@ -1755,7 +1752,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
       for (AlignFrame afr : frames)
       {
-        if (sequenceSetId==null || afr.getViewport().getSequenceSetId().equals(sequenceSetId))
+        if (sequenceSetId == null
+                || afr.getViewport().getSequenceSetId()
+                        .equals(sequenceSetId))
         {
           if (afr.alignPanels != null)
           {
@@ -1894,8 +1893,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                           Desktop.desktop,
                           MessageManager.formatMessage(
                                   "label.couldnt_import_as_vamsas_session",
-                                  new Object[]
-                                  { fle }),
+                                  new Object[] { fle }),
                           MessageManager
                                   .getString("label.vamsas_document_import_failed"),
                           JOptionPane.ERROR_MESSAGE);
@@ -1972,16 +1970,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
 
     setProgressBar(MessageManager.formatMessage(
-            "status.importing_vamsas_session_from", new Object[]
-            { file.getName() }), file.hashCode());
+            "status.importing_vamsas_session_from",
+            new Object[] { file.getName() }), file.hashCode());
     try
     {
       v_client = new jalview.gui.VamsasApplication(this, file, null);
     } catch (Exception ex)
     {
       setProgressBar(MessageManager.formatMessage(
-              "status.importing_vamsas_session_from", new Object[]
-              { file.getName() }), file.hashCode());
+              "status.importing_vamsas_session_from",
+              new Object[] { file.getName() }), file.hashCode());
       jalview.bin.Cache.log.error(
               "New vamsas session from existing session file failed:", ex);
       return false;
@@ -1989,8 +1987,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     setupVamsasConnectedGui();
     v_client.initial_update(); // TODO: thread ?
     setProgressBar(MessageManager.formatMessage(
-            "status.importing_vamsas_session_from", new Object[]
-            { file.getName() }), file.hashCode());
+            "status.importing_vamsas_session_from",
+            new Object[] { file.getName() }), file.hashCode());
     return v_client.inSession();
   }
 
@@ -2097,8 +2095,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           JMenuItem sessit = new JMenuItem();
           sessit.setText(sess[i]);
           sessit.setToolTipText(MessageManager.formatMessage(
-                  "label.connect_to_session", new Object[]
-                  { sess[i] }));
+                  "label.connect_to_session", new Object[] { sess[i] }));
           final Desktop dsktp = this;
           final String mysesid = sess[i];
           sessit.addActionListener(new ActionListener()
@@ -2151,8 +2148,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       JalviewFileChooser chooser = new JalviewFileChooser(
               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
               { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
-              new String[]
-              { "Vamsas Document" }, "Vamsas Document");
+              new String[] { "Vamsas Document" }, "Vamsas Document");
 
       chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager
@@ -2164,8 +2160,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         java.io.File choice = chooser.getSelectedFile();
         JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
-                "label.saving_vamsas_doc", new Object[]
-                { choice.getName() }));
+                "label.saving_vamsas_doc",
+                new Object[] { choice.getName() }));
         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
         String warnmsg = null;
         String warnttl = null;
@@ -2331,9 +2327,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           g.drawString(MessageManager.formatMessage(
                   "label.memory_stats",
-                  new Object[]
-                  { df.format(totalFreeMemory), df.format(maxMemory),
-                      df.format(percentUsage) }), 10,
+                  new Object[] { df.format(totalFreeMemory),
+                      df.format(maxMemory), df.format(percentUsage) }), 10,
                   getHeight() - fm.getHeight());
         }
       }
@@ -2463,12 +2458,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               "groovy.ui.Console");
       Constructor gccons = gcClass.getConstructor();
       java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
-              new Class[]
-              { String.class, Object.class });
+              new Class[] { String.class, Object.class });
       java.lang.reflect.Method run = gcClass.getMethod("run");
       Object gc = gccons.newInstance();
-      setvar.invoke(gc, new Object[]
-      { "Jalview", this });
+      setvar.invoke(gc, new Object[] { "Jalview", this });
       run.invoke(gc);
     } catch (Exception ex)
     {
@@ -2546,9 +2539,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           handler.cancelActivity(id);
           us.setProgressBar(MessageManager.formatMessage(
-                  "label.cancelled_params", new Object[]
-                  { ((JLabel) progressPanel.getComponent(0)).getText() }),
-                  id);
+                  "label.cancelled_params",
+                  new Object[] { ((JLabel) progressPanel.getComponent(0))
+                          .getText() }), id);
         }
       });
       progressPanel.add(cancel, BorderLayout.EAST);
@@ -2570,8 +2563,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * This will return the first AlignFrame holding the given viewport instance. It
-   * will break if there are more than one AlignFrames viewing a particular av.
+   * This will return the first AlignFrame holding the given viewport instance.
+   * It will break if there are more than one AlignFrames viewing a particular
+   * av.
    * 
    * @param viewport
    * @return alignFrame for viewport
@@ -2580,8 +2574,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (desktop != null)
     {
-      AlignmentPanel[] aps = getAlignmentPanels(viewport
-              .getSequenceSetId());
+      AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
       for (int panel = 0; aps != null && panel < aps.length; panel++)
       {
         if (aps[panel] != null && aps[panel].av == viewport)
@@ -2790,8 +2783,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           if (progress != null)
           {
             progress.setProgressBar(MessageManager.formatMessage(
-                    "status.opening_params", new Object[]
-                    { url }), this.hashCode());
+                    "status.opening_params", new Object[] { url }), this
+                    .hashCode());
           }
           jalview.util.BrowserLauncher.openURL(url);
         } catch (Exception ex)
@@ -3020,7 +3013,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     myBottomFrame.viewport.setGatherViewsHere(true);
     String topViewId = myTopFrame.viewport.getSequenceSetId();
     String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
-  
+
     JInternalFrame[] frames = desktop.getAllFrames();
     for (JInternalFrame frame : frames)
     {
@@ -3048,7 +3041,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             myBottomFrame.addAlignmentPanel(bottomPanel, false);
           }
         }
-  
+
         if (gatherThis)
         {
           topFrame.getAlignPanels().clear();
@@ -3075,5 +3068,4 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     Desktop.currentAlignFrame = currentAlignFrame;
   }
 
-
 }
diff --git a/src/jalview/gui/EPSOptions.java b/src/jalview/gui/EPSOptions.java
index b5c3762..69fde89 100644
--- a/src/jalview/gui/EPSOptions.java
+++ b/src/jalview/gui/EPSOptions.java
@@ -22,9 +22,19 @@ package jalview.gui;
 
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
 
 public class EPSOptions extends JPanel
 {
@@ -49,8 +59,7 @@ public class EPSOptions extends JPanel
     bg.add(text);
 
     JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
-            JOptionPane.DEFAULT_OPTION, null, new Object[]
-            { this });
+            JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
 
     dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");
     dialog.setVisible(true);
diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java
index e88dcae..baad794 100644
--- a/src/jalview/gui/EditNameDialog.java
+++ b/src/jalview/gui/EditNameDialog.java
@@ -22,8 +22,15 @@ package jalview.gui;
 
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
 
 public class EditNameDialog
 {
diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java
index 7f76760..625cccc 100644
--- a/src/jalview/gui/FeatureColourChooser.java
+++ b/src/jalview/gui/FeatureColourChooser.java
@@ -20,19 +20,32 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.border.LineBorder;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.GraphLine;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
 import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
+
+import javax.swing.BorderFactory;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.border.LineBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
 
 public class FeatureColourChooser extends JalviewDialog
 {
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 9e09bfb..a0f1b80 100644
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -55,7 +55,9 @@ import javax.swing.SwingConstants;
  * @author $author$
  * @version $Revision$
  */
-public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer implements jalview.api.FeatureRenderer
+public class FeatureRenderer extends
+        jalview.renderer.seqfeatures.FeatureRenderer implements
+        jalview.api.FeatureRenderer
 {
   Color resBoxColour;
 
@@ -72,7 +74,8 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
     super();
     this.ap = ap;
     this.av = ap.av;
-    if (ap != null && ap.getSeqPanel() != null && ap.getSeqPanel().seqCanvas != null
+    if (ap != null && ap.getSeqPanel() != null
+            && ap.getSeqPanel().seqCanvas != null
             && ap.getSeqPanel().seqCanvas.fr != null)
     {
       transferSettings(ap.getSeqPanel().seqCanvas.fr);
@@ -123,7 +126,8 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
         if (fcol instanceof Color)
         {
           Color col = JColorChooser.showDialog(Desktop.desktop,
-                  MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
+                  MessageManager.getString("label.select_feature_colour"),
+                  ((Color) fcol));
           if (col != null)
           {
             fcol = col;
@@ -306,21 +310,22 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
     Object[] options;
     if (!newFeatures)
     {
-      options = new Object[]
-      { "Amend", "Delete", "Cancel" };
+      options = new Object[] { "Amend", "Delete", "Cancel" };
     }
     else
     {
-      options = new Object[]
-      { "OK", "Cancel" };
+      options = new Object[] { "OK", "Cancel" };
     }
 
-    String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
-            : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
+    String title = newFeatures ? MessageManager
+            .getString("label.create_new_sequence_features")
+            : MessageManager.formatMessage("label.amend_delete_features",
+                    new String[] { sequences[0].getName() });
 
     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
-            JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
+            JOptionPane.QUESTION_MESSAGE, null, options,
+            MessageManager.getString("action.ok"));
 
     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 
@@ -406,7 +411,6 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
     return true;
   }
 
-
   /**
    * update the amend feature button dependent on the given style
    * 
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 940a216..6b58b51 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -125,7 +125,8 @@ public class FeatureSettings extends JPanel implements
     this.af = af;
     fr = af.getFeatureRenderer();
     // allow transparency to be recovered
-    transparency.setMaximum(100 - (int) ((originalTransparency=fr.getTransparency()) * 100));
+    transparency.setMaximum(100 - (int) ((originalTransparency = fr
+            .getTransparency()) * 100));
 
     try
     {
@@ -135,15 +136,18 @@ public class FeatureSettings extends JPanel implements
       ex.printStackTrace();
     }
 
-    table = new JTable() {
+    table = new JTable()
+    {
       @Override
-      public String getToolTipText(MouseEvent e) {
-        if (table.columnAtPoint(e.getPoint()) == 0) {
+      public String getToolTipText(MouseEvent e)
+      {
+        if (table.columnAtPoint(e.getPoint()) == 0)
+        {
           /*
            * Tooltip for feature name only
            */
-          return JvSwingUtils.wrapTooltip(true,
-                MessageManager.getString("label.feature_settings_click_drag"));
+          return JvSwingUtils.wrapTooltip(true, MessageManager
+                  .getString("label.feature_settings_click_drag"));
         }
         return null;
       }
@@ -187,8 +191,7 @@ public class FeatureSettings extends JPanel implements
         {
           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
-                  evt.getX(),
-                  evt.getY());
+                  evt.getX(), evt.getY());
         }
       }
     });
@@ -217,8 +220,8 @@ public class FeatureSettings extends JPanel implements
         }
       }
     });
-//    table.setToolTipText(JvSwingUtils.wrapTooltip(true,
-//            MessageManager.getString("label.feature_settings_click_drag")));
+    // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
+    // MessageManager.getString("label.feature_settings_click_drag")));
     scrollPane.setViewportView(table);
 
     dassourceBrowser = new DasSourceBrowser(this);
@@ -278,8 +281,7 @@ public class FeatureSettings extends JPanel implements
           final Object typeCol, final Hashtable minmax, int x, int y)
   {
     JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
-            "label.settings_for_param", new String[]
-            { type }));
+            "label.settings_for_param", new String[] { type }));
     JMenuItem scr = new JMenuItem(
             MessageManager.getString("label.sort_by_score"));
     men.add(scr);
@@ -289,8 +291,7 @@ public class FeatureSettings extends JPanel implements
 
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureScore(new String[]
-        { type });
+        me.af.avc.sortAlignmentByFeatureScore(new String[] { type });
       }
 
     });
@@ -301,8 +302,7 @@ public class FeatureSettings extends JPanel implements
 
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureDensity(new String[]
-        { type });
+        me.af.avc.sortAlignmentByFeatureDensity(new String[] { type });
       }
 
     });
@@ -516,8 +516,7 @@ public class FeatureSettings extends JPanel implements
           af.alignPanel.overviewPanel.updateOverviewImage();
         }
 
-        resetTable(new String[]
-        { grp });
+        resetTable(new String[] { grp });
       }
     });
     groupPanel.add(check);
@@ -705,11 +704,13 @@ public class FeatureSettings extends JPanel implements
   void load()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "fc" }, new String[]
-            { "Sequence Feature Colours" }, "Sequence Feature Colours");
+            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(MessageManager.getString("label.load_feature_colours"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.load_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.load"));
 
     int value = chooser.showOpenDialog(this);
@@ -724,8 +725,7 @@ public class FeatureSettings extends JPanel implements
                 file), "UTF-8");
 
         jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-        jucs = jucs
-                .unmarshal(in);
+        jucs = jucs.unmarshal(in);
 
         for (int i = jucs.getColourCount() - 1; i >= 0; i--)
         {
@@ -803,11 +803,13 @@ public class FeatureSettings extends JPanel implements
   void save()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "fc" }, new String[]
-            { "Sequence Feature Colours" }, "Sequence Feature Colours");
+            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(MessageManager.getString("label.save_feature_colours"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -942,9 +944,9 @@ public class FeatureSettings extends JPanel implements
       }
     }
     if (sort)
-     {
+    {
       jalview.util.QuickSort.sort(width, data);
-    // update global priority order
+      // update global priority order
     }
 
     updateFeatureRenderer(data, false);
@@ -1169,8 +1171,10 @@ public class FeatureSettings extends JPanel implements
       }
     });
     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-    tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane);
-    tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane);
+    tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
+            settingsPane);
+    tabbedPane.addTab(MessageManager.getString("label.das_settings"),
+            dasSettingsPane);
     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
     transbuttons.add(optimizeOrder);
     transbuttons.add(invert);
@@ -1364,8 +1368,10 @@ public class FeatureSettings extends JPanel implements
       this.data = data;
     }
 
-    private String[] columnNames =
-    { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") };
+    private String[] columnNames = {
+        MessageManager.getString("label.feature_type"),
+        MessageManager.getString("action.colour"),
+        MessageManager.getString("label.display") };
 
     private Object[][] data;
 
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5d07562..6bff69a 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -20,6 +20,13 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.KeyEvent;
 import java.util.Vector;
@@ -33,13 +40,6 @@ import javax.swing.JLayeredPane;
 import javax.swing.JOptionPane;
 import javax.swing.KeyStroke;
 
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GFinder;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-
 /**
  * Performs the menu option for searching the alignment, for the next or all
  * matches. If matches are found, they are highlighted, and the user has the
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index 2ffb166..535196e 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -20,6 +20,10 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
+import jalview.jbgui.GFontChooser;
+import jalview.util.MessageManager;
+
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.event.ActionEvent;
@@ -29,10 +33,6 @@ import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JOptionPane;
 
-import jalview.bin.Cache;
-import jalview.jbgui.GFontChooser;
-import jalview.util.MessageManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -249,11 +249,10 @@ public class FontChooser extends GFontChooser
     {
       final String messageKey = iBounds.getHeight() < 1 ? "label.font_doesnt_have_letters_defined"
               : "label.font_too_small";
-      JOptionPane
-              .showInternalMessageDialog(
-                      this,
+      JOptionPane.showInternalMessageDialog(this,
               MessageManager.getString(messageKey),
-                      MessageManager.getString("label.invalid_font"), JOptionPane.WARNING_MESSAGE);
+              MessageManager.getString("label.invalid_font"),
+              JOptionPane.WARNING_MESSAGE);
       /*
        * Restore the changed value - note this will reinvoke this method via the
        * ActionListener, but now validation should pass
diff --git a/src/jalview/gui/HTMLOptions.java b/src/jalview/gui/HTMLOptions.java
index 0ef4710..97cbcb0 100644
--- a/src/jalview/gui/HTMLOptions.java
+++ b/src/jalview/gui/HTMLOptions.java
@@ -39,8 +39,7 @@ public class HTMLOptions extends JPanel
     bg.add(text);
 
     JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
-            JOptionPane.DEFAULT_OPTION, null, new Object[]
-            { this });
+            JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
 
     dialog = pane.createDialog(Desktop.desktop, "HTML Rendering options");
     dialog.setVisible(true);
diff --git a/src/jalview/gui/Help.java b/src/jalview/gui/Help.java
index b07cc4e..1224645 100644
--- a/src/jalview/gui/Help.java
+++ b/src/jalview/gui/Help.java
@@ -52,7 +52,9 @@ public class Help
    * 
    * This is a workaround for issue JAL-914 - both Desktop and AlignFrame
    * responding to F1 key, resulting in duplicate help windows opened.
-   * @param id TODO
+   * 
+   * @param id
+   *          TODO
    * 
    * @throws HelpSetException
    */
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index fe42e1e..c89a9d5 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -98,8 +98,7 @@ public class IdCanvas extends JPanel
    *          DOCUMENT ME!
    */
   public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
-          int i, int starty,
-          int ypos)
+          int i, int starty, int ypos)
   {
     int xPos = 0;
     int panelWidth = getWidth();
@@ -453,11 +452,9 @@ public class IdCanvas extends JPanel
     if (below)
     {
       gg.fillPolygon(
-              new int[]
-              { getWidth() - av.getCharHeight(),
-                  getWidth() - av.getCharHeight(),
-                  getWidth() }, new int[]
-              {
+              new int[] { getWidth() - av.getCharHeight(),
+                  getWidth() - av.getCharHeight(), getWidth() },
+              new int[] {
                   (i - starty) * av.getCharHeight() + yoffset,
                   (i - starty) * av.getCharHeight() + yoffset
                           + av.getCharHeight() / 4,
@@ -466,11 +463,9 @@ public class IdCanvas extends JPanel
     if (above)
     {
       gg.fillPolygon(
-              new int[]
-              { getWidth() - av.getCharHeight(),
-                  getWidth() - av.getCharHeight(),
-                  getWidth() }, new int[]
-              {
+              new int[] { getWidth() - av.getCharHeight(),
+                  getWidth() - av.getCharHeight(), getWidth() },
+              new int[] {
                   (i - starty + 1) * av.getCharHeight() + yoffset,
                   (i - starty + 1) * av.getCharHeight() + yoffset
                           - av.getCharHeight() / 4,
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 88d0c69..5dfe581 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -109,10 +109,9 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       SequenceI sequence = av.getAlignment().getSequenceAt(seq);
       StringBuffer tip = new StringBuffer(64);
-      seqAnnotReport
-              .createSequenceAnnotationReport(tip, sequence,
+      seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
               av.isShowDBRefs(), av.isShowNPFeats(),
-                      sp.seqCanvas.fr.getMinMax());
+              sp.seqCanvas.fr.getMinMax());
       setToolTipText("" + sequence.getDisplayId(true) + " "
               + tip.toString() + "");
     }
@@ -245,11 +244,10 @@ public class IdPanel extends JPanel implements MouseListener,
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
-      JOptionPane
-              .showInternalMessageDialog(
-                      Desktop.desktop,
-                      MessageManager.getString("label.web_browser_not_found_unix"),
-                      MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager.getString("label.web_browser_not_found_unix"),
+              MessageManager.getString("label.web_browser_not_found"),
+              JOptionPane.WARNING_MESSAGE);
       ex.printStackTrace();
     }
   }
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 3d82256..0c03db1 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
+
 import java.awt.Color;
 import java.awt.Graphics;
 import java.awt.Image;
@@ -29,8 +31,6 @@ import java.awt.event.MouseMotionListener;
 
 import javax.swing.JPanel;
 
-import jalview.api.AlignViewportI;
-
 /**
  * DOCUMENT ME!
  * 
diff --git a/src/jalview/gui/JDatabaseTree.java b/src/jalview/gui/JDatabaseTree.java
index 207c600..a886723 100644
--- a/src/jalview/gui/JDatabaseTree.java
+++ b/src/jalview/gui/JDatabaseTree.java
@@ -88,7 +88,9 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
 
   public JDatabaseTree(jalview.ws.SequenceFetcher sfetch)
   {
-    initDialogFrame(this, true, false, MessageManager.getString("label.select_database_retrieval_source"),
+    initDialogFrame(this, true, false,
+            MessageManager
+                    .getString("label.select_database_retrieval_source"),
             650, 490);
     /*
      * Dynamically generated database list will need a translation function from
@@ -221,7 +223,9 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
       }
       else
       {
-        throw new Error(MessageManager.getString("error.implementation_error_cant_reorder_tree"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_cant_reorder_tree"));
       }
     }
     jalview.util.QuickSort.sort(names, nodes);
@@ -412,8 +416,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
     if (allowMultiSelections)
     {
       dbstatus.setText(MessageManager.formatMessage(
-              "label.selected_database_to_fetch_from", new String[]
-              {
+              "label.selected_database_to_fetch_from", new String[] {
                   Integer.valueOf(srcs.size()).toString(),
                   (srcs.size() == 1 ? "" : "s"),
                   (srcs.size() > 0 ? " with " + x + " test quer"
@@ -425,13 +428,11 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
       if (nm.length() > 0)
       {
         dbstatus.setText(MessageManager.formatMessage(
-                "label.database_param", new String[]
-                { nm }));
+                "label.database_param", new String[] { nm }));
         if (qr.length() > 0)
         {
           dbstatex.setText(MessageManager.formatMessage(
-                  "label.example_param", new String[]
-                  { qr }));
+                  "label.example_param", new String[] { qr }));
         }
         else
         {
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 2f90e91..f87fbe5 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1854,8 +1854,8 @@ public class Jalview2XML
       }
     }
     throw new Error(MessageManager.formatMessage(
-            "error.unsupported_version_calcIdparam", new Object[]
-            { calcIdParam.toString() }));
+            "error.unsupported_version_calcIdparam",
+            new Object[] { calcIdParam.toString() }));
   }
 
   /**
@@ -2839,8 +2839,8 @@ public class Jalview2XML
             else
             {
               // defer to later
-              frefedSequence.add(new Object[]
-              { maps[m].getDnasq(), cf, mapping });
+              frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
+                  mapping });
             }
           }
         }
@@ -4583,8 +4583,8 @@ public class Jalview2XML
       /**
        * Kludge for magic autoannotation names (see JAL-811)
        */
-      String[] magicNames = new String[]
-      { "Consensus", "Quality", "Conservation" };
+      String[] magicNames = new String[] { "Consensus", "Quality",
+          "Conservation" };
       JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
       Hashtable visan = new Hashtable();
       for (String nm : magicNames)
@@ -4994,8 +4994,7 @@ public class Jalview2XML
         }
         else
         {
-          frefedSequence.add(new Object[]
-          { dsfor, jmap });
+          frefedSequence.add(new Object[] { dsfor, jmap });
         }
       }
       else
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index cb572cd..b551f5d 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -161,8 +161,7 @@ public class Jalview2XML_V1
                     + "\n");
             JOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage("label.couldnt_locate",
-                            new String[]
-                            { file }), MessageManager
+                            new String[] { file }), MessageManager
                             .getString("label.url_not_found"),
                     JOptionPane.WARNING_MESSAGE);
           }
@@ -181,7 +180,10 @@ public class Jalview2XML_V1
           {
 
             JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                    MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
+                    MessageManager.formatMessage(
+                            "label.error_loading_file_params", new String[]
+                            { file }), MessageManager
+                            .getString("label.error_loading_jalview_file"),
                     JOptionPane.WARNING_MESSAGE);
           }
         });
@@ -348,8 +350,7 @@ public class Jalview2XML_V1
 
         for (int s = 0; s < ids.length; s++)
         {
-          seqs.addElement(seqids
-                  .elementAt(ids[s]));
+          seqs.addElement(seqids.elementAt(ids[s]));
         }
 
         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
@@ -435,19 +436,21 @@ public class Jalview2XML_V1
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
 
-        featureColours.put(
-                setting.getType(), new java.awt.Color(setting.getColour()));
+        featureColours.put(setting.getType(),
+                new java.awt.Color(setting.getColour()));
 
         renderOrder[fs] = setting.getType();
 
         if (setting.getDisplay())
         {
-          featuresDisplayed.put(setting.getType(), new Integer(
-                  setting.getColour()));
+          featuresDisplayed.put(setting.getType(),
+                  new Integer(setting.getColour()));
         }
       }
-      FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
-      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(frs);
+      FeatureRendererSettings frs = new FeatureRendererSettings(
+              renderOrder, new Hashtable(), featureColours, 1.0f, null);
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+              .transferSettings(frs);
     }
 
     af.setMenusFromViewport(af.viewport);
diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index a5af244..892e094 100644
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -21,8 +21,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   }
 
   @Override
-  public FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
     AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
             : (AlignmentPanel) alignment;
@@ -103,17 +102,17 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
       @Override
       public void run()
       {
-    long stm = cvf.startProgressBar(progressMsg);
-    try
-    {
-      sendChimeraCommand(command, false);
-    } finally
-    {
-      cvf.stopProgressBar(null, stm);
-    }
+        long stm = cvf.startProgressBar(progressMsg);
+        try
+        {
+          sendChimeraCommand(command, false);
+        } finally
+        {
+          cvf.stopProgressBar(null, stm);
+        }
       }
     });
-  thread.start();
+    thread.start();
 
   }
 }
diff --git a/src/jalview/gui/JvSwingUtils.java b/src/jalview/gui/JvSwingUtils.java
index 2cba586..052c314 100644
--- a/src/jalview/gui/JvSwingUtils.java
+++ b/src/jalview/gui/JvSwingUtils.java
@@ -86,9 +86,9 @@ public final class JvSwingUtils
       return enclose ? "" + ttext + "" : ttext;
     }
 
-      return (enclose ? "" : "")
-              + "
"
-              + ttext + "
" + ((enclose ? "" : ""));
+    return (enclose ? "" : "")
+            + "
"
+            + ttext + "
" + ((enclose ? "" : ""));
 
   }
 
diff --git a/src/jalview/gui/OOMWarning.java b/src/jalview/gui/OOMWarning.java
index 319c283..eb4425e 100644
--- a/src/jalview/gui/OOMWarning.java
+++ b/src/jalview/gui/OOMWarning.java
@@ -77,12 +77,11 @@ public class OOMWarning implements Runnable
 
   public void run()
   {
-    javax.swing.JOptionPane
-            .showInternalMessageDialog(
-                    desktop,
-                    MessageManager.formatMessage("warn.out_of_memory_when_action", new String[]{action}),
-                    MessageManager.getString("label.out_of_memory"),
-                    javax.swing.JOptionPane.WARNING_MESSAGE);
+    javax.swing.JOptionPane.showInternalMessageDialog(desktop,
+            MessageManager.formatMessage("warn.out_of_memory_when_action",
+                    new String[] { action }), MessageManager
+                    .getString("label.out_of_memory"),
+            javax.swing.JOptionPane.WARNING_MESSAGE);
     // hope that there's enough memory left that no more appear.
     oomInprogress = false;
   }
diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 9b805d1..8a0fe77 100644
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -41,7 +41,6 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 
@@ -111,21 +110,21 @@ public class OptsAndParamsPage
       {
         hasLink = true;
 
-        enabled.setToolTipText(
-             JvSwingUtils
-                        .wrapTooltip(true, ((desc == null || desc.trim().length() == 0) ? MessageManager.getString("label.opt_and_params_further_details ")
+        enabled.setToolTipText(JvSwingUtils
+                .wrapTooltip(
+                        true,
+                        ((desc == null || desc.trim().length() == 0) ? MessageManager
+                                .getString("label.opt_and_params_further_details ")
                                 : desc)
-                                + "
")
-                );
+                                + "
"));
         enabled.addMouseListener(this);
       }
       else
       {
         if (desc != null && desc.trim().length() > 0)
         {
-          enabled.setToolTipText(
-                   JvSwingUtils.wrapTooltip(true, opt.getDescription())
-                 );
+          enabled.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                  opt.getDescription()));
         }
       }
       add(enabled, BorderLayout.NORTH);
@@ -345,10 +344,14 @@ public class OptsAndParamsPage
       {
         // Only create description boxes if there actually is a description.
         ttipText = (JvSwingUtils
-                        .wrapTooltip(true, parm.getDescription()
+                .wrapTooltip(
+                        true,
+                        parm.getDescription()
                                 + (finfo != null ? "
"+MessageManager.getString("label.opt_and_params_further_detail")
+                                        + "\"/>"
+                                        + MessageManager
+                                                .getString("label.opt_and_params_further_detail")
                                         : "")));
       }
 
@@ -390,12 +393,21 @@ public class OptsAndParamsPage
         // Only create description boxes if there actually is a description.
         if (finfo != null)
         {
-          showDesc.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.opt_and_params_show_brief_desc_image_link", new String[]{linkImageURL.toExternalForm()})));
+          showDesc.setToolTipText(JvSwingUtils.wrapTooltip(
+                  true,
+                  MessageManager
+                          .formatMessage(
+                                  "label.opt_and_params_show_brief_desc_image_link",
+                                  new String[] { linkImageURL
+                                          .toExternalForm() })));
           showDesc.addMouseListener(this);
         }
         else
         {
-          showDesc.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.opt_and_params_show_brief_desc")));
+          showDesc.setToolTipText(JvSwingUtils.wrapTooltip(
+                  true,
+                  MessageManager
+                          .getString("label.opt_and_params_show_brief_desc")));
         }
         showDesc.addActionListener(new ActionListener()
         {
@@ -678,8 +690,7 @@ public class OptsAndParamsPage
           {
             slider.setVisible(false);
           }
-          return new int[]
-          { iVal };
+          return new int[] { iVal };
         }
         else
         {
@@ -721,8 +732,7 @@ public class OptsAndParamsPage
           {
             slider.setVisible(false);
           }
-          return new float[]
-          { fVal };
+          return new float[] { fVal };
         }
       }
       else
@@ -730,13 +740,11 @@ public class OptsAndParamsPage
         if (!choice)
         {
           slider.setVisible(false);
-          return new String[]
-          { valueField.getText().trim() };
+          return new String[] { valueField.getText().trim() };
         }
         else
         {
-          return new String[]
-          { (String) choicebox.getSelectedItem() };
+          return new String[] { (String) choicebox.getSelectedItem() };
         }
       }
 
@@ -767,8 +775,7 @@ public class OptsAndParamsPage
 
     JPopupMenu mnu = new JPopupMenu();
     JMenuItem mitem = new JMenuItem(MessageManager.formatMessage(
-            "label.view_params", new String[]
-            { finfo }));
+            "label.view_params", new String[] { finfo }));
     mitem.addActionListener(new ActionListener()
     {
 
@@ -854,7 +861,9 @@ public class OptsAndParamsPage
       }
       else
       {
-        throw new Error(MessageManager.formatMessage("error.invalid_value_for_option", new String[]{string,option.getName()}));
+        throw new Error(MessageManager.formatMessage(
+                "error.invalid_value_for_option", new String[] { string,
+                    option.getName() }));
       }
 
     }
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 609e010..de0dbe5 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -92,7 +92,7 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.renderGaps = false;
     sr.forOverview = true;
     fr = new FeatureRenderer(ap);
-    
+
     // scale the initial size of overviewpanel to shape of alignment
     float initialScale = (float) av.getAlignment().getWidth()
             / (float) av.getAlignment().getHeight();
@@ -364,8 +364,8 @@ public class OverviewPanel extends JPanel implements Runnable
         }
 
         if (hiddenRow
-                || (hasHiddenCols && !av.getColumnSelection()
-                        .isVisible(lastcol)))
+                || (hasHiddenCols && !av.getColumnSelection().isVisible(
+                        lastcol)))
         {
           color = new Color(color).darker().darker().getRGB();
         }
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index f4fd70b..b6e5b94 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -20,6 +20,17 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPCAPanel;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Graphics;
@@ -37,17 +48,6 @@ import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.JRadioButtonMenuItem;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GPCAPanel;
-import jalview.schemes.ResidueProperties;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.PCAModel;
-
 /**
  * DOCUMENT ME!
  * 
@@ -113,11 +113,10 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
     if (!sameLength)
     {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager.getString("label.pca_sequences_not_aligned"),
-                      MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showMessageDialog(Desktop.desktop,
+              MessageManager.getString("label.pca_sequences_not_aligned"),
+              MessageManager.getString("label.sequences_not_aligned"),
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -170,7 +169,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
   public void bgcolour_actionPerformed(ActionEvent e)
   {
-    Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_backgroud_colour"),
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_backgroud_colour"),
             rc.bgColour);
 
     if (col != null)
@@ -397,8 +397,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
         // msaorder);
 
         Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.original_data_for_params", new String[]
-                { this.title }), AlignFrame.DEFAULT_WIDTH,
+                "label.original_data_for_params",
+                new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -488,15 +488,14 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (type == jalview.util.ImageMaker.TYPE.PNG)
     {
       im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.PNG,
-              "Make PNG image from PCA", width, height, null, null);
+              jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
+              width, height, null, null);
     }
     else if (type == jalview.util.ImageMaker.TYPE.EPS)
     {
       im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.EPS,
-              "Make EPS file from PCA", width, height, null,
-              this.getTitle());
+              jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
+              width, height, null, this.getTitle());
     }
     else
     {
@@ -597,8 +596,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.points_for_params", new String[]
-              { this.getTitle() }), 500, 500);
+              "label.points_for_params", new String[] { this.getTitle() }),
+              500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting PCA points", oom);
@@ -622,14 +621,15 @@ public class PCAPanel extends GPCAPanel implements Runnable,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.transformed_points_for_params", new String[]
-              { this.getTitle() }), 500, 500);
+              "label.transformed_points_for_params",
+              new String[] { this.getTitle() }), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting transformed PCA points", oom);
       cap.dispose();
     }
   }
+
   /*
    * (non-Javadoc)
    * 
diff --git a/src/jalview/gui/PDBSearchPanel.java b/src/jalview/gui/PDBSearchPanel.java
index 4e23f57..4c89f12 100644
--- a/src/jalview/gui/PDBSearchPanel.java
+++ b/src/jalview/gui/PDBSearchPanel.java
@@ -54,7 +54,6 @@ public class PDBSearchPanel extends GPDBSearchPanel
             .getProgressIndicator();
   }
 
-
   /**
    * Action performed when an input is detected on txt_search field.
    */
@@ -161,7 +160,6 @@ public class PDBSearchPanel extends GPDBSearchPanel
     return foundSearchTerms;
   }
 
-
   @Override
   public void btn_ok_ActionPerformed()
   {
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index a11b40d..fee47e5 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -137,7 +137,7 @@ public class PopupMenu extends JPopupMenu
   JMenuItem sequenceDetails = new JMenuItem();
 
   JMenuItem sequenceSelDetails = new JMenuItem();
-  
+
   JMenuItem makeReferenceSeq = new JMenuItem();
 
   JMenuItem chooseAnnotations = new JMenuItem();
@@ -319,7 +319,9 @@ public class PopupMenu extends JPopupMenu
       {
         makeReferenceSeq.setText(MessageManager
                 .getString("action.unmark_as_reference"));
-      } else {
+      }
+      else
+      {
         makeReferenceSeq.setText(MessageManager
                 .getString("action.set_as_reference"));
       }
@@ -348,8 +350,8 @@ public class PopupMenu extends JPopupMenu
                */
               menuItem = new JMenuItem();
               menuItem.setText(MessageManager.formatMessage(
-                      "label.2d_rna_structure_line", new Object[]
-                      { aa.label }));
+                      "label.2d_rna_structure_line",
+                      new Object[] { aa.label }));
               menuItem.addActionListener(new java.awt.event.ActionListener()
               {
                 @Override
@@ -376,8 +378,8 @@ public class PopupMenu extends JPopupMenu
               // TODO: make rnastrucF a bit more nice
               menuItem = new JMenuItem();
               menuItem.setText(MessageManager.formatMessage(
-                      "label.2d_rna_sequence_name", new Object[]
-                      { seq.getName() }));
+                      "label.2d_rna_sequence_name",
+                      new Object[] { seq.getName() }));
               menuItem.addActionListener(new java.awt.event.ActionListener()
               {
                 @Override
@@ -413,8 +415,8 @@ public class PopupMenu extends JPopupMenu
               && ap.av.getSelectionGroup().getSize() > 1)
       {
         menuItem = new JMenuItem(MessageManager.formatMessage(
-                "label.represent_group_with", new Object[]
-                { seq.getName() }));
+                "label.represent_group_with",
+                new Object[] { seq.getName() }));
         menuItem.addActionListener(new java.awt.event.ActionListener()
         {
           @Override
@@ -482,8 +484,7 @@ public class PopupMenu extends JPopupMenu
     if (sg != null && sg.getSize() > 0)
     {
       groupName.setText(MessageManager.formatMessage("label.name_param",
-              new Object[]
-              { sg.getName() }));
+              new Object[] { sg.getName() }));
       groupName.setText(MessageManager
               .getString("label.edit_name_and_description_current_group"));
 
@@ -641,8 +642,7 @@ public class PopupMenu extends JPopupMenu
 
           // collect matching db-refs
           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
-                  seq.getDBRef(), new String[]
-                  { urlLink.getTarget() });
+                  seq.getDBRef(), new String[] { urlLink.getTarget() });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
@@ -773,17 +773,15 @@ public class PopupMenu extends JPopupMenu
      */
     Map>> shownTypes = new LinkedHashMap>>();
     Map>> hiddenTypes = new LinkedHashMap>>();
-    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
-            hiddenTypes,
-            AlignmentAnnotationUtils.asList(annotations),
-            forSequences);
+    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+            AlignmentAnnotationUtils.asList(annotations), forSequences);
 
     for (String calcId : hiddenTypes.keySet())
     {
       for (List type : hiddenTypes.get(calcId))
       {
-        addAnnotationTypeToShowHide(showMenu, forSequences,
-                calcId, type, false, true);
+        addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+                false, true);
       }
     }
     // grey out 'show annotations' if none are hidden
@@ -793,8 +791,8 @@ public class PopupMenu extends JPopupMenu
     {
       for (List type : shownTypes.get(calcId))
       {
-        addAnnotationTypeToShowHide(hideMenu, forSequences,
-                calcId, type, false, false);
+        addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+                false, false);
       }
     }
     // grey out 'hide annotations' if none are shown
@@ -855,8 +853,8 @@ public class PopupMenu extends JPopupMenu
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
-                forSequences, allTypes, actionIsShow);
+        AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+                types, forSequences, allTypes, actionIsShow);
         refresh();
       }
     });
@@ -872,8 +870,8 @@ public class PopupMenu extends JPopupMenu
     // ID/regex match URLs
     groupLinksMenu = new JMenu(
             MessageManager.getString("action.group_link"));
-    JMenu[] linkMenus = new JMenu[]
-    { null, new JMenu(MessageManager.getString("action.ids")),
+    JMenu[] linkMenus = new JMenu[] { null,
+        new JMenu(MessageManager.getString("action.ids")),
         new JMenu(MessageManager.getString("action.sequences")),
         new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
                                                                        // types
@@ -908,8 +906,7 @@ public class PopupMenu extends JPopupMenu
           if (sarray == null)
           {
             sarray = new Object[2];
-            sarray[0] = new int[]
-            { 0 };
+            sarray[0] = new int[] { 0 };
             sarray[1] = new String[seqs.length];
 
             commonDbrefs.put(src, sarray);
@@ -1029,8 +1026,7 @@ public class PopupMenu extends JPopupMenu
   {
     JMenuItem item = new JMenuItem(label);
     item.setToolTipText(MessageManager.formatMessage(
-            "label.open_url_param", new Object[]
-            { url }));
+            "label.open_url_param", new Object[] { url }));
     item.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
@@ -1069,8 +1065,7 @@ public class PopupMenu extends JPopupMenu
     JMenuItem item = new JMenuItem(label);
     item.setToolTipText(MessageManager.formatMessage(
             "label.open_url_seqs_param",
-            new Object[]
-            { urlgenerator.getUrl_prefix(),
+            new Object[] { urlgenerator.getUrl_prefix(),
                 urlgenerator.getNumberInvolved(urlstub) }));
     // TODO: put in info about what is being sent.
     item.addActionListener(new java.awt.event.ActionListener()
@@ -1356,8 +1351,7 @@ public class PopupMenu extends JPopupMenu
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        SequenceI[] selectedSeqs = new SequenceI[]
-        { sequence };
+        SequenceI[] selectedSeqs = new SequenceI[] { sequence };
         if (ap.av.getSelectionGroup() != null)
         {
           selectedSeqs = ap.av.getSequenceSelection();
@@ -1384,15 +1378,16 @@ public class PopupMenu extends JPopupMenu
             .getString("label.mark_as_representative"));
     makeReferenceSeq.addActionListener(new ActionListener()
     {
-      
+
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         makeReferenceSeq_actionPerformed(actionEvent);
-        
+
       }
     });
-    hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
+    hideInsertions.setText(MessageManager
+            .getString("label.hide_insertions"));
     hideInsertions.addActionListener(new ActionListener()
     {
 
@@ -1413,7 +1408,7 @@ public class PopupMenu extends JPopupMenu
     add(sequenceMenu);
     add(rnaStructureMenu);
     add(pdbStructureDialog);
-    if (sequence!=null)
+    if (sequence != null)
     {
       add(hideInsertions);
     }
@@ -1671,8 +1666,8 @@ public class PopupMenu extends JPopupMenu
    * @param menuItem
    * @param forSequences
    */
-  protected void configureReferenceAnnotationsMenu(
-          JMenuItem menuItem, List forSequences)
+  protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
+          List forSequences)
   {
     menuItem.setEnabled(false);
 
@@ -1768,6 +1763,7 @@ public class PopupMenu extends JPopupMenu
     }
     refresh();
   }
+
   protected void sequenceSelectionDetails_actionPerformed()
   {
     createSequenceDetailsReport(ap.av.getSequenceSelection());
@@ -1775,8 +1771,7 @@ public class PopupMenu extends JPopupMenu
 
   protected void sequenceDetails_actionPerformed()
   {
-    createSequenceDetailsReport(new SequenceI[]
-    { sequence });
+    createSequenceDetailsReport(new SequenceI[] { sequence });
   }
 
   public void createSequenceDetailsReport(SequenceI[] sequences)
@@ -1789,8 +1784,8 @@ public class PopupMenu extends JPopupMenu
               + MessageManager
                       .formatMessage(
                               "label.create_sequence_details_report_annotation_for",
-                              new Object[]
-                              { seq.getDisplayId(true) }) + "
");
+                              new Object[] { seq.getDisplayId(true) })
+              + "
");
       new SequenceAnnotationReport(null)
               .createSequenceAnnotationReport(
                       contents,
@@ -1799,8 +1794,7 @@ public class PopupMenu extends JPopupMenu
                       true,
                       false,
                       (ap.getSeqPanel().seqCanvas.fr != null) ? ap
-                              .getSeqPanel().seqCanvas.fr
-                              .getMinMax()
+                              .getSeqPanel().seqCanvas.fr.getMinMax()
                               : null);
       contents.append("
");
     }
@@ -1808,9 +1802,9 @@ public class PopupMenu extends JPopupMenu
 
     Desktop.addInternalFrame(cap, MessageManager.formatMessage(
             "label.sequence_details_for",
-            (sequences.length == 1 ? new Object[]
-            { sequences[0].getDisplayId(true) } : new Object[]
-            { MessageManager.getString("label.selection") })), 500, 400);
+            (sequences.length == 1 ? new Object[] { sequences[0]
+                    .getDisplayId(true) } : new Object[] { MessageManager
+                    .getString("label.selection") })), 500, 400);
 
   }
 
@@ -2316,8 +2310,7 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup sg = ap.av.getSelectionGroup();
     if (sg == null || sg.getSize() < 1)
     {
-      ap.av.hideSequence(new SequenceI[]
-      { sequence });
+      ap.av.hideSequence(new SequenceI[] { sequence });
       return;
     }
 
@@ -2356,8 +2349,7 @@ public class PopupMenu extends JPopupMenu
     if (sg != null)
     {
       List startEnd = ap.av.getVisibleRegionBoundaries(
-              sg.getStartRes(),
-              sg.getEndRes() + 1);
+              sg.getStartRes(), sg.getEndRes() + 1);
 
       String description;
       int caseChange;
@@ -2395,8 +2387,8 @@ public class PopupMenu extends JPopupMenu
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
     Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-            "label.alignment_output_command", new Object[]
-            { e.getActionCommand() }), 600, 500);
+            "label.alignment_output_command",
+            new Object[] { e.getActionCommand() }), 600, 500);
 
     String[] omitHidden = null;
 
@@ -2414,11 +2406,11 @@ public class PopupMenu extends JPopupMenu
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle(MessageManager.formatMessage(
-            "label.select_pdb_file_for", new Object[]
-            { sequence.getDisplayId(false) }));
+            "label.select_pdb_file_for",
+            new Object[] { sequence.getDisplayId(false) }));
     chooser.setToolTipText(MessageManager.formatMessage(
-            "label.load_pdb_file_associate_with_sequence", new Object[]
-            { sequence.getDisplayId(false) }));
+            "label.load_pdb_file_associate_with_sequence",
+            new Object[] { sequence.getDisplayId(false) }));
 
     int value = chooser.showOpenDialog(null);
 
@@ -2433,7 +2425,6 @@ public class PopupMenu extends JPopupMenu
 
   }
 
-
   public void enterPDB_actionPerformed()
   {
     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 88f5df3..5cb6512 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -263,8 +263,7 @@ public class Preferences extends GPreferences
 
     sortAutocalc.addItem("Autocalculated first");
     sortAutocalc.addItem("Autocalculated last");
-    final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
-            true);
+    final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
             : sortAutocalc.getItemAt(1));
     startupCheckbox
@@ -298,8 +297,7 @@ public class Preferences extends GPreferences
     structFromPdb.setSelected(structSelected);
     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
     useRnaView.setEnabled(structSelected);
-    addSecondaryStructure
-            .setSelected(Cache.getDefault(ADD_SS_ANN, false));
+    addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
     addSecondaryStructure.setEnabled(structSelected);
     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
     addTempFactor.setEnabled(structSelected);
@@ -465,8 +463,8 @@ public class Preferences extends GPreferences
     }
 
     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
-    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
-            Boolean.valueOf(showAutocalcFirst).toString());
+    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
+            .valueOf(showAutocalcFirst).toString());
 
     /*
      * Save Colours settings
@@ -645,20 +643,21 @@ public class Preferences extends GPreferences
     return validateChimeraPath();
 
   }
+
   /**
    * DOCUMENT ME!
    */
   public void startupFileTextfield_mouseClicked()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[]
-            { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
-            new String[]
-            { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+            jalview.bin.Cache.getProperty("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(MessageManager.getString("label.select_startup_file"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.select_startup_file"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -800,7 +799,8 @@ public class Preferences extends GPreferences
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     JFileChooser chooser = new JFileChooser(".");
-    chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.select_default_browser"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -833,7 +833,8 @@ public class Preferences extends GPreferences
   public void minColour_actionPerformed(JPanel panel)
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
+            MessageManager.getString("label.select_colour_minimum_value"),
+            minColour.getBackground());
     if (col != null)
     {
       panel.setBackground(col);
@@ -845,7 +846,8 @@ public class Preferences extends GPreferences
   public void maxColour_actionPerformed(JPanel panel)
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
+            MessageManager.getString("label.select_colour_maximum_value"),
+            maxColour.getBackground());
     if (col != null)
     {
       panel.setBackground(col);
@@ -870,12 +872,10 @@ public class Preferences extends GPreferences
       }
     } catch (NumberFormatException x)
     {
-      JOptionPane
-              .showInternalMessageDialog(
-                      Desktop.desktop,
-                      MessageManager.getString("warn.user_defined_width_requirements"),
-                      MessageManager.getString("label.invalid_id_column_width"),
-                      JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+              .getString("warn.user_defined_width_requirements"),
+              MessageManager.getString("label.invalid_id_column_width"),
+              JOptionPane.WARNING_MESSAGE);
       userIdWidth.setText("");
     }
   }
@@ -936,14 +936,13 @@ public class Preferences extends GPreferences
     }
     if (!found)
     {
-      String[] options =
-      { "OK", "Help" };
+      String[] options = { "OK", "Help" };
       int showHelp = JOptionPane.showInternalOptionDialog(
               Desktop.desktop,
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
-              "", JOptionPane.YES_NO_OPTION,
-              JOptionPane.WARNING_MESSAGE, null, options, options[0]);
+              "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+              null, options, options[0]);
       if (showHelp == JOptionPane.NO_OPTION)
       {
         try
diff --git a/src/jalview/gui/ProgressBar.java b/src/jalview/gui/ProgressBar.java
index c7db535..bb5e780 100644
--- a/src/jalview/gui/ProgressBar.java
+++ b/src/jalview/gui/ProgressBar.java
@@ -102,7 +102,7 @@ public class ProgressBar implements IProgressIndicator
   public void setProgressBar(String message, long id)
   {
     Long longId = Long.valueOf(id);
-  
+
     JPanel progressPanel = progressBars.get(longId);
     if (progressPanel != null)
     {
@@ -126,15 +126,15 @@ public class ProgressBar implements IProgressIndicator
        * No progress bar for this id - add one now
        */
       progressPanel = new JPanel(new BorderLayout(10, 5));
-  
+
       JProgressBar progressBar = new JProgressBar();
       progressBar.setIndeterminate(true);
-  
+
       progressPanel.add(new JLabel(message), BorderLayout.WEST);
       progressPanel.add(progressBar, BorderLayout.CENTER);
-  
+
       addRow(progressPanel);
-  
+
       progressBars.put(longId, progressPanel);
     }
 
@@ -223,8 +223,9 @@ public class ProgressBar implements IProgressIndicator
       {
         handler.cancelActivity(id);
         us.setProgressBar(MessageManager.formatMessage(
-                "label.cancelled_params", new Object[]
-                { ((JLabel) progressPanel.getComponent(0)).getText() }), id);
+                "label.cancelled_params",
+                new Object[] { ((JLabel) progressPanel.getComponent(0))
+                        .getText() }), id);
       }
     });
     progressPanel.add(cancel, BorderLayout.EAST);
diff --git a/src/jalview/gui/PromptUserConfig.java b/src/jalview/gui/PromptUserConfig.java
index 7655251..d7449d0 100644
--- a/src/jalview/gui/PromptUserConfig.java
+++ b/src/jalview/gui/PromptUserConfig.java
@@ -24,7 +24,7 @@ import jalview.bin.Cache;
 
 import java.awt.Component;
 
-import javax.swing.*;
+import javax.swing.JOptionPane;
 
 public class PromptUserConfig implements Runnable
 {
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index e541540..7fb0593 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -171,7 +171,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress.setVisible(false);
     progress = null;
 
-    label.setText(MessageManager.getString("label.enter_redundancy_thereshold"));
+    label.setText(MessageManager
+            .getString("label.enter_redundancy_thereshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
@@ -240,7 +241,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         }
       }
 
-      EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
+      EditCommand cut = new EditCommand(
+              MessageManager.getString("action.remove_redundancy"),
               Action.CUT, deleted, 0, width, ap.av.getAlignment());
 
       for (int i = 0; i < del.size(); i++)
@@ -257,7 +259,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       ap.alignFrame.addHistoryItem(cut);
 
       PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
-       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
     }
 
   }
@@ -270,17 +273,19 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    */
   public void undoButton_actionPerformed(ActionEvent e)
   {
-    if(historyList == null || historyList.isEmpty()){
-        undoButton.setEnabled(false);
-    	return;
+    if (historyList == null || historyList.isEmpty())
+    {
+      undoButton.setEnabled(false);
+      return;
     }
-    
+
     CommandI command = historyList.pop();
     if (ap.av.getHistoryList().contains(command))
     {
       command.undoCommand(af.getViewAlignments());
       ap.av.getHistoryList().remove(command);
-      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
       af.updateEditMenuBar();
     }
 
diff --git a/src/jalview/gui/RestInputParamEditDialog.java b/src/jalview/gui/RestInputParamEditDialog.java
index 9a71770..8056189 100644
--- a/src/jalview/gui/RestInputParamEditDialog.java
+++ b/src/jalview/gui/RestInputParamEditDialog.java
@@ -20,6 +20,13 @@
  */
 package jalview.gui;
 
+import jalview.jbgui.GRestInputParamEditDialog;
+import jalview.ws.params.InvalidArgumentException;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.rest.InputType;
+import jalview.ws.rest.RestServiceDescription;
+
 import java.util.ArrayList;
 import java.util.Hashtable;
 
@@ -29,13 +36,6 @@ import javax.swing.event.ListSelectionEvent;
 
 import net.miginfocom.swing.MigLayout;
 
-import jalview.jbgui.GRestInputParamEditDialog;
-import jalview.ws.params.InvalidArgumentException;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.rest.InputType;
-import jalview.ws.rest.RestServiceDescription;
-
 public class RestInputParamEditDialog extends GRestInputParamEditDialog
         implements OptsParametersContainerI
 {
diff --git a/src/jalview/gui/RestServiceEditorPane.java b/src/jalview/gui/RestServiceEditorPane.java
index 8a77329..ec8e7f1 100644
--- a/src/jalview/gui/RestServiceEditorPane.java
+++ b/src/jalview/gui/RestServiceEditorPane.java
@@ -435,8 +435,7 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
               parseRes.setText(MessageManager
                       .formatMessage(
                               "label.parsing_failed_syntax_errors_shown_below_param",
-                              new String[]
-                              { rsd.getInvalidMessage() }));
+                              new String[] { rsd.getInvalidMessage() }));
               parseWarnings.setVisible(true);
             }
           } catch (Throwable e)
@@ -445,8 +444,7 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
             parseRes.setText(MessageManager
                     .formatMessage(
                             "label.parsing_failed_unrecoverable_exception_thrown_param",
-                            new String[]
-                            { e.toString() }));
+                            new String[] { e.toString() }));
             parseWarnings.setVisible(true);
           }
         }
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 4241c5f..0719fa0 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -20,18 +20,34 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
 import jalview.api.RotatableCanvasI;
-import jalview.datamodel.*;
-import jalview.math.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
+
 /**
  * DOCUMENT ME!
  * 
@@ -826,8 +842,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     }
     else
     {
-      return new AlignmentPanel[]
-      { ap };
+      return new AlignmentPanel[] { ap };
     }
   }
 
diff --git a/src/jalview/gui/SVGOptions.java b/src/jalview/gui/SVGOptions.java
index c3bdc70..a64819a 100644
--- a/src/jalview/gui/SVGOptions.java
+++ b/src/jalview/gui/SVGOptions.java
@@ -59,8 +59,7 @@ public class SVGOptions extends JPanel
     bg.add(text);
 
     JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
-            JOptionPane.DEFAULT_OPTION, null, new Object[]
-            { this });
+            JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
 
     dialog = pane.createDialog(Desktop.desktop, "SVG Rendering options");
     dialog.setVisible(true);
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 519f2e2..62cd3f1 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -482,13 +482,13 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
         gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
                 y + 2,
-                ((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
-                y + (fm.getDescent() * 2));
+                ((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
+                        + (fm.getDescent() * 2));
       }
       else
       {
-        gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
-                y + fm.getDescent(), ((i - startx - 1) * avCharWidth)
+        gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
+                + fm.getDescent(), ((i - startx - 1) * avCharWidth)
                 + (avCharWidth / 2), y + (fm.getDescent() * 2));
       }
     }
@@ -512,12 +512,10 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
             continue;
           }
 
-          gg.fillPolygon(new int[]
-          { res * avCharWidth - avCharHeight / 4,
+          gg.fillPolygon(new int[] { res * avCharWidth - avCharHeight / 4,
               res * avCharWidth + avCharHeight / 4, res * avCharWidth },
-                  new int[]
-                  { y - avCharHeight / 2, y - avCharHeight / 2, y + 8 },
-                  3);
+                  new int[] { y - avCharHeight / 2, y - avCharHeight / 2,
+                      y + 8 }, 3);
 
         }
       }
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 4c04ad3..5706fe7 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -106,6 +106,7 @@ public class SeqCanvas extends JComponent
     charHeight = av.getCharHeight();
     charWidth = av.getCharWidth();
   }
+
   /**
    * DOCUMENT ME!
    * 
@@ -138,8 +139,7 @@ public class SeqCanvas extends JComponent
 
       g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
               (ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
-                      + (charWidth / 2),
-              ypos - 2);
+                      + (charWidth / 2), ypos - 2);
     }
   }
 
@@ -557,12 +557,12 @@ public class SeqCanvas extends JComponent
             continue;
           }
 
-          gg.fillPolygon(new int[]
-          { res * charWidth - charHeight / 4,
-              res * charWidth + charHeight / 4, res * charWidth },
-                  new int[]
-                  { ypos - (charHeight / 2), ypos - (charHeight / 2),
-                      ypos - (charHeight / 2) + 8 }, 3);
+          gg.fillPolygon(
+                  new int[] { res * charWidth - charHeight / 4,
+                      res * charWidth + charHeight / 4, res * charWidth },
+                  new int[] { ypos - (charHeight / 2),
+                      ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+                  3);
 
         }
       }
@@ -591,8 +591,8 @@ public class SeqCanvas extends JComponent
           annotations = new AnnotationPanel(av);
         }
 
-        annotations.renderer.drawComponent(annotations, av, g,
-                -1, startRes, endx + 1);
+        annotations.renderer.drawComponent(annotations, av, g, -1,
+                startRes, endx + 1);
         g.translate(0, -cHeight - ypos - 3);
       }
       g.setClip(clip);
@@ -638,8 +638,7 @@ public class SeqCanvas extends JComponent
    *          DOCUMENT ME!
    */
   public void drawPanel(Graphics g1, int startRes, int endRes,
-          int startSeq,
-          int endSeq, int offset)
+          int startSeq, int endSeq, int offset)
   {
     updateViewport();
     if (!av.hasHiddenColumns())
@@ -700,8 +699,7 @@ public class SeqCanvas extends JComponent
   // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
   // int x1, int x2, int y1, int y2, int startx, int starty,
   private void draw(Graphics g, int startRes, int endRes, int startSeq,
-          int endSeq,
-          int offset)
+          int endSeq, int offset)
   {
     g.setFont(av.getFont());
     sr.prepare(g, av.isRenderGaps());
@@ -831,8 +829,8 @@ public class SeqCanvas extends JComponent
               if (group == av.getSelectionGroup())
               {
                 g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
-                        BasicStroke.JOIN_ROUND, 3f, new float[]
-                        { 5f, 3f }, 0f));
+                        BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f },
+                        0f));
                 g.setColor(Color.RED);
               }
               else
@@ -941,8 +939,7 @@ public class SeqCanvas extends JComponent
           break;
         }
 
-        group = av.getAlignment().getGroups()
-                .get(groupIndex);
+        group = av.getAlignment().getGroups().get(groupIndex);
 
       } while (groupIndex < av.getAlignment().getGroups().size());
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 01653b6..d379764 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -192,8 +192,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
@@ -250,8 +249,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       y -= hgap;
 
@@ -668,11 +666,12 @@ public class SeqPanel extends JPanel implements MouseListener,
   @Override
   public void highlightSequence(SearchResults results)
   {
-    if (results == null || results.equals(lastSearchResults)) {
+    if (results == null || results.equals(lastSearchResults))
+    {
       return;
     }
     lastSearchResults = results;
-    
+
     if (av.isFollowHighlight())
     {
       /*
@@ -696,6 +695,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     return this.ap == null ? null : this.ap.av;
   }
+
   @Override
   public void updateColours(SequenceI seq, int index)
   {
@@ -767,9 +767,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (av.isShowSequenceFeatures())
     {
       int rpos;
-      List features = ap.getFeatureRenderer().findFeaturesAtRes(
-              sequence.getDatasetSequence(),
-              rpos = sequence.findPosition(res));
+      List features = ap.getFeatureRenderer()
+              .findFeaturesAtRes(sequence.getDatasetSequence(),
+                      rpos = sequence.findPosition(res));
       seqARep.appendFeatures(tooltipText, rpos, features,
               this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
     }
@@ -1034,7 +1034,8 @@ public class SeqPanel extends JPanel implements MouseListener,
       message.append("Edit group:");
       if (editCommand == null)
       {
-        editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
+        editCommand = new EditCommand(
+                MessageManager.getString("action.edit_group"));
       }
     }
     else
@@ -1047,7 +1048,8 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       if (editCommand == null)
       {
-        editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
+        editCommand = new EditCommand(MessageManager.formatMessage(
+                "label.edit_params", new String[] { label }));
       }
     }
 
@@ -1285,14 +1287,13 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           for (int j = lastres; j < startres; j++)
           {
-            insertChar(j, new SequenceI[]
-            { seq }, fixedRight);
+            insertChar(j, new SequenceI[] { seq }, fixedRight);
           }
         }
         else
         {
-          appendEdit(Action.INSERT_GAP, new SequenceI[]
-          { seq }, lastres, startres - lastres);
+          appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
+                  startres - lastres);
         }
       }
       else
@@ -1309,8 +1310,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                 endEditing();
                 break;
               }
-              deleteChar(startres, new SequenceI[]
-              { seq }, fixedRight);
+              deleteChar(startres, new SequenceI[] { seq }, fixedRight);
             }
           }
           else
@@ -1328,8 +1328,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (max > 0)
             {
-              appendEdit(Action.DELETE_GAP, new SequenceI[]
-              { seq }, startres, max);
+              appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
+                      startres, max);
             }
           }
         }
@@ -1339,14 +1339,13 @@ public class SeqPanel extends JPanel implements MouseListener,
           {
             for (int j = lastres; j < startres; j++)
             {
-              insertChar(j, new SequenceI[]
-              { seq }, fixedRight);
+              insertChar(j, new SequenceI[] { seq }, fixedRight);
             }
           }
           else
           {
-            appendEdit(Action.INSERT_NUC, new SequenceI[]
-            { seq }, lastres, startres - lastres);
+            appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
+                    startres - lastres);
           }
         }
       }
@@ -1402,8 +1401,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
             av.getAlignment().getGapCharacter());
 
-    editCommand.appendEdit(edit, av.getAlignment(),
-            true, null);
+    editCommand.appendEdit(edit, av.getAlignment(), true, null);
   }
 
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
@@ -1469,21 +1467,23 @@ public class SeqPanel extends JPanel implements MouseListener,
         av.setSelectionGroup(null);
       }
 
-      List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes(
-              sequence.getDatasetSequence(),
-              sequence.findPosition(findRes(evt)));
+      List features = seqCanvas.getFeatureRenderer()
+              .findFeaturesAtRes(sequence.getDatasetSequence(),
+                      sequence.findPosition(findRes(evt)));
 
-      if (features != null && features.size()> 0)
+      if (features != null && features.size() > 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence, features.get(0).getBegin(),
-                features.get(0).getEnd());
+        highlight.addResult(sequence, features.get(0).getBegin(), features
+                .get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
-      if (features != null && features.size()> 0)
+      if (features != null && features.size() > 0)
       {
-        seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
-        { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap);
+        seqCanvas.getFeatureRenderer().amendFeatures(
+                new SequenceI[] { sequence },
+                features.toArray(new SequenceFeature[features.size()]),
+                false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -1598,10 +1598,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes(
-              sequence.getDatasetSequence(), sequence.findPosition(res));
+      List allFeatures = ap.getFeatureRenderer()
+              .findFeaturesAtRes(sequence.getDatasetSequence(),
+                      sequence.findPosition(res));
       Vector links = new Vector();
-      for (SequenceFeature sf:allFeatures)
+      for (SequenceFeature sf : allFeatures)
       {
         if (sf.links != null)
         {
@@ -1917,8 +1918,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     // handles selection messages...
     // TODO: extend config options to allow user to control if selections may be
     // shared between viewports.
-    boolean iSentTheSelection = (av == source
-            || (source instanceof AlignViewport && ((AlignmentViewport) source)
+    boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
             .getSequenceSetId().equals(av.getSequenceSetId())));
     if (iSentTheSelection || !av.followSelection)
     {
@@ -2034,11 +2034,13 @@ public class SeqPanel extends JPanel implements MouseListener,
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
           ColumnSelection colsel, SelectionSource source)
   {
-    if (!(source instanceof AlignViewportI)) {
+    if (!(source instanceof AlignViewportI))
+    {
       return false;
     }
     final AlignViewportI sourceAv = (AlignViewportI) source;
-    if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+    if (sourceAv.getCodingComplement() != av
+            && av.getCodingComplement() != sourceAv)
     {
       return false;
     }
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 6a0d010..a973757 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -115,6 +115,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   private static Thread initingThread = null;
 
   int debounceTrap = 0;
+
   /**
    * Blocking method that initialises and returns the shared instance of the
    * SequenceFetcher client
@@ -130,9 +131,11 @@ public class SequenceFetcher extends JPanel implements Runnable
     {
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(
-                MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
-                Thread.currentThread().hashCode());
+        guiWindow
+                .setProgressBar(
+                        MessageManager
+                                .getString("status.waiting_sequence_database_fetchers_init"),
+                        Thread.currentThread().hashCode());
       }
       // initting happening on another thread - so wait around to see if it
       // finishes.
@@ -149,9 +152,11 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(
-        		MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
-                Thread.currentThread().hashCode());
+        guiWindow
+                .setProgressBar(
+                        MessageManager
+                                .getString("status.waiting_sequence_database_fetchers_init"),
+                        Thread.currentThread().hashCode());
       }
     }
     if (sfetch == null
@@ -168,7 +173,8 @@ public class SequenceFetcher extends JPanel implements Runnable
        */
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
+        guiWindow.setProgressBar(MessageManager
+                .getString("status.init_sequence_database_fetchers"),
                 Thread.currentThread().hashCode());
       }
       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
@@ -189,6 +195,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   }
 
   private IProgressIndicator progressIndicator;
+
   public SequenceFetcher(IProgressIndicator guiIndic)
   {
     this.progressIndicator = guiIndic;
@@ -214,8 +221,10 @@ public class SequenceFetcher extends JPanel implements Runnable
               JOptionPane
                       .showInternalMessageDialog(
                               Desktop.desktop,
-                              MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
-                              MessageManager.getString("label.couldnt_create_sequence_fetcher"),
+                              MessageManager
+                                      .getString("warn.couldnt_create_sequence_fetcher_client"),
+                              MessageManager
+                                      .getString("label.couldnt_create_sequence_fetcher"),
                               JOptionPane.ERROR_MESSAGE);
             }
           });
@@ -272,7 +281,9 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private String getFrameTitle()
   {
-    return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
+    return ((alignFrame == null) ? MessageManager
+            .getString("label.new_sequence_fetcher") : MessageManager
+            .getString("label.additional_sequence_fetcher"));
   }
 
   private void jbInit() throws Exception
@@ -360,7 +371,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         String currentSelection = database.getSelectedItem();
         if (!currentSelection.equalsIgnoreCase("pdb"))
         {
-            otherSourceAction();
+          otherSourceAction();
         }
         if (currentSelection.equalsIgnoreCase("pdb")
                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
@@ -404,8 +415,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                       : ""));
       String eq = database.getExampleQueries();
       dbeg.setText(MessageManager.formatMessage(
-              "label.example_query_param", new String[]
-              { eq }));
+              "label.example_query_param", new String[] { eq }));
       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
       for (DbSourceProxy dbs : database.getSelectedSources())
       {
@@ -443,8 +453,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     jPanel3.repaint();
   }
 
-
-
   public void close_actionPerformed(ActionEvent e)
   {
     try
@@ -537,8 +545,13 @@ public class SequenceFetcher extends JPanel implements Runnable
       try
       {
         // update status
-        guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
-                .currentThread().hashCode());
+        guiWindow
+                .setProgressBar(MessageManager.formatMessage(
+                        "status.fetching_sequence_queries_from",
+                        new String[] {
+                            Integer.valueOf(nqueries).toString(),
+                            proxy.getDbName() }), Thread.currentThread()
+                        .hashCode());
         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
         if (proxy.getAccessionSeparator() == null)
         {
@@ -735,11 +748,15 @@ public class SequenceFetcher extends JPanel implements Runnable
           presultTitle.add(titl);
         }
       }
-      guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
+      guiWindow.setProgressBar(MessageManager
+              .getString("status.finshed_querying"), Thread.currentThread()
               .hashCode());
     }
-    guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
-            : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
+    guiWindow.setProgressBar(
+            (presult.size() > 0) ? MessageManager
+                    .getString("status.parsing_results") : MessageManager
+                    .getString("status.processing"), Thread.currentThread()
+                    .hashCode());
     // process results
     while (presult.size() > 0)
     {
@@ -891,8 +908,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     return progressIndicator;
   }
 
-
-
   public void setProgressIndicator(IProgressIndicator progressIndicator)
   {
     this.progressIndicator = progressIndicator;
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 273bfd9..258a229 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -217,7 +217,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           int y1)
   {
     if (seq == null)
-     {
+    {
       return; // fix for racecondition
     }
     int i = start;
@@ -425,8 +425,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
         graphics.drawString(String.valueOf(s),
-                charOffset + av.getCharWidth()
-                * (i - start), y1);
+                charOffset + av.getCharWidth() * (i - start), y1);
 
       }
     }
diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index af6bfff..e1e70dc 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -140,7 +140,10 @@ public class SliderPanel extends GSliderPanel
       sp.cs = cs;
     }
 
-    conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));
+    conservationSlider
+            .setTitle(MessageManager.formatMessage(
+                    "label.conservation_colour_increment",
+                    new String[] { source }));
 
     if (ap.av.getAlignment().getGroups() != null)
     {
@@ -216,7 +219,9 @@ public class SliderPanel extends GSliderPanel
       pid.cs = cs;
     }
 
-    PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));
+    PIDSlider.setTitle(MessageManager
+            .formatMessage("label.percentage_identity_thereshold",
+                    new String[] { source }));
 
     if (ap.av.getAlignment().getGroups() != null)
     {
diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index aa658ce..9e2281e 100644
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -72,7 +72,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
     adjustLayout();
 
     addCloseFrameListener();
-    
+
     addKeyListener();
 
     addKeyBindings();
@@ -155,7 +155,8 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
    */
   protected void addKeyListener()
   {
-    addKeyListener(new KeyAdapter() {
+    addKeyListener(new KeyAdapter()
+    {
 
       @Override
       public void keyPressed(KeyEvent e)
@@ -189,7 +190,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
           }
         }
       }
-      
+
     });
   }
 
@@ -638,4 +639,3 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
     overrideKeyBinding(key_cmdF, action);
   }
 }
-
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 510ce78..347c1b2 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -75,7 +75,6 @@ public class StructureChooser extends GStructureChooser
 
   private boolean isValidPBDEntry;
 
-
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
@@ -210,7 +209,8 @@ public class StructureChooser extends GStructureChooser
       if (seq.getDatasetSequence() != null
               && seq.getDatasetSequence().getAllPDBEntries() != null)
       {
-        for (PDBEntry pdbEntry : seq.getDatasetSequence().getAllPDBEntries())
+        for (PDBEntry pdbEntry : seq.getDatasetSequence()
+                .getAllPDBEntries())
         {
           if (pdbEntry.getFile() != null)
           {
@@ -224,7 +224,6 @@ public class StructureChooser extends GStructureChooser
     tbl_local_pdb.setModel(tableModelx);
   }
 
-
   /**
    * Builds a query string for a given sequences using its DBRef entries
    * 
@@ -390,14 +389,12 @@ public class StructureChooser extends GStructureChooser
           // Update table selection model here
           tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
           mainFrame.setTitle(MessageManager.formatMessage(
-                  "label.structure_chooser_filter_time",
- totalTime));
+                  "label.structure_chooser_filter_time", totalTime));
         }
         else
         {
           mainFrame.setTitle(MessageManager.formatMessage(
-                  "label.structure_chooser_filter_time",
- totalTime));
+                  "label.structure_chooser_filter_time", totalTime));
           if (errors.size() > 0)
           {
             StringBuilder errorMsg = new StringBuilder();
@@ -405,7 +402,9 @@ public class StructureChooser extends GStructureChooser
             {
               errorMsg.append(error).append("\n");
             }
-            JOptionPane.showMessageDialog(null, errorMsg.toString(),
+            JOptionPane.showMessageDialog(
+                    null,
+                    errorMsg.toString(),
                     MessageManager.getString("label.pdb_web-service_error"),
                     JOptionPane.ERROR_MESSAGE);
           }
@@ -546,9 +545,9 @@ public class StructureChooser extends GStructureChooser
     lbl_pdbManualFetchStatus.setToolTipText("");
     if (txt_search.getText().length() > 0)
     {
-      lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
-              true, MessageManager.formatMessage(
-                      "info.no_pdb_entry_found_for",
+      lbl_pdbManualFetchStatus
+              .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+                      .formatMessage("info.no_pdb_entry_found_for",
                               txt_search.getText())));
     }
 
@@ -715,11 +714,9 @@ public class StructureChooser extends GStructureChooser
         selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
       }
 
-      PDBEntry[] pdbEntriesToView = new PDBEntry[]
-      { pdbEntry };
+      PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
       launchStructureViewer(ap.getStructureSelectionManager(),
-              pdbEntriesToView, ap, new SequenceI[]
-              { selectedSequence });
+              pdbEntriesToView, ap, new SequenceI[] { selectedSequence });
     }
     else if (currentView == VIEWS_FROM_FILE)
     {
@@ -735,9 +732,8 @@ public class StructureChooser extends GStructureChooser
                       selectedSequence, true, Desktop.instance);
 
       launchStructureViewer(ap.getStructureSelectionManager(),
-              new PDBEntry[]
-              { fileEntry }, ap, new SequenceI[]
-              { selectedSequence });
+              new PDBEntry[] { fileEntry }, ap,
+              new SequenceI[] { selectedSequence });
     }
     mainFrame.dispose();
   }
@@ -756,8 +752,7 @@ public class StructureChooser extends GStructureChooser
           ArrayList seqsMap = new ArrayList();
           for (SequenceI seq : sequences)
           {
-            seqsMap.add(new SequenceI[]
-            { seq });
+            seqsMap.add(new SequenceI[] { seq });
           }
           SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
           sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
@@ -820,40 +815,40 @@ public class StructureChooser extends GStructureChooser
     {
       public void run()
       {
-    errorWarning.setLength(0);
-    isValidPBDEntry = false;
-    if (txt_search.getText().length() > 0)
-    {
-      List wantedFields = new ArrayList();
-      wantedFields.add(PDBDocField.PDB_ID);
-      PDBRestRequest pdbRequest = new PDBRestRequest();
-      pdbRequest.setAllowEmptySeq(false);
-      pdbRequest.setResponseSize(1);
-      pdbRequest.setFieldToSearchBy("(pdb_id:");
-      pdbRequest.setWantedFields(wantedFields);
-      pdbRequest.setSearchTerm(txt_search.getText() + ")");
-      pdbRequest.setAssociatedSequence(selectedSequence);
-      pdbRestCleint = new PDBRestClient();
-      PDBRestResponse resultList;
-      try
-      {
-        resultList = pdbRestCleint.executeRequest(pdbRequest);
-      } catch (Exception e)
-      {
-        errorWarning.append(e.getMessage());
-        return;
-      } finally
-      {
+        errorWarning.setLength(0);
+        isValidPBDEntry = false;
+        if (txt_search.getText().length() > 0)
+        {
+          List wantedFields = new ArrayList();
+          wantedFields.add(PDBDocField.PDB_ID);
+          PDBRestRequest pdbRequest = new PDBRestRequest();
+          pdbRequest.setAllowEmptySeq(false);
+          pdbRequest.setResponseSize(1);
+          pdbRequest.setFieldToSearchBy("(pdb_id:");
+          pdbRequest.setWantedFields(wantedFields);
+          pdbRequest.setSearchTerm(txt_search.getText() + ")");
+          pdbRequest.setAssociatedSequence(selectedSequence);
+          pdbRestCleint = new PDBRestClient();
+          PDBRestResponse resultList;
+          try
+          {
+            resultList = pdbRestCleint.executeRequest(pdbRequest);
+          } catch (Exception e)
+          {
+            errorWarning.append(e.getMessage());
+            return;
+          } finally
+          {
+            validateSelections();
+          }
+          if (resultList.getSearchSummary() != null
+                  && resultList.getSearchSummary().size() > 0)
+          {
+            isValidPBDEntry = true;
+          }
+        }
         validateSelections();
       }
-      if (resultList.getSearchSummary() != null
-              && resultList.getSearchSummary().size() > 0)
-      {
-        isValidPBDEntry = true;
-      }
-    }
-    validateSelections();
-      }
     }.start();
   }
 
@@ -878,8 +873,7 @@ public class StructureChooser extends GStructureChooser
 
   public class PDBEntryTableModel extends AbstractTableModel
   {
-    String[] columns =
-    { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
+    String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
 
     private List pdbEntries;
 
diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 2285765..21b2984 100644
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -20,10 +20,6 @@
  */
 package jalview.gui;
 
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.List;
-
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
@@ -31,6 +27,10 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
 import jalview.structure.StructureSelectionManager;
 
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * proxy for handling structure viewers.
  * 
@@ -98,8 +98,7 @@ public class StructureViewer
    * @return
    */
   private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
-          SequenceI[][] seqsForPdbs,
-          AlignmentPanel ap)
+          SequenceI[][] seqsForPdbs, AlignmentPanel ap)
   {
     List seqs = new ArrayList();
     if (pdbs == null || pdbs.length == 0)
@@ -190,8 +189,8 @@ public class StructureViewer
    */
   public JalviewStructureDisplayI createView(ViewerType type,
           String[] pdbf, String[] id, SequenceI[][] sq,
-          AlignmentPanel alignPanel, StructureViewerModel viewerData, String fileloc,
-          Rectangle rect, String vid)
+          AlignmentPanel alignPanel, StructureViewerModel viewerData,
+          String fileloc, Rectangle rect, String vid)
   {
     final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
     final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 587e08a..9ba50ca 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -32,20 +32,28 @@ public abstract class StructureViewerBase extends GStructureViewer
    * list of sequenceSet ids associated with the view
    */
   protected List _aps = new ArrayList();
+
   /**
    * list of alignment panels to use for superposition
    */
   protected Vector _alignwith = new Vector();
+
   /**
    * list of alignment panels that are used for colouring structures by aligned
    * sequences
    */
   protected Vector _colourwith = new Vector();
+
   private String viewId = null;
+
   private AlignmentPanel ap;
+
   protected boolean alignAddedStructures = false;
+
   protected boolean _started = false;
+
   protected boolean addingStructures = false;
+
   protected Thread worker = null;
 
   /**
@@ -60,7 +68,7 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   public boolean isUsedforaligment(AlignmentPanel ap2)
   {
-  
+
     return (_alignwith != null) && _alignwith.contains(ap2);
   }
 
@@ -138,7 +146,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         list = t;
       }
     }
-  
+
     return list;
   }
 
@@ -209,7 +217,8 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
-  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
+  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
+          boolean enableColourBySeq)
   {
     useAlignmentPanelForColourbyseq(nap);
     getBinding().setColourBySequence(enableColourBySeq);
@@ -250,7 +259,8 @@ public abstract class StructureViewerBase extends GStructureViewer
    *          alignment
    * @param alignFrame
    */
-  protected void addStructure(final PDBEntry pdbentry, final SequenceI[] seqs, final String[] chains,
+  protected void addStructure(final PDBEntry pdbentry,
+          final SequenceI[] seqs, final String[] chains,
           final boolean align, final IProgressIndicator alignFrame)
   {
     if (pdbentry.getFile() == null)
@@ -268,7 +278,7 @@ public abstract class StructureViewerBase extends GStructureViewer
               try
               {
                 Thread.sleep(100 + ((int) Math.random() * 100));
-  
+
               } catch (Exception e)
               {
               }
@@ -299,12 +309,13 @@ public abstract class StructureViewerBase extends GStructureViewer
    * @param view
    * @return YES, NO or CANCEL JOptionPane code
    */
-  protected int chooseAlignStructureToViewer(String pdbId, StructureViewerBase view)
+  protected int chooseAlignStructureToViewer(String pdbId,
+          StructureViewerBase view)
   {
     int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
             MessageManager.formatMessage("label.add_pdbentry_to_view",
-                    new Object[]
-                    { pdbId, view.getTitle() }), MessageManager
+                    new Object[] { pdbId, view.getTitle() }),
+            MessageManager
                     .getString("label.align_to_existing_structure_view"),
             JOptionPane.YES_NO_CANCEL_OPTION);
     return option;
@@ -356,7 +367,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         // NO_OPTION - offer the next viewer if any
       }
     }
-  
+
     /*
      * nothing offered and selected
      */
@@ -379,9 +390,9 @@ public abstract class StructureViewerBase extends GStructureViewer
     /*
      * create the mappings
      */
-    apanel.getStructureSelectionManager().setMapping(seq, chains, pdbFilename,
-            AppletFormatAdapter.FILE);
-  
+    apanel.getStructureSelectionManager().setMapping(seq, chains,
+            pdbFilename, AppletFormatAdapter.FILE);
+
     /*
      * alert the FeatureRenderer to show new (PDB RESNUM) features
      */
@@ -390,7 +401,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
       apanel.paintAlignment(true);
     }
-  
+
     /*
      * add the sequences to any other viewers (of the same type) for this pdb
      * file
@@ -411,7 +422,8 @@ public abstract class StructureViewerBase extends GStructureViewer
            */
           viewer.useAlignmentPanelForColourbyseq(apanel);
           viewer.buildActionMenu();
-          apanel.getStructureSelectionManager().sequenceColoursChanged(apanel);
+          apanel.getStructureSelectionManager().sequenceColoursChanged(
+                  apanel);
           break;
         }
       }
@@ -434,18 +446,20 @@ public abstract class StructureViewerBase extends GStructureViewer
     boolean finished = false;
     String alreadyMapped = apanel.getStructureSelectionManager()
             .alreadyMappedToFile(pdbId);
-  
+
     if (alreadyMapped != null)
     {
       /*
        * the PDB file is already loaded
        */
       int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-      MessageManager.formatMessage(
-              "label.pdb_entry_is_already_displayed", new Object[]
-              { pdbId }), MessageManager.formatMessage(
-              "label.map_sequences_to_visible_window", new Object[]
-              { pdbId }), JOptionPane.YES_NO_CANCEL_OPTION);
+              MessageManager.formatMessage(
+                      "label.pdb_entry_is_already_displayed",
+                      new Object[] { pdbId }), MessageManager
+                      .formatMessage(
+                              "label.map_sequences_to_visible_window",
+                              new Object[] { pdbId }),
+              JOptionPane.YES_NO_CANCEL_OPTION);
       if (option == JOptionPane.CANCEL_OPTION)
       {
         finished = true;
diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index c8a4a08..6bac6df 100644
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -78,8 +78,11 @@ public class TextColourChooser
     JPanel panel = new JPanel();
     bigpanel.add(panel, BorderLayout.CENTER);
     bigpanel.add(
-            new JLabel(""+MessageManager.getString("label.select_dark_light_set_thereshold")+""),
-            BorderLayout.NORTH);
+            new JLabel(
+                    ""
+                            + MessageManager
+                                    .getString("label.select_dark_light_set_thereshold")
+                            + ""), BorderLayout.NORTH);
     panel.add(col1);
     panel.add(slider);
     panel.add(col2);
@@ -89,7 +92,8 @@ public class TextColourChooser
       public void mousePressed(MouseEvent e)
       {
         Color col = JColorChooser.showDialog(bigpanel,
-                MessageManager.getString("label.select_colour_for_text"), col1.getBackground());
+                MessageManager.getString("label.select_colour_for_text"),
+                col1.getBackground());
         if (col != null)
         {
           colour1Changed(col);
@@ -103,7 +107,8 @@ public class TextColourChooser
       public void mousePressed(MouseEvent e)
       {
         Color col = JColorChooser.showDialog(bigpanel,
-        		MessageManager.getString("label.select_colour_for_text"), col2.getBackground());
+                MessageManager.getString("label.select_colour_for_text"),
+                col2.getBackground());
         if (col != null)
         {
           colour2Changed(col);
@@ -120,10 +125,14 @@ public class TextColourChooser
       }
     });
 
-    int reply = JOptionPane.showInternalOptionDialog(ap, bigpanel,
-            MessageManager.getString("label.adjunst_foreground_text_colour_thereshold"),
-            JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
-            null, null, null);
+    int reply = JOptionPane
+            .showInternalOptionDialog(
+                    ap,
+                    bigpanel,
+                    MessageManager
+                            .getString("label.adjunst_foreground_text_colour_thereshold"),
+                    JOptionPane.OK_CANCEL_OPTION,
+                    JOptionPane.QUESTION_MESSAGE, null, null, null);
 
     if (reply == JOptionPane.CANCEL_OPTION)
     {
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 1bce84b..9cb3d18 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -294,8 +294,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       SequenceGroup selected = av.getSelectionGroup();
 
       if ((selected != null)
-              && selected.getSequences(null).contains(
-                      node.element()))
+              && selected.getSequences(null).contains(node.element()))
       {
         g.setColor(Color.gray);
 
@@ -713,8 +712,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
 
-    float wscale = (width - labelLength - (offx * 2))
-            / tree.getMaxHeight();
+    float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
 
@@ -788,7 +786,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       if (SwingUtilities.isRightMouseButton(evt))
       {
         Color col = JColorChooser.showDialog(this,
-                MessageManager.getString("label.select_subtree_colour"), highlightNode.color);
+                MessageManager.getString("label.select_subtree_colour"),
+                highlightNode.color);
         if (col != null)
         {
           setColor(highlightNode, col);
@@ -1008,7 +1007,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     if (av.getCodingComplement() != null)
     {
-      ((AlignViewport) av.getCodingComplement()).getAlignPanel().updateAnnotation();
+      ((AlignViewport) av.getCodingComplement()).getAlignPanel()
+              .updateAnnotation();
       /*
        * idPanel. repaint ()
        */
@@ -1059,8 +1059,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      return new AlignmentPanel[]
-      { ap };
+      return new AlignmentPanel[] { ap };
     }
   }
 }
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index a806183..d2c86c8 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -439,7 +439,8 @@ public class TreePanel extends GTreePanel
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_tree_as_newick"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(null);
@@ -533,8 +534,8 @@ public class TreePanel extends GTreePanel
         // msaorder);
 
         Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.original_data_for_params", new Object[]
-                { this.title }), AlignFrame.DEFAULT_WIDTH,
+                "label.original_data_for_params",
+                new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -733,10 +734,11 @@ public class TreePanel extends GTreePanel
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "eps" }, new String[]
-              { "Encapsulated Postscript" }, "Encapsulated Postscript");
+              { "eps" }, new String[] { "Encapsulated Postscript" },
+              "Encapsulated Postscript");
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
+      chooser.setDialogTitle(MessageManager
+              .getString("label.create_eps_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
@@ -779,11 +781,12 @@ public class TreePanel extends GTreePanel
     {
       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");
+              { "png" }, new String[] { "Portable network graphics" },
+              "Portable network graphics");
 
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
+      chooser.setDialogTitle(MessageManager
+              .getString("label.create_png_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
@@ -837,8 +840,8 @@ public class TreePanel extends GTreePanel
           {
             // search dbrefs, features and annotation
             DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
-                    sq.getDBRef(), new String[]
-                    { labelClass.toUpperCase() });
+                    sq.getDBRef(),
+                    new String[] { labelClass.toUpperCase() });
             if (refs != null)
             {
               for (int i = 0; i < refs.length; i++)
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a907187..c9c1531 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -20,6 +20,16 @@
  */
 package jalview.gui;
 
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.JalviewFileChooser;
+import jalview.jbgui.GUserDefinedColours;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+
 import java.awt.Color;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
@@ -40,16 +50,6 @@ import javax.swing.JOptionPane;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.datamodel.SequenceGroup;
-import jalview.io.JalviewFileChooser;
-import jalview.jbgui.GUserDefinedColours;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.util.ColorUtils;
-import jalview.util.MessageManager;
-
 /**
  * This panel allows the user to assign colours to Amino Acid residue codes, and
  * save the colour scheme.
@@ -486,7 +486,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
             || upperCaseButtons.isEmpty();
     final boolean noLowerCaseSelected = caseSensitive.isSelected()
             && (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
-    final boolean noSelectionMade = noUpperCaseSelected || noLowerCaseSelected;
+    final boolean noSelectionMade = noUpperCaseSelected
+            || noLowerCaseSelected;
     return noSelectionMade;
   }
 
@@ -501,12 +502,13 @@ public class UserDefinedColours extends GUserDefinedColours implements
   {
     if (isNoSelectionMade())
     {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                MessageManager.getString("label.no_colour_selection_in_scheme"),MessageManager.getString("label.no_colour_selection_warn"),
-                JOptionPane.WARNING_MESSAGE);
-		
-	}
-	UserColourScheme ucs = getSchemeFromButtons();
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .getString("label.no_colour_selection_in_scheme"),
+              MessageManager.getString("label.no_colour_selection_warn"),
+              JOptionPane.WARNING_MESSAGE);
+
+    }
+    UserColourScheme ucs = getSchemeFromButtons();
     ucs.setName(schemeName.getText());
 
     if (seqGroup != null)
@@ -530,17 +532,22 @@ public class UserDefinedColours extends GUserDefinedColours implements
     Color[] newColours = new Color[24];
 
     int length = upperCaseButtons.size();
-    if (length<24){
-    	int i = 0;
-    	for (JButton btn:upperCaseButtons){
-    		newColours[i] = btn.getBackground();
-    		i++;
-    	}
-    }else{
-    	for (int i = 0; i < 24; i++){
-    		JButton button = upperCaseButtons.get(i);
-    		newColours[i] = button.getBackground();
-    	}
+    if (length < 24)
+    {
+      int i = 0;
+      for (JButton btn : upperCaseButtons)
+      {
+        newColours[i] = btn.getBackground();
+        i++;
+      }
+    }
+    else
+    {
+      for (int i = 0; i < 24; i++)
+      {
+        JButton button = upperCaseButtons.get(i);
+        newColours[i] = button.getBackground();
+      }
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
@@ -549,17 +556,22 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       newColours = new Color[23];
       length = lowerCaseButtons.size();
-      if (length<23){
-    	  int i = 0;
-    	  for (JButton btn:lowerCaseButtons){
-    		  newColours[i] = btn.getBackground();
-    		  i++;
-    	  }
-      }else{
-    	  for (int i = 0; i < 23; i++){
-    		  JButton button = lowerCaseButtons.get(i);
-    		  newColours[i] = button.getBackground();
-    	  }
+      if (length < 23)
+      {
+        int i = 0;
+        for (JButton btn : lowerCaseButtons)
+        {
+          newColours[i] = btn.getBackground();
+          i++;
+        }
+      }
+      else
+      {
+        for (int i = 0; i < 23; i++)
+        {
+          JButton button = lowerCaseButtons.get(i);
+          newColours[i] = button.getBackground();
+        }
       }
       ucs.setLowerCaseColours(newColours);
     }
@@ -585,9 +597,9 @@ public class UserDefinedColours extends GUserDefinedColours implements
     lowerCaseButtons = new ArrayList();
 
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "jc" }, new String[]
-            { "Jalview User Colours" }, "Jalview User Colours");
+            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(MessageManager
             .getString("label.load_colour_scheme"));
@@ -710,8 +722,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
         name = jucs.getColour(i).getName();
         if (ResidueProperties.aa3Hash.containsKey(name))
         {
-          index = ResidueProperties.aa3Hash.get(name)
-                  .intValue();
+          index = ResidueProperties.aa3Hash.get(name).intValue();
         }
         else
         {
@@ -810,8 +821,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
               MessageManager.formatMessage(
-                      "label.colour_scheme_exists_overwrite", new Object[]
-                      { schemeName.getText(), schemeName.getText() }),
+                      "label.colour_scheme_exists_overwrite", new Object[] {
+                          schemeName.getText(), schemeName.getText() }),
               MessageManager.getString("label.duplicate_scheme_name"),
               JOptionPane.YES_NO_OPTION);
       if (reply != JOptionPane.YES_OPTION)
@@ -822,12 +833,13 @@ public class UserDefinedColours extends GUserDefinedColours implements
       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");
+            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(MessageManager.getString("label.save_colour_scheme"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_colour_scheme"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
diff --git a/src/jalview/gui/UserQuestionnaireCheck.java b/src/jalview/gui/UserQuestionnaireCheck.java
index 02f6054..eb38ee6 100644
--- a/src/jalview/gui/UserQuestionnaireCheck.java
+++ b/src/jalview/gui/UserQuestionnaireCheck.java
@@ -22,10 +22,11 @@ package jalview.gui;
 
 import jalview.util.MessageManager;
 
-import java.io.*;
-import java.net.*;
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.net.URL;
 
-import javax.swing.*;
+import javax.swing.JOptionPane;
 
 public class UserQuestionnaireCheck implements Runnable
 {
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 6444667..7588e07 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -156,7 +156,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       {
         if (sess != null)
         {
-          throw new Error(MessageManager.getString("error.implementation_error_cannot_import_vamsas_doc"));
+          throw new Error(
+                  MessageManager
+                          .getString("error.implementation_error_cannot_import_vamsas_doc"));
         }
         try
         {
@@ -176,8 +178,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   .showInternalMessageDialog(
                           Desktop.desktop,
 
-                          MessageManager.getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
-                          MessageManager.getString("label.vamsas_document_import_failed"),
+                          MessageManager
+                                  .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
+                          MessageManager
+                                  .getString("label.vamsas_document_import_failed"),
                           JOptionPane.ERROR_MESSAGE);
 
         }
@@ -263,7 +267,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
   {
     if (!inSession())
     {
-      throw new Error(MessageManager.getString("error.implementation_error_vamsas_operation_not_init"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_vamsas_operation_not_init"));
     }
     addDocumentUpdateHandler();
     addStoreDocumentHandler();
@@ -348,7 +354,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
   {
     if (!inSession())
     {
-      throw new Error(MessageManager.getString("error.jalview_no_connected_vamsas_session"));
+      throw new Error(
+              MessageManager
+                      .getString("error.jalview_no_connected_vamsas_session"));
     }
     Cache.log.info("Jalview disconnecting from the Vamsas Session.");
     try
@@ -717,7 +725,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         return;
       }
 
-      throw new Error(MessageManager.getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
     }
     jv2vobj.clear();
     Iterator el = _backup_jv2vobj.entrySet().iterator();
@@ -1013,9 +1023,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                 if (source instanceof AlignViewport)
                 {
                   // the empty selection.
-                  sm = new SelectionMessage("jalview", new String[]
-                  { ((AlignmentViewport) source).getSequenceSetId() }, null,
-                          true);
+                  sm = new SelectionMessage("jalview",
+                          new String[] { ((AlignmentViewport) source)
+                                  .getSequenceSetId() }, null, true);
                 }
                 else
                 {
diff --git a/src/jalview/gui/ViewSelectionMenu.java b/src/jalview/gui/ViewSelectionMenu.java
index e12fb5b..f1e2467 100644
--- a/src/jalview/gui/ViewSelectionMenu.java
+++ b/src/jalview/gui/ViewSelectionMenu.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import jalview.util.MessageManager;
+
 import java.awt.Component;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -35,8 +37,6 @@ import javax.swing.JMenuItem;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
-import jalview.util.MessageManager;
-
 /**
  * this is an implementation of an abstract Jalview GUI class that provides a
  * dialog/menu which allows the user to select/deselect specific views from a
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 8e78b93..dd0e6c2 100644
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -20,6 +20,10 @@
  */
 package jalview.gui;
 
+import jalview.jbgui.GWebserviceInfo;
+import jalview.util.MessageManager;
+import jalview.ws.WSClientI;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Font;
@@ -45,10 +49,6 @@ import javax.swing.event.HyperlinkListener;
 import javax.swing.text.html.HTMLEditorKit;
 import javax.swing.text.html.StyleSheet;
 
-import jalview.jbgui.GWebserviceInfo;
-import jalview.util.MessageManager;
-import jalview.ws.WSClientI;
-
 /**
  * Base class for web service client thread and gui TODO: create StAX parser to
  * extract html body content reliably when preparing html formatted job statuses
@@ -386,7 +386,9 @@ public class WebserviceInfo extends GWebserviceInfo implements
   {
     if (jobpane < 0 || jobpane >= jobPanes.size())
     {
-      throw new Error(MessageManager.formatMessage("error.setstatus_called_non_existent_job_pane", new String[]{Integer.valueOf(jobpane).toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.setstatus_called_non_existent_job_pane",
+              new String[] { Integer.valueOf(jobpane).toString() }));
     }
     switch (status)
     {
@@ -680,7 +682,9 @@ public class WebserviceInfo extends GWebserviceInfo implements
       // anyhow - it has to stop threads and clean up
       // JBPNote : TODO: Instead of a warning, we should have an optional 'Are
       // you sure?' prompt
-      warnUser(MessageManager.getString("warn.job_cannot_be_cancelled_close_window"),
+      warnUser(
+              MessageManager
+                      .getString("warn.job_cannot_be_cancelled_close_window"),
               MessageManager.getString("action.cancel_job"));
     }
     else
diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index a3a61b7..c4d215e 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -20,6 +20,19 @@
  */
 package jalview.gui;
 
+import jalview.gui.OptsAndParamsPage.OptionBox;
+import jalview.gui.OptsAndParamsPage.ParamBox;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.WsParamSetI;
+
 import java.awt.BorderLayout;
 import java.awt.Component;
 import java.awt.Dimension;
@@ -66,19 +79,6 @@ import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
-import jalview.gui.OptsAndParamsPage.OptionBox;
-import jalview.gui.OptsAndParamsPage.ParamBox;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.params.WsParamSetI;
-
 /**
  * job parameter editing/browsing dialog box. User can browse existing settings
  * (user + presets + Defaults), and any changes to parameters creates a modified
@@ -219,8 +219,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     frame = new JDialog(Desktop.instance, true);
 
     frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
-            new String[]
-            { service.getActionText() }));
+            new String[] { service.getActionText() }));
     Rectangle deskr = Desktop.instance.getBounds();
     Dimension pref = this.getPreferredSize();
     frame.setBounds(new Rectangle(
@@ -1101,8 +1100,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
             WsJobParameters pgui = new WsJobParameters(lastserv,
                     new JabaPreset(lastserv, pr));
             JFrame jf = new JFrame(MessageManager.formatMessage(
-                    "label.ws_parameters_for", new String[]
-                    { lastserv.getActionText() }));
+                    "label.ws_parameters_for",
+                    new String[] { lastserv.getActionText() }));
             JPanel cont = new JPanel(new BorderLayout());
             pgui.validate();
             cont.setPreferredSize(pgui.getPreferredSize());
diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
index f00f50c..b6a7672 100644
--- a/src/jalview/gui/WsParamSetManager.java
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -178,17 +178,20 @@ public class WsParamSetManager implements ParamManager
     }
     if (parser == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_cannot_find_marshaller_for_param_set"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_cannot_find_marshaller_for_param_set"));
     }
     if (filename == null)
     {
       JalviewFileChooser chooser = new JalviewFileChooser(
               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "wsparams" }, new String[]
-              { "Web Service Parameter File" },
+              { "wsparams" },
+              new String[] { "Web Service Parameter File" },
               "Web Service Parameter File");
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(MessageManager.getString("label.choose_filename_for_param_file"));
+      chooser.setDialogTitle(MessageManager
+              .getString("label.choose_filename_for_param_file"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
       int value = chooser.showSaveDialog(Desktop.instance);
       if (value == JalviewFileChooser.APPROVE_OPTION)
diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index 25ada33..6ec25b2 100644
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -128,7 +128,8 @@ public class WsPreferences extends GWsPreferences
     }
 
     wsList.setModel(new WsUrlTableModel(tdat));
-    wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(10);
+    wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(
+            10);
   }
 
   private class JabaWSStatusRenderer extends JPanel implements
@@ -187,8 +188,10 @@ public class WsPreferences extends GWsPreferences
   {
 
     private Object[][] data;
-    private String[] columnNames = new String[]
-    { MessageManager.getString("label.service_url"), MessageManager.getString("label.status") };
+
+    private String[] columnNames = new String[] {
+        MessageManager.getString("label.service_url"),
+        MessageManager.getString("label.status") };
 
     public WsUrlTableModel(Object[][] tdat)
     {
@@ -204,7 +207,7 @@ public class WsPreferences extends GWsPreferences
     @Override
     public String getColumnName(int column)
     {
-        return columnNames[column];
+      return columnNames[column];
     }
 
     @Override
@@ -483,11 +486,10 @@ public class WsPreferences extends GWsPreferences
     }
     if (valid && resp == JOptionPane.OK_OPTION)
     {
-      int validate = JOptionPane
-              .showInternalConfirmDialog(
-                      Desktop.desktop,
-                      MessageManager.getString("info.validate_jabaws_server"),
-                      MessageManager.getString("label.test_server"), JOptionPane.YES_NO_OPTION);
+      int validate = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+              MessageManager.getString("info.validate_jabaws_server"),
+              MessageManager.getString("label.test_server"),
+              JOptionPane.YES_NO_OPTION);
 
       if (validate == JOptionPane.OK_OPTION)
       {
@@ -519,7 +521,6 @@ public class WsPreferences extends GWsPreferences
                                     .getString("warn.server_didnt_pass_validation"));
           }
 
-
         }
       }
       else
@@ -540,7 +541,8 @@ public class WsPreferences extends GWsPreferences
   @Override
   protected void newWsUrl_actionPerformed(ActionEvent e)
   {
-    String url = editUrl(null, MessageManager.getString("label.add_jabaws_url"));
+    String url = editUrl(null,
+            MessageManager.getString("label.add_jabaws_url"));
     if (url != null)
     {
       if (!wsUrls.contains(url))
@@ -625,8 +627,8 @@ public class WsPreferences extends GWsPreferences
         public void run()
         {
           long ct = System.currentTimeMillis();
-          Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_web_service_menus"),
-                  ct);
+          Desktop.instance.setProgressBar(MessageManager
+                  .getString("status.refreshing_web_service_menus"), ct);
           if (lastrefresh != update)
           {
             lastrefresh = update;
diff --git a/src/jalview/httpserver/HttpServer.java b/src/jalview/httpserver/HttpServer.java
index 7ab0d63..59eef26 100644
--- a/src/jalview/httpserver/HttpServer.java
+++ b/src/jalview/httpserver/HttpServer.java
@@ -72,7 +72,8 @@ public class HttpServer
   {
     synchronized (HttpServer.class)
     {
-      if (instance == null) {
+      if (instance == null)
+      {
         instance = new HttpServer();
       }
       return instance;
@@ -229,8 +230,7 @@ public class HttpServer
     ch.setAllowNullPathInfo(true);
     ch.setContextPath("/" + JALVIEW_PATH + "/" + path);
     ch.setResourceBase(".");
-    ch.setClassLoader(Thread.currentThread()
-            .getContextClassLoader());
+    ch.setClassLoader(Thread.currentThread().getContextClassLoader());
     ch.setHandler(handler);
 
     /*
diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 2fc17d5..f82407e 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -20,7 +20,8 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 
 public class AMSAFile extends jalview.io.FastaFile
 {
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 3b46760..7e0cabd 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -97,9 +97,10 @@ public abstract class AlignFile extends FileParse
   {
     this(true, inFile, type);
   }
-  
+
   /**
-   * Constructor which (optionally delays) parsing of data from a file of some specified type.
+   * Constructor which (optionally delays) parsing of data from a file of some
+   * specified type.
    * 
    * @param parseImmediately
    *          if false, need to call 'doParse()' to begin parsing data
@@ -109,14 +110,17 @@ public abstract class AlignFile extends FileParse
    *          What type of file to read from (File, URL)
    * @throws IOException
    */
-  public AlignFile(boolean parseImmediately, String inFile, String type) throws IOException
+  public AlignFile(boolean parseImmediately, String inFile, String type)
+          throws IOException
   {
     super(inFile, type);
     initData();
-    if (parseImmediately) {
+    if (parseImmediately)
+    {
       doParse();
     }
   }
+
   /**
    * Attempt to read from the position where some other parsing process left
    * off.
@@ -126,25 +130,31 @@ public abstract class AlignFile extends FileParse
    */
   public AlignFile(FileParse source) throws IOException
   {
-    this(true,source);
+    this(true, source);
   }
+
   /**
-   * Construct a new parser to read from the position where some other parsing process left
+   * Construct a new parser to read from the position where some other parsing
+   * process left
    * 
    * @param parseImmediately
    *          if false, need to call 'doParse()' to begin parsing data
    * @param source
    */
-  public AlignFile(boolean parseImmediately, FileParse source) throws IOException
+  public AlignFile(boolean parseImmediately, FileParse source)
+          throws IOException
   {
     super(source);
     initData();
-    if (parseImmediately) {
+    if (parseImmediately)
+    {
       doParse();
     }
   }
+
   /**
    * called if parsing was delayed till after parser was constructed
+   * 
    * @throws IOException
    */
   public void doParse() throws IOException
@@ -155,7 +165,7 @@ public abstract class AlignFile extends FileParse
               "Implementation error: Parser called twice for same data.\n"
                       + "Need to call initData() again before parsing can be reattempted.");
     }
-    parseCalled=true;
+    parseCalled = true;
     parse();
     // sets the index of each sequence in the alignment
     for (int i = 0, c = seqs.size(); i < c; i++)
@@ -164,7 +174,6 @@ public abstract class AlignFile extends FileParse
     }
   }
 
-
   /**
    * Return the seqs Vector
    */
@@ -211,8 +220,7 @@ public abstract class AlignFile extends FileParse
        * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
        * Rna.HelixMap(pairArray);
        */
-      AlignmentAnnotation an = annotations
-              .elementAt(i);
+      AlignmentAnnotation an = annotations.elementAt(i);
       an.validateRangeAndDisplay();
       al.addAnnotation(an);
     }
@@ -264,7 +272,9 @@ public abstract class AlignFile extends FileParse
   {
     if (key == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_cannot_have_null_alignment"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_cannot_have_null_alignment"));
     }
     if (value == null)
     {
@@ -294,7 +304,7 @@ public abstract class AlignFile extends FileParse
     seqs = new Vector();
     annotations = new Vector();
     seqGroups = new ArrayList();
-    parseCalled=false;
+    parseCalled = false;
   }
 
   /**
@@ -373,8 +383,7 @@ public abstract class AlignFile extends FileParse
     {
       newickStrings = new Vector();
     }
-    newickStrings.addElement(new String[]
-    { treeName, newickString });
+    newickStrings.addElement(new String[] { treeName, newickString });
   }
 
   protected int getTreeCount()
diff --git a/src/jalview/io/AlignmentProperties.java b/src/jalview/io/AlignmentProperties.java
index cb4b7ad..f2a6150 100644
--- a/src/jalview/io/AlignmentProperties.java
+++ b/src/jalview/io/AlignmentProperties.java
@@ -20,14 +20,14 @@
  */
 package jalview.io;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+
 import java.io.PrintWriter;
 import java.io.StringWriter;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-
 /**
  * Render associated attributes of an alignment. The heart of this code was
  * refactored from jalview.gui.AlignFrame and jalview.appletgui.AlignFrame TODO:
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index dcca491..8b3aa98 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -294,8 +294,7 @@ public class AnnotationFile
             }
             else
             {
-              graphGroup_refs.put(key, new Object[]
-              { refSeq, refGroup });
+              graphGroup_refs.put(key, new Object[] { refSeq, refGroup });
               graphGroup.put(key, row.label);
             }
           }
@@ -472,8 +471,9 @@ public class AnnotationFile
         text.append(properties.get(key));
       }
       // TODO: output alignment visualization settings here if required
-      // iterate through one or more views, defining, marking columns and rows as visible/hidden, and emmitting view properties.
-      // View specific annotation is 
+      // iterate through one or more views, defining, marking columns and rows
+      // as visible/hidden, and emmitting view properties.
+      // View specific annotation is
     }
 
     return text.toString();
@@ -670,14 +670,14 @@ public class AnnotationFile
     }
     boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
             file, protocol);
-    if (rslt
-            && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+    if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
     {
       viewport.setColumnSelection(colSel);
     }
 
     return rslt;
   }
+
   public boolean readAnnotationFile(AlignmentI al, String file,
           String protocol)
   {
@@ -737,8 +737,7 @@ public class AnnotationFile
   private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
 
   public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
-          BufferedReader in)
-          throws Exception
+          BufferedReader in) throws Exception
   {
     nlinesread = 0;
     ArrayList combineAnnotation_calls = new ArrayList();
@@ -831,8 +830,8 @@ public class AnnotationFile
         else if (token.equalsIgnoreCase(COMBINE))
         {
           // keep a record of current state and resolve groupRef at end
-          combineAnnotation_calls.add(new Object[]
-          { st, refSeq, groupRef });
+          combineAnnotation_calls
+                  .add(new Object[] { st, refSeq, groupRef });
           modified = true;
           continue;
         }
@@ -845,8 +844,8 @@ public class AnnotationFile
         else if (token.equalsIgnoreCase(GRAPHLINE))
         {
           // resolve at end
-          deferredAnnotation_calls.add(new Object[]
-          { GRAPHLINE, st, refSeq, groupRef });
+          deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
+              refSeq, groupRef });
           modified = true;
           continue;
         }
@@ -1154,7 +1153,7 @@ public class AnnotationFile
                   (SequenceI) _deferred_args[2], // refSeq
                   (_deferred_args[3] == null) ? null : groupRefLookup
                           .get(_deferred_args[3]) // the reference
-                                                           // group, or null
+                                                  // group, or null
           );
         }
       }
@@ -1174,7 +1173,7 @@ public class AnnotationFile
                 (SequenceI) _combine_args[1], // refSeq
                 (_combine_args[2] == null) ? null : groupRefLookup
                         .get(_combine_args[2]) // the reference group,
-                                                        // or null
+                                               // or null
         );
       }
     }
@@ -1183,7 +1182,7 @@ public class AnnotationFile
 
   private void parseHideCols(ColumnSelection colSel, String nextToken)
   {
-    StringTokenizer inval = new StringTokenizer(nextToken,",");
+    StringTokenizer inval = new StringTokenizer(nextToken, ",");
     while (inval.hasMoreTokens())
     {
       String range = inval.nextToken().trim();
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 7dc263b..239c531 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -83,52 +83,51 @@ public class AppletFormatAdapter
   /**
    * List of valid format strings used in the isValidFormat method
    */
-  public static final String[] READABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
-      "HTML" };
+  public static final String[] READABLE_FORMATS = new String[] { "BLC",
+      "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
+      "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
+      IdentifyFile.GFF3File, "HTML" };
 
   /**
    * List of readable format file extensions by application in order
    * corresponding to READABLE_FNAMES
    */
-  public static final String[] READABLE_EXTENSIONS = new String[]
-  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+  public static final String[] READABLE_EXTENSIONS = new String[] {
+      "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
       "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
-      ".gff2,gff3",
-      "jar,jvp", HtmlFile.FILE_EXT };
+      ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT };
 
   /**
    * List of readable formats by application in order corresponding to
    * READABLE_EXTENSIONS
    */
-  public static final String[] READABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
-      "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview",
-      HtmlFile.FILE_DESC };
+  public static final String[] READABLE_FNAMES = new String[] { "Fasta",
+      "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
+      "Jalview", HtmlFile.FILE_DESC };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
    * method
    */
-  public static final String[] WRITEABLE_FORMATS = new String[]
-          { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA",
-    "STH", PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
+  public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
+      "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
    * that are writable by the application.
    */
-  public static final String[] WRITABLE_EXTENSIONS = new String[]
-  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+  public static final String[] WRITABLE_EXTENSIONS = new String[] {
+      "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
       "sto,stk", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
    * WRITABLE_EXTENSIONS list of formats.
    */
-  public static final String[] WRITABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
+  public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
+      "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
       PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
@@ -170,7 +169,6 @@ public class AppletFormatAdapter
     return list.toString();
   }
 
-
   public void setNewlineString(String nl)
   {
     newline = nl;
@@ -480,7 +478,6 @@ public class AppletFormatAdapter
     }
   }
 
-
   /**
    * boilerplate method to handle data from an AlignFile and construct a new
    * alignment or import to an existing alignment
@@ -504,6 +501,7 @@ public class AppletFormatAdapter
 
   /**
    * create an alignment flatfile from a Jalview alignment view
+   * 
    * @param format
    * @param jvsuffix
    * @param av
@@ -592,10 +590,10 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile();
       }
-       else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
-       {
+      else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
+      {
         afile = new JSONFile();
-       }
+      }
       else if (format.equalsIgnoreCase("RNAML"))
       {
         afile = new RnamlFile();
@@ -603,7 +601,9 @@ public class AppletFormatAdapter
 
       else
       {
-        throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
+        throw new Exception(
+                MessageManager
+                        .getString("error.implementation_error_unknown_file_format_string"));
       }
 
       afile.setNewlineString(newline);
@@ -684,7 +684,7 @@ public class AppletFormatAdapter
             } catch (Exception e)
             {
               System.err
-              .println("Couln't format the alignment for output as a FASTA file.");
+                      .println("Couln't format the alignment for output as a FASTA file.");
               e.printStackTrace(System.err);
             }
           }
@@ -694,8 +694,8 @@ public class AppletFormatAdapter
           }
           System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
           System.out
-          .println("Difference between free memory now and before is "
-                  + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
+                  .println("Difference between free memory now and before is "
+                          + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
         } catch (Exception e)
         {
           System.err.println("Exception when dealing with " + i
@@ -761,7 +761,7 @@ public class AppletFormatAdapter
     } catch (Exception ex)
     {
       System.err
-      .println("Exception checking resources: " + file + " " + ex);
+              .println("Exception checking resources: " + file + " " + ex);
     }
 
     if (file.indexOf("://") > -1)
@@ -863,7 +863,7 @@ public class AppletFormatAdapter
           if (debug)
           {
             System.out
-            .println("File deemed not accessible via " + protocol);
+                    .println("File deemed not accessible via " + protocol);
           }
           fp.close();
           return null;
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index c7cf2d6..a499f75 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -153,7 +153,7 @@ public class BLCFile extends AlignFile
         }
       } while (!idsFound);
       if (line == null)
-       {
+      {
         break; // end of file.
       }
       int starCol = line.indexOf("*");
diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 50486f2..f5a4136 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -20,7 +20,6 @@ import java.net.URL;
 import java.util.Objects;
 import java.util.TreeMap;
 
-
 public class BioJsHTMLOutput
 {
   private AlignmentViewPanel ap;
@@ -94,8 +93,7 @@ public class BioJsHTMLOutput
 
       };
       AlignmentExportData exportData = jalview.gui.AlignFrame
-              .getAlignmentForExport(
-JSONFile.FILE_DESC,
+              .getAlignmentForExport(JSONFile.FILE_DESC,
                       ap.getAlignViewport(), exportSettings);
       if (exportData.getSettings().isCancelled())
       {
@@ -109,8 +107,7 @@ JSONFile.FILE_DESC,
 
       String bioJSTemplateString = getBioJsTemplateAsString();
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
-              .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
+              .replaceAll("#sequenceData#", jalviewAlignmentJson)
               .toString();
 
       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
@@ -132,9 +129,9 @@ JSONFile.FILE_DESC,
   {
     String selectedFile = null;
     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "html" }, new String[]
-            { "HTML files" }, "HTML files");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "html" }, new String[] { "HTML files" },
+            "HTML files");
     jvFileChooser.setFileView(new JalviewFileView());
 
     jvFileChooser.setDialogTitle(MessageManager
@@ -155,9 +152,7 @@ JSONFile.FILE_DESC,
     return selectedFile;
   }
 
-
-  public static String getBioJsTemplateAsString()
-          throws IOException
+  public static String getBioJsTemplateAsString() throws IOException
   {
     InputStreamReader isReader = null;
     BufferedReader buffReader = null;
@@ -257,7 +252,6 @@ JSONFile.FILE_DESC,
 
   }
 
-
   public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
   {
     for (BioJSReleasePojo bjsRelease : repo.getReleases())
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 1b29b52..a9295a3 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -20,11 +20,15 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
 public class ClustalFile extends AlignFile
 {
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 8dbfbfd..b867ba4 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -20,9 +20,13 @@
  */
 package jalview.io;
 
-import java.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.io.IOException;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index fbe871b..498226b 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -214,7 +214,8 @@ public class FeaturesFile extends AlignFile
     {
       SequenceI seq = null;
       /**
-       * keep track of any sequences we try to create from the data if it is a GFF3 file
+       * keep track of any sequences we try to create from the data if it is a
+       * GFF3 file
        */
       ArrayList newseqs = new ArrayList();
       String type, desc, token = null;
@@ -833,18 +834,19 @@ public class FeaturesFile extends AlignFile
    * @return true if sf was actually added to the sequence, false if it was
    *         processed in another way
    */
-  public boolean processOrAddSeqFeature(AlignmentI align, List newseqs, SequenceI seq, SequenceFeature sf,
+  public boolean processOrAddSeqFeature(AlignmentI align,
+          List newseqs, SequenceI seq, SequenceFeature sf,
           boolean gFFFile, boolean relaxedIdMatching)
   {
     String attr = (String) sf.getValue("ATTRIBUTES");
     boolean add = true;
     if (gFFFile && attr != null)
     {
-      int nattr=8;
+      int nattr = 8;
 
       for (String attset : attr.split("\t"))
       {
-        if (attset==null || attset.trim().length()==0)
+        if (attset == null || attset.trim().length() == 0)
         {
           continue;
         }
@@ -860,22 +862,25 @@ public class FeaturesFile extends AlignFile
             continue;
           }
 
-          // expect either space seperated (gff2) or '=' separated (gff3) 
+          // expect either space seperated (gff2) or '=' separated (gff3)
           // key/value pairs here
 
-          int eqpos = pair.indexOf('='),sppos = pair.indexOf(' ');
+          int eqpos = pair.indexOf('='), sppos = pair.indexOf(' ');
           String key = null, value = null;
 
           if (sppos > -1 && (eqpos == -1 || sppos < eqpos))
           {
             key = pair.substring(0, sppos);
             value = pair.substring(sppos + 1);
-          } else {
+          }
+          else
+          {
             if (eqpos > -1 && (sppos == -1 || eqpos < sppos))
             {
               key = pair.substring(0, eqpos);
               value = pair.substring(eqpos + 1);
-            } else
+            }
+            else
             {
               key = pair;
             }
@@ -898,8 +903,8 @@ public class FeaturesFile extends AlignFile
         {
           add &= processGffKey(set, nattr, seq, sf, align, newseqs,
                   relaxedIdMatching); // process decides if
-                                                     // feature is actually
-                                                     // added
+                                      // feature is actually
+                                      // added
         } catch (InvalidGFF3FieldException ivfe)
         {
           System.err.println(ivfe);
@@ -948,20 +953,20 @@ public class FeaturesFile extends AlignFile
     {
       int strand = sf.getStrand();
       // exonerate cdna/protein map
-      // look for fields 
+      // look for fields
       List querySeq = findNames(align, newseqs,
-              relaxedIdMatching, set.get(attr="Query"));
-      if (querySeq==null || querySeq.size()!=1)
+              relaxedIdMatching, set.get(attr = "Query"));
+      if (querySeq == null || querySeq.size() != 1)
       {
-        throw new InvalidGFF3FieldException( attr, set,
+        throw new InvalidGFF3FieldException(attr, set,
                 "Expecting exactly one sequence in Query field (got "
                         + set.get(attr) + ")");
       }
-      if (set.containsKey(attr="Align"))
+      if (set.containsKey(attr = "Align"))
       {
         // process the align maps and create cdna/protein maps
         // ideally, the query sequences are in the alignment, but maybe not...
-        
+
         AlignedCodonFrame alco = new AlignedCodonFrame();
         MapList codonmapping = constructCodonMappingFromAlign(set, attr,
                 strand);
@@ -979,8 +984,8 @@ public class FeaturesFile extends AlignFile
   }
 
   private MapList constructCodonMappingFromAlign(
-          Map> set,
-          String attr, int strand) throws InvalidGFF3FieldException
+          Map> set, String attr, int strand)
+          throws InvalidGFF3FieldException
   {
     if (strand == 0)
     {
@@ -1134,21 +1139,21 @@ public class FeaturesFile extends AlignFile
           }
         }
       }
-      
+
     }
-    if (match==null && newseqs!=null)
+    if (match == null && newseqs != null)
     {
       match = new SequenceDummy(seqId);
       if (relaxedIdMatching)
       {
-        matcher.addAll(Arrays.asList(new SequenceI[]
-        { match }));
+        matcher.addAll(Arrays.asList(new SequenceI[] { match }));
       }
       // add dummy sequence to the newseqs list
       newseqs.add(match);
     }
     return match;
   }
+
   public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
   {
     if (sf.getDescription() == null)
@@ -1176,7 +1181,8 @@ public class FeaturesFile extends AlignFile
    *          hash of feature types and colours
    * @return features file contents
    */
-  public String printJalviewFormat(SequenceI[] seqs, Map visible)
+  public String printJalviewFormat(SequenceI[] seqs,
+          Map visible)
   {
     return printJalviewFormat(seqs, visible, true, true);
   }
@@ -1424,13 +1430,13 @@ public class FeaturesFile extends AlignFile
    * @param visible
    * @return
    */
-  public String printGFFFormat(SequenceI[] seqs, Map visible)
+  public String printGFFFormat(SequenceI[] seqs, Map visible)
   {
     return printGFFFormat(seqs, visible, true, true);
   }
 
-  public String printGFFFormat(SequenceI[] seqs, Map visible,
-          boolean visOnly, boolean nonpos)
+  public String printGFFFormat(SequenceI[] seqs,
+          Map visible, boolean visOnly, boolean nonpos)
   {
     StringBuffer out = new StringBuffer();
     SequenceFeature[] next;
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index e2e7d19..9ff3ef9 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -399,8 +399,8 @@ public class FileLoader implements Runnable
             }
 
             alignFrame.statusBar.setText(MessageManager.formatMessage(
-                    "label.successfully_loaded_file", new String[]
-                    { title }));
+                    "label.successfully_loaded_file",
+                    new String[] { title }));
 
             if (raiseGUI)
             {
@@ -470,8 +470,8 @@ public class FileLoader implements Runnable
           {
             javax.swing.JOptionPane.showInternalMessageDialog(
                     Desktop.desktop, MessageManager.formatMessage(
-                            "label.problems_opening_file", new String[]
-                            { file }), MessageManager
+                            "label.problems_opening_file",
+                            new String[] { file }), MessageManager
                             .getString("label.file_open_error"),
                     javax.swing.JOptionPane.WARNING_MESSAGE);
           }
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 1ab99db..405363d 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -80,7 +80,7 @@ public class FileParse
 
   public void setNewlineString(String nl)
   {
-      newline = nl;
+    newline = nl;
   }
 
   public String getNewlineString()
@@ -124,7 +124,9 @@ public class FileParse
   {
     if (from == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_null_fileparse"));
     }
     if (from == this)
     {
@@ -239,7 +241,10 @@ public class FileParse
     {
       if (e != null)
       {
-        throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
+        throw new IOException(
+                MessageManager
+                        .getString("exception.failed_to_resolve_gzip_stream"),
+                e);
       }
       throw q;
     }
@@ -294,12 +299,17 @@ public class FileParse
         {
           if (checkFileSource(suffixLess))
           {
-            throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage}));
+            throw new IOException(MessageManager.formatMessage(
+                    "exception.problem_opening_file_also_tried",
+                    new String[] { inFile.getName(), suffixLess,
+                        errormessage }));
           }
         }
         else
         {
-          throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage}));
+          throw new IOException(MessageManager.formatMessage(
+                  "exception.problem_opening_file",
+                  new String[] { inFile.getName(), errormessage }));
         }
       }
     }
@@ -311,7 +321,7 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
-           {
+          {
             extractSuffix(fileStr); // URL lref is stored for later reference.
           }
         } catch (IOException e)
@@ -378,7 +388,9 @@ public class FileParse
     if (dataIn == null || error)
     {
       // pass up the reason why we have no source to read from
-      throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage}));
+      throw new IOException(MessageManager.formatMessage(
+              "exception.failed_to_read_data_from_source",
+              new String[] { errormessage }));
     }
     error = false;
     dataIn.mark(READAHEAD_LIMIT);
@@ -398,7 +410,8 @@ public class FileParse
     }
     else
     {
-      throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
+      throw new IOException(
+              MessageManager.getString("exception.no_init_source_stream"));
     }
   }
 
@@ -408,7 +421,9 @@ public class FileParse
     {
       return dataIn.readLine();
     }
-    throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
+    throw new IOException(MessageManager.formatMessage(
+            "exception.invalid_source_stream",
+            new String[] { errormessage }));
   }
 
   /**
@@ -453,7 +468,9 @@ public class FileParse
     }
     else
     {
-      throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));
+      throw new IOException(
+              MessageManager
+                      .getString("error.implementation_error_reset_called_for_invalid_source"));
     }
   }
 
@@ -558,7 +575,8 @@ public class FileParse
    */
   public void configureForView(AlignmentViewPanel avpanel)
   {
-    if (avpanel!=null) {
+    if (avpanel != null)
+    {
       setViewport(avpanel.getAlignViewport());
     }
     // could also set export/import settings
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 63a14d7..ebca31b 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -63,9 +63,9 @@ public class FormatAdapter extends AppletFormatAdapter
       annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
               true);
       localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
-            true);
-    serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
-            true);
+              true);
+      serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+              true);
     }
     else
     {
@@ -108,7 +108,6 @@ public class FormatAdapter extends AppletFormatAdapter
         startRes = seqs[i].getStart();
         endRes = seqs[i].getEnd();
 
-
         if (startEnd != null)
         {
           startIndex = startEnd[0];
@@ -271,14 +270,12 @@ public class FormatAdapter extends AppletFormatAdapter
           ColumnSelection colSel)
   {
     return formatSequences(format, alignment, omitHidden, exportRange,
-            suffix, colSel,
-            null);
+            suffix, colSel, null);
   }
 
   public String formatSequences(String format, AlignmentI alignment,
           String[] omitHidden, int[] exportRange, boolean suffix,
-          ColumnSelection colSel,
-          jalview.datamodel.SequenceGroup selgp)
+          ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
   {
     if (omitHidden != null)
     {
@@ -363,5 +360,4 @@ public class FormatAdapter extends AppletFormatAdapter
             selectedOnly);
   }
 
-
 }
diff --git a/src/jalview/io/Gff3File.java b/src/jalview/io/Gff3File.java
index 1f8c3be..6f0442a 100644
--- a/src/jalview/io/Gff3File.java
+++ b/src/jalview/io/Gff3File.java
@@ -100,6 +100,7 @@ public class Gff3File extends FeaturesFile
   AlignmentI dataset;
 
   List alignments;
+
   @Override
   public void parse()
   {
@@ -118,8 +119,7 @@ public class Gff3File extends FeaturesFile
     }
     else
     {
-      dataset = new Alignment(new SequenceI[]
-      {});
+      dataset = new Alignment(new SequenceI[] {});
     }
 
     boolean parseResult = parse(dataset, null, null, false, true);
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 3c31b7f..df0dc06 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -20,14 +20,18 @@
  */
 package jalview.io;
 
-import java.io.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.SequenceRenderer;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.Font;
+import java.io.PrintWriter;
+
 public class HTMLOutput
 {
   AlignViewport av;
@@ -48,9 +52,9 @@ public class HTMLOutput
     fr.transferSettings(fr1);
 
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "html" }, new String[]
-            { "HTML files" }, "HTML files");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "html" }, new String[] { "HTML files" },
+            "HTML files");
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index dc14cc0..06c2717 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -103,8 +103,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
         throw new IOException(errormessage);
       }
       JSONFile jsonFile = new JSONFile().parse(new StringReader(
-              contentFromDiv ? content.text() : content
-              .val()));
+              contentFromDiv ? content.text() : content.val()));
       this.seqs = jsonFile.getSeqs();
       this.seqGroups = jsonFile.getSeqGroups();
       this.annotations = jsonFile.getAnnotations();
@@ -119,7 +118,6 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     }
   }
 
-
   @Override
   public String print()
   {
diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index a93cd7f..387d374 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -26,8 +26,8 @@ public class HtmlSvgOutput
   AlignViewport av;
 
   FeatureRenderer fr;
-  AlignmentPanel ap;
 
+  AlignmentPanel ap;
 
   public HtmlSvgOutput(File file, AlignmentPanel ap)
   {
@@ -44,18 +44,18 @@ public class HtmlSvgOutput
       if (file == null)
       {
 
-      JalviewFileChooser chooser = getHTMLChooser();
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(ap.alignFrame.getTitle());
-      chooser.setToolTipText(MessageManager.getString("action.save"));
-      int value = chooser.showSaveDialog(ap.alignFrame);
+        JalviewFileChooser chooser = getHTMLChooser();
+        chooser.setFileView(new jalview.io.JalviewFileView());
+        chooser.setDialogTitle(ap.alignFrame.getTitle());
+        chooser.setToolTipText(MessageManager.getString("action.save"));
+        int value = chooser.showSaveDialog(ap.alignFrame);
 
-      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
-      {
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
-                .getSelectedFile().getParent());
-        file = chooser.getSelectedFile();
-      }
+        if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        {
+          jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+                  .getSelectedFile().getParent());
+          file = chooser.getSelectedFile();
+        }
       }
 
       AlignmentDimension aDimension = ap.getAlignmentDimension();
@@ -99,7 +99,8 @@ public class HtmlSvgOutput
               .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
       if (isEmbbedBioJSON)
       {
-        AlignExportSettingI exportSettings = new AlignExportSettingI(){
+        AlignExportSettingI exportSettings = new AlignExportSettingI()
+        {
           @Override
           public boolean isExportHiddenSequences()
           {
@@ -135,14 +136,15 @@ public class HtmlSvgOutput
           {
             return false;
           }
-          
+
         };
         AlignmentExportData exportData = jalview.gui.AlignFrame
                 .getAlignmentForExport(JSONFile.FILE_DESC, av,
                         exportSettings);
         jsonData = new FormatAdapter(ap, exportData.getSettings())
-              .formatSequences(JSONFile.FILE_DESC, exportData
-                      .getAlignment(), exportData.getOmitHidden(),
+                .formatSequences(JSONFile.FILE_DESC,
+                        exportData.getAlignment(),
+                        exportData.getOmitHidden(),
                         exportData.getStartEndPostions(),
                         av.getColumnSelection());
       }
@@ -154,20 +156,21 @@ public class HtmlSvgOutput
       if (!(System.getProperty("java.awt.headless") != null && System
               .getProperty("java.awt.headless").equals("true")))
       {
-      jalview.util.BrowserLauncher.openURL("file:///" + file);
+        jalview.util.BrowserLauncher.openURL("file:///" + file);
       }
     } catch (Exception e)
     {
       e.printStackTrace();
     }
   }
-  
+
   static JalviewFileChooser getHTMLChooser()
   {
     return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "html" }, new String[]
-            { "Hypertext Markup Language" }, "Hypertext Markup Language");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "html" },
+            new String[] { "Hypertext Markup Language" },
+            "Hypertext Markup Language");
   }
 
   public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
@@ -266,9 +269,7 @@ public class HtmlSvgOutput
                 - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
                 - 4;
       }
-      pg[0].drawString(
-              seq.getDisplayId(av.getShowJVSuffix()),
-              xPos,
+      pg[0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
               (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
@@ -302,7 +303,7 @@ public class HtmlSvgOutput
 
     return Printable.PAGE_EXISTS;
   }
-  
+
   private String getHtml(String titleSvg, String alignmentSvg,
           String jsonData)
   {
@@ -355,9 +356,7 @@ public class HtmlSvgOutput
     htmlSvg.append("
");
     htmlSvg.append(
             "
 
")
-            .append(alignmentSvg)
-.append("
")
-            .append("
");
+            .append(alignmentSvg).append("").append("");
     htmlSvg.append("");
 
     htmlSvg.append("\n"
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index a5e7fbc..ff0f0cc 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -306,19 +306,18 @@ public class IdentifyFile
           break;
         }
 
-
         /*
          * // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else
          * if (!lineswereskipped && data.indexOf("BLAST")<4) { reply =
          * "SimpleBLAST"; break;
-         *
+         * 
          * } // end comments for Jalview 2.4.1
          */
         else if (!lineswereskipped && data.charAt(0) != '*'
                 && data.charAt(0) != ' '
                 && data.indexOf(":") < data.indexOf(",")) // &&
-          // data.indexOf(",") -1)
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index f54ad9c..9570552 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -35,10 +35,10 @@ package jalview.io;
  * found in Emboss (thanks David Martin!)
  * 
  */
-import java.io.*;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
 
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
 
 public class PileUpfile extends MSFfile
 {
diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index c15bc6c..0941a6f 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -100,21 +100,29 @@ public class RnamlFile extends AlignFile
       _parse();
     } catch (ExceptionPermissionDenied pdx)
     {
-      errormessage = MessageManager.formatMessage("exception.rnaml_couldnt_access_datasource", new String[]{pdx.getMessage()});
+      errormessage = MessageManager.formatMessage(
+              "exception.rnaml_couldnt_access_datasource",
+              new String[] { pdx.getMessage() });
       throw new IOException(pdx);
     } catch (ExceptionLoadingFailed lf)
     {
-      errormessage = MessageManager.formatMessage("exception.ranml_couldnt_process_data", new String[]{lf.getMessage()});
+      errormessage = MessageManager.formatMessage(
+              "exception.ranml_couldnt_process_data",
+              new String[] { lf.getMessage() });
       throw new IOException(lf);
     } catch (ExceptionFileFormatOrSyntax iff)
     {
-        errormessage = MessageManager.formatMessage("exception.ranml_invalid_file", new String[]{iff.getMessage()});
+      errormessage = MessageManager.formatMessage(
+              "exception.ranml_invalid_file",
+              new String[] { iff.getMessage() });
       throw new IOException(iff);
     } catch (Exception x)
     {
       error = true;
-      errormessage = MessageManager.formatMessage("exception.ranml_problem_parsing_data", new String[]{x.getMessage()});
-      throw new IOException(errormessage , x);
+      errormessage = MessageManager.formatMessage(
+              "exception.ranml_problem_parsing_data",
+              new String[] { x.getMessage() });
+      throw new IOException(errormessage, x);
     }
   }
 
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 6d8ce5f..72f8044 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,7 +20,6 @@
  */
 package jalview.io;
 
-
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -30,7 +29,6 @@ import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
 
-
 /**
  * generate HTML reports for a sequence
  * 
@@ -67,12 +65,11 @@ public class SequenceAnnotationReport
     String tmpString;
     if (features != null)
     {
-      for (SequenceFeature feature:features)
+      for (SequenceFeature feature : features)
       {
         if (feature.getType().equals("disulfide bond"))
         {
-          if (feature.getBegin() == rpos
-                  || feature.getEnd() == rpos)
+          if (feature.getBegin() == rpos || feature.getEnd() == rpos)
           {
             if (tooltipText2.length() > 6)
             {
@@ -104,8 +101,7 @@ public class SequenceAnnotationReport
             }
 
             if (feature.getDescription() != null
-                    && !feature.description.equals(feature
-                            .getType()))
+                    && !feature.description.equals(feature.getType()))
             {
               tmpString = feature.getDescription();
               String tmp2up = tmpString.toUpperCase();
@@ -235,8 +231,7 @@ public class SequenceAnnotationReport
 
       // collect matching db-refs
       DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
-              new String[]
-              { target });
+              new String[] { target });
       // collect id string too
       String id = seq.getName();
       String descr = seq.getDescription();
@@ -263,8 +258,8 @@ public class SequenceAnnotationReport
               String unq = urls[u] + "|" + urls[u + 1];
               if (!uniques.contains(unq))
               {
-                urlSets.add(new String[]
-                { target, label, urls[u], urls[u + 1] });
+                urlSets.add(new String[] { target, label, urls[u],
+                    urls[u + 1] });
                 uniques.add(unq);
               }
             }
@@ -282,8 +277,8 @@ public class SequenceAnnotationReport
             String unq = urls[u] + "|" + urls[u + 1];
             if (!uniques.contains(unq))
             {
-              urlSets.add(new String[]
-              { target, label, urls[u], urls[u + 1] });
+              urlSets.add(new String[] { target, label, urls[u],
+                  urls[u + 1] });
               uniques.add(unq);
             }
           }
@@ -300,8 +295,8 @@ public class SequenceAnnotationReport
             String unq = urls[u] + "|" + urls[u + 1];
             if (!uniques.contains(unq))
             {
-              urlSets.add(new String[]
-              { target, label, urls[u], urls[u + 1] });
+              urlSets.add(new String[] { target, label, urls[u],
+                  urls[u + 1] });
               uniques.add(unq);
             }
           }
@@ -316,13 +311,12 @@ public class SequenceAnnotationReport
       {
         uniques.add(unq);
         // Add a non-dynamic link
-        urlSets.add(new String[]
-        { target, label, null, urlLink.getUrl_prefix() });
+        urlSets.add(new String[] { target, label, null,
+            urlLink.getUrl_prefix() });
       }
     }
 
-    return urlSets.toArray(new String[][]
-    {});
+    return urlSets.toArray(new String[][] {});
   }
 
   public void createSequenceAnnotationReport(final StringBuffer tip,
diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index cebe47d..f4dc5a2 100644
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -20,10 +20,13 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 /**
  * parse a simple blast report. Attempt to cope with query anchored and pairwise
@@ -197,9 +200,8 @@ public class SimpleBlastFile extends AlignFile
             if (seqentry == null)
             {
               padseq = true; // prepend gaps to new sequences in this block
-              seqentry = new Object[]
-              { new StringBuffer(), new long[]
-              { rstart, rend } };
+              seqentry = new Object[] { new StringBuffer(),
+                  new long[] { rstart, rend } };
               seqentries.addElement(seqentry);
               seqhash.put(sqid, seqentry);
 
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index f652035..9135b92 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -420,8 +420,8 @@ public class StockholmFile extends AlignFile
         {
           // logger.error("Could not parse sequence line: " + line);
           throw new IOException(MessageManager.formatMessage(
-                  "exception.couldnt_parse_sequence_line", new String[]
-                  { line }));
+                  "exception.couldnt_parse_sequence_line",
+                  new String[] { line }));
         }
         String ns = seqs.get(x.stringMatched(1));
         if (ns == null)
@@ -665,8 +665,8 @@ public class StockholmFile extends AlignFile
         else
         {
           throw new IOException(MessageManager.formatMessage(
-                  "exception.unknown_annotation_detected", new String[]
-                  { annType, annContent }));
+                  "exception.unknown_annotation_detected", new String[] {
+                      annType, annContent }));
         }
       }
     }
@@ -779,9 +779,8 @@ public class StockholmFile extends AlignFile
     {
       for (DBRefEntry d : dbrs)
       {
-        jalview.util.MapList mp = new jalview.util.MapList(new int[]
-        { seqO.getStart(), seqO.getEnd() }, new int[]
-        { st, en }, 1, 1);
+        jalview.util.MapList mp = new jalview.util.MapList(new int[] {
+            seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1, 1);
         jalview.datamodel.Mapping mping = new Mapping(mp);
         d.setMap(mping);
       }
@@ -826,7 +825,7 @@ public class StockholmFile extends AlignFile
       // be written out
       if (ss)
       {
-        //if (" .-_".indexOf(pos) == -1)
+        // if (" .-_".indexOf(pos) == -1)
         {
           if (detectbrackets.search(pos))
           {
@@ -848,7 +847,7 @@ public class StockholmFile extends AlignFile
             ann.displayCharacter = " " + ann.displayCharacter;
           }
         }
-        
+
       }
 
       els[i] = ann;
@@ -1068,21 +1067,19 @@ public class StockholmFile extends AlignFile
    * @param ann
    * @param sequenceI
    */
-  private char outputCharacter(String key, int k,
-          boolean isrna, Annotation[] ann, SequenceI sequenceI)
+  private char outputCharacter(String key, int k, boolean isrna,
+          Annotation[] ann, SequenceI sequenceI)
   {
     char seq = ' ';
     Annotation annot = ann[k];
     String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
-            .toString(sequenceI.getCharAt(k)))
-            : annot.displayCharacter;
+            .toString(sequenceI.getCharAt(k))) : annot.displayCharacter;
     if (key != null && key.equals("SS"))
     {
       if (annot == null)
       {
         // sensible gap character if one is available or make one up
-        return sequenceI == null ? '-' : sequenceI
-                .getCharAt(k);
+        return sequenceI == null ? '-' : sequenceI.getCharAt(k);
       }
       else
       {
diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index ca8a22a..07d7be4 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -525,8 +525,7 @@ public class TCoffeeScoreFile extends AlignFile
   /**
    * TCOFFEE score colourscheme
    */
-  static final Color[] colors =
-  { new Color(102, 102, 255), // #6666FF
+  static final Color[] colors = { new Color(102, 102, 255), // #6666FF
       new Color(0, 255, 0), // #00FF00
       new Color(102, 255, 0), // #66FF00
       new Color(204, 255, 0), // #CCFF00
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index d67293a..a093ebe 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -246,9 +246,12 @@ public class VamsasAppDatastore
     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(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
+      Cache.log
+              .debug("Warning? Overwriting existing vamsas id binding for "
+                      + vobj.getVorbaId(),
+                      new Exception(
+                              MessageManager
+                                      .getString("exception.overwriting_vamsas_id_binding")));
     }
     else if (jv2vobj.containsKey(jvobj)
             && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
@@ -335,7 +338,9 @@ public class VamsasAppDatastore
                 if (vbound.getV_parent() != null
                         && dataset != vbound.getV_parent())
                 {
-                  throw new Error(MessageManager.getString("error.implementation_error_cannot_map_alignment_sequences"));
+                  throw new Error(
+                          MessageManager
+                                  .getString("error.implementation_error_cannot_map_alignment_sequences"));
                   // This occurs because the dataset for the alignment we are
                   // trying to
                 }
@@ -1258,8 +1263,7 @@ public class VamsasAppDatastore
       end = start;
       start = t;
     }
-    return new int[]
-    { start, end, pol < 0 ? 1 : 0 };
+    return new int[] { start, end, pol < 0 ? 1 : 0 };
   }
 
   /**
@@ -1500,7 +1504,9 @@ public class VamsasAppDatastore
     {
       // NOTE: this happens if user deletes object in one session then updates
       // from another client
-      throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_old_jalview_object_not_bound",
+              new String[] { oldjvobject.toString() }));
     }
     if (newjvobject != null)
     {
@@ -2029,8 +2035,7 @@ public class VamsasAppDatastore
     // 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[][]
     { new jalview.datamodel.Annotation[rangeMap.length],
@@ -2165,15 +2170,13 @@ public class VamsasAppDatastore
           anot[1][i].description = anot[1][i].description + " (after)";
         }
       }
-      return new Object[]
-      { AeContent, rangeMap, anot[0], anot[1] };
+      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;
   }
@@ -2446,7 +2449,9 @@ public class VamsasAppDatastore
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -2469,8 +2474,7 @@ public class VamsasAppDatastore
         // 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();
@@ -2504,7 +2508,9 @@ public class VamsasAppDatastore
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-          throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -2757,7 +2763,9 @@ public class VamsasAppDatastore
       }
     } catch (Exception e)
     {
-      throw new Exception(MessageManager.formatMessage("exception.couldnt_store_sequence_mappings", new String[]{title}),e);
+      throw new Exception(MessageManager.formatMessage(
+              "exception.couldnt_store_sequence_mappings",
+              new String[] { title }), e);
     }
   }
 
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index db4acc4..a6c1111 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -20,15 +20,29 @@
  */
 package jalview.io;
 
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
 
-import javax.swing.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
-import uk.ac.ebi.www.*;
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+import uk.ac.ebi.www.Data;
+import uk.ac.ebi.www.InputParams;
+import uk.ac.ebi.www.WSFile;
+import uk.ac.ebi.www.WSWUBlast;
+import uk.ac.ebi.www.WSWUBlastService;
+import uk.ac.ebi.www.WSWUBlastServiceLocator;
 
 /**
  * DOCUMENT ME!
@@ -122,8 +136,7 @@ public class WSWUBlastClient
             {
               maxFound = value;
               buffer.append(" " + id2 + " " + value + "%; ");
-              suggestedIds.addElement(new Object[]
-              { seq, id2 });
+              suggestedIds.addElement(new Object[] { seq, id2 });
             }
           }
         }
@@ -208,7 +221,9 @@ public class WSWUBlastClient
           imageIndex++;
           imageIndex %= 9;
           output.setFrameIcon(imageIcon[imageIndex]);
-          output.setTitle(MessageManager.formatMessage("label.blasting_for_unidentified_sequence_jobs_running", new String[]{Integer.valueOf(jobsRunning).toString()}));
+          output.setTitle(MessageManager.formatMessage(
+                  "label.blasting_for_unidentified_sequence_jobs_running",
+                  new String[] { Integer.valueOf(jobsRunning).toString() }));
         } catch (Exception ex)
         {
         }
diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java
index 9c86557..f1b9f1a 100644
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -23,6 +23,7 @@ package jalview.io.vamsas;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
+
 import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Sequence;
diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index 11c7e91..1560ad0 100644
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -130,16 +130,22 @@ public abstract class DatastoreItem
     if (vobj2jv.containsKey(vobj.getVorbaId())
             && !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
     {
-      Cache.log.debug(
-              "Warning? Overwriting existing vamsas id binding for "
-                      + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
+      Cache.log
+              .debug("Warning? Overwriting existing vamsas id binding for "
+                      + vobj.getVorbaId(),
+                      new Exception(
+                              MessageManager
+                                      .getString("exception.overwriting_vamsas_id_binding")));
     }
     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(MessageManager.getString("exception.overwriting_jalview_id_binding")));
+      Cache.log
+              .debug("Warning? Overwriting existing jalview object binding for "
+                      + jvobj,
+                      new Exception(
+                              MessageManager
+                                      .getString("exception.overwriting_jalview_id_binding")));
     }
     /*
      * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
@@ -189,7 +195,9 @@ public abstract class DatastoreItem
     Object vobject = jv2vobj.remove(oldjvobject);
     if (vobject == null)
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_old_jalview_object_not_bound",
+              new String[] { oldjvobject.toString() }));
     }
     if (newjvobject != null)
     {
@@ -228,8 +236,13 @@ public abstract class DatastoreItem
     tojalview = true;
     if (jvobj != null && !(boundType.isAssignableFrom(jvobj.getClass())))
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_vamsas_doc_class_should_bind_to_type"
-    		  	, new String[]{vobj.getClass().toString(),boundType.toString(),jvobj.getClass().toString()}));
+      throw new Error(
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+                              new String[] { vobj.getClass().toString(),
+                                  boundType.toString(),
+                                  jvobj.getClass().toString() }));
     }
     dsReg.registerDsObj(this);
   }
@@ -255,8 +268,13 @@ public abstract class DatastoreItem
     vobj = getjv2vObj(jvobj);
     if (vobj != null && !(boundToType.isAssignableFrom(vobj.getClass())))
     {
-        throw new Error(MessageManager.formatMessage("error.implementation_error_vamsas_doc_class_should_bind_to_type"
-    		  	, new String[]{jvobj2.getClass().toString(),boundToType.toString(),vobj.getClass().toString()}));
+      throw new Error(
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+                              new String[] { jvobj2.getClass().toString(),
+                                  boundToType.toString(),
+                                  vobj.getClass().toString() }));
     }
     dsReg.registerDsObj(this);
   }
@@ -429,8 +447,7 @@ public abstract class DatastoreItem
       end = start;
       start = t;
     }
-    return new int[]
-    { start, end, pol < 0 ? 1 : 0 };
+    return new int[] { start, end, pol < 0 ? 1 : 0 };
   }
 
   /**
diff --git a/src/jalview/io/vamsas/DatastoreRegistry.java b/src/jalview/io/vamsas/DatastoreRegistry.java
index 7467d4d..2879889 100644
--- a/src/jalview/io/vamsas/DatastoreRegistry.java
+++ b/src/jalview/io/vamsas/DatastoreRegistry.java
@@ -83,8 +83,7 @@ public class DatastoreRegistry
     if (dsregitem == null)
     {
       // create a new item entry
-      dsregitem = new Object[]
-      { dsitem.jvobj, dsitem.vobj };
+      dsregitem = new Object[] { dsitem.jvobj, dsitem.vobj };
       dsItemReg.put(dsitem, dsregitem);
       dsObjReg.put(dsitem.jvobj, dsitem);
       dsObjReg.put(dsitem.vobj, dsitem);
diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index aacdecf..3e2f4e5 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -22,11 +22,12 @@ package jalview.io.vamsas;
 
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+
 import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Map;
 import uk.ac.vamsas.objects.core.Sequence;
-import jalview.io.VamsasAppDatastore;
 
 public class Dbref extends Rangetype
 {
diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index 08b1b52..96820d3 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -78,7 +78,9 @@ public abstract class Rangetype extends DatastoreItem
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -101,8 +103,7 @@ public abstract class Rangetype extends DatastoreItem
         // 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();
@@ -136,7 +137,9 @@ public abstract class Rangetype extends DatastoreItem
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -183,7 +186,9 @@ public abstract class Rangetype extends DatastoreItem
       int[] se = null;
       if (range.getSegCount() > 0 && range.getPosCount() > 0)
       {
-        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (range.getSegCount() > 0)
       {
@@ -299,7 +304,9 @@ public abstract class Rangetype extends DatastoreItem
   {
     if (ml == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_maplist_is_null"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_maplist_is_null"));
     }
     maprange.setLocal(new Local());
     maprange.setMapped(new Mapped());
diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index ffc9998..6e93f45 100644
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -200,8 +200,7 @@ public class Sequencefeature extends Rangetype
               .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
                       + dsa.getVorbaId() + ")");
     }
-    dsa.setSeg(new Seg[]
-    { vSeg });
+    dsa.setSeg(new Seg[] { vSeg });
     dsa.setDescription(feature.getDescription());
     dsa.setStatus(feature.getStatus());
     if (feature.links != null && feature.links.size() > 0)
@@ -224,8 +223,7 @@ public class Sequencefeature extends Rangetype
     if (!Float.isNaN(feature.getScore()))
     {
       Score fscore = new Score();
-      dsa.setScore(new Score[]
-      { fscore });
+      dsa.setScore(new Score[] { fscore });
       fscore.setContent(feature.getScore());
       fscore.setName(feature.getType());
     }
diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index d23b264..31ccc48 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -364,7 +364,8 @@ public class Sequencemapping extends Rangetype
     }
     bindjvvobj(mapping, sequenceMapping);
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance).registerMapping(acf);
+            .getStructureSelectionManager(Desktop.instance)
+            .registerMapping(acf);
     // Try to link up any conjugate database references in the two sequences
     // matchConjugateDBRefs(from, to, mapping);
     // Try to propagate any dbrefs across this mapping.
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index b5ada26..0bf4096 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -20,12 +20,6 @@
  */
 package jalview.io.vamsas;
 
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.analysis.NJTree;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -39,6 +33,13 @@ import jalview.gui.TreePanel;
 import jalview.io.NewickFile;
 import jalview.io.VamsasAppDatastore;
 import jalview.viewmodel.AlignmentViewport;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.AlignmentSequence;
 import uk.ac.vamsas.objects.core.Entry;
@@ -421,8 +422,7 @@ public class Tree extends DatastoreItem
       tnv.copyInto(tn);
       return tn;
     }
-    return new Treenode[]
-    {};
+    return new Treenode[] {};
   }
 
   private String makeNodeSpec(Hashtable nodespecs,
@@ -595,8 +595,7 @@ public class Tree extends DatastoreItem
           // off by
           // one for to
         }
-        return new Object[]
-        { new AlignmentView(view), jal };
+        return new Object[] { new AlignmentView(view), jal };
       }
     }
     Cache.log
diff --git a/src/jalview/javascript/JSFunctionExec.java b/src/jalview/javascript/JSFunctionExec.java
index cd9ca88..4d7c0d4 100644
--- a/src/jalview/javascript/JSFunctionExec.java
+++ b/src/jalview/javascript/JSFunctionExec.java
@@ -20,11 +20,12 @@
  */
 package jalview.javascript;
 
+import jalview.bin.JalviewLite;
+
 import java.net.URL;
 import java.util.Vector;
 
 import netscape.javascript.JSObject;
-import jalview.bin.JalviewLite;
 
 public class JSFunctionExec implements Runnable
 {
diff --git a/src/jalview/javascript/JsSelectionSender.java b/src/jalview/javascript/JsSelectionSender.java
index e4a0916..60cff9a 100644
--- a/src/jalview/javascript/JsSelectionSender.java
+++ b/src/jalview/javascript/JsSelectionSender.java
@@ -62,10 +62,8 @@ public class JsSelectionSender extends JSFunctionExec implements
 
         }
       }
-      String[] seqs = new String[]
-      {};
-      String[] cols = new String[]
-      {};
+      String[] seqs = new String[] {};
+      String[] cols = new String[] {};
       int strt = 0, end = (src == null) ? -1 : src.alignPanel.av
               .getAlignment().getWidth();
       if (seqsel != null && seqsel.getSize() > 0)
@@ -111,10 +109,8 @@ public class JsSelectionSender extends JSFunctionExec implements
 
       }
       System.err.println("Relaying selection to jsfunction:" + _listener);
-      executeJavascriptFunction(
-              _listener,
-              new Object[]
-              { src, setid, jvlite.arrayToSeparatorList(seqs),
+      executeJavascriptFunction(_listener,
+              new Object[] { src, setid, jvlite.arrayToSeparatorList(seqs),
                   jvlite.arrayToSeparatorList(cols) });
     } catch (Exception ex)
     {
diff --git a/src/jalview/javascript/MouseOverListener.java b/src/jalview/javascript/MouseOverListener.java
index 9d0279b..7b751f8 100644
--- a/src/jalview/javascript/MouseOverListener.java
+++ b/src/jalview/javascript/MouseOverListener.java
@@ -64,10 +64,8 @@ public class MouseOverListener extends JSFunctionExec implements
           // function, then only events from that alignFrame are sent to that
           // function
         }
-        executeJavascriptFunction(
-                _listener,
-                new Object[]
-                { src, seq.getDisplayId(false), "" + (1 + i),
+        executeJavascriptFunction(_listener,
+                new Object[] { src, seq.getDisplayId(false), "" + (1 + i),
                     "" + seq.findPosition(i) });
       } catch (Exception ex)
       {
diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index e3534ce..2ef957e 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -154,10 +154,10 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         // field that is interpreted (in 2.8.2) as pdbId?
         // JBPComment: yep - this is right! the Javascript harness uses the
         // absolute pdbFile URI to locate the PDB file in the external viewer
-        executeJavascriptFunction(_listenerfn, new String[]
-        { "mouseover", "" + atom.getPdbFile(),
-                    "" + atom.getChain(),
-            "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
+        executeJavascriptFunction(_listenerfn,
+                new String[] { "mouseover", "" + atom.getPdbFile(),
+                    "" + atom.getChain(), "" + (atom.getPdbResNum()),
+                    "" + atom.getAtomIndex() });
       } catch (Exception ex)
       {
         System.err.println("Couldn't execute callback with " + _listenerfn
@@ -253,8 +253,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       {
         jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
         // and notify javascript handler
-        String st[] = new String[]
-        {
+        String st[] = new String[] {
             "colourstruct",
             "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
             "" + ccomandset.length,
diff --git a/src/jalview/jbgui/GAlignExportSettings.java b/src/jalview/jbgui/GAlignExportSettings.java
index 58005e8..8b2e4e1 100644
--- a/src/jalview/jbgui/GAlignExportSettings.java
+++ b/src/jalview/jbgui/GAlignExportSettings.java
@@ -53,8 +53,7 @@ public abstract class GAlignExportSettings extends JPanel
   {
     this.hasHiddenSeq = hasHiddenSeq;
     this.hasHiddenCols = hasHiddenCols;
-    String[] complexFormats =
-    { "JSON", "HTML" };
+    String[] complexFormats = { "JSON", "HTML" };
 
     for (String format : complexFormats)
     {
@@ -143,7 +142,7 @@ public abstract class GAlignExportSettings extends JPanel
     add(actionPanel, BorderLayout.SOUTH);
 
   }
-  
+
   private void checkAllAction()
   {
     boolean isSelected = chkAll.isSelected();
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 3504ea4..8d18064 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -491,8 +491,7 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
-            MessageManager
-            .getString("action.select_all"));
+            MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -703,8 +702,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
-.getString("action.remove_redundancy"));
+    JMenuItem removeRedundancyMenuItem = new JMenuItem(
+            MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1959,8 +1958,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.ALT_MASK, false);
     al = new ActionListener()
     {
@@ -2803,6 +2802,7 @@ public class GAlignFrame extends JInternalFrame
   {
 
   }
+
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -3057,7 +3057,8 @@ public class GAlignFrame extends JInternalFrame
     return annotationSortOrder;
   }
 
-  protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
+  protected void setAnnotationSortOrder(
+          SequenceAnnotationOrder annotationSortOrder)
   {
     this.annotationSortOrder = annotationSortOrder;
   }
diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index 474a92d..6e09799 100755
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -20,9 +20,16 @@
  */
 package jalview.jbgui;
 
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.border.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JPanel;
+import javax.swing.JScrollBar;
+import javax.swing.JScrollPane;
+import javax.swing.border.Border;
 
 public class GAlignmentPanel extends JPanel
 {
diff --git a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
index 03154ee..a9e3112 100644
--- a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
@@ -23,10 +23,22 @@ package jalview.jbgui;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index 4ac3a67..acf1581 100755
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -23,9 +23,21 @@ package jalview.jbgui;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JButton;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/jbgui/GDasSourceBrowser.java b/src/jalview/jbgui/GDasSourceBrowser.java
index d74900a..a2612e8 100755
--- a/src/jalview/jbgui/GDasSourceBrowser.java
+++ b/src/jalview/jbgui/GDasSourceBrowser.java
@@ -22,11 +22,30 @@ package jalview.jbgui;
 
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.border.*;
-import javax.swing.event.*;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JEditorPane;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
 
 public class GDasSourceBrowser extends JPanel
 {
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 1c37e86..d22fd88 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -75,7 +75,7 @@ public class GDesktop extends JFrame
   JMenuItem saveState = new JMenuItem();
 
   JMenuItem loadState = new JMenuItem();
-  
+
   JMenu inputMenu = new JMenu();
 
   protected JMenuItem vamsasStart = new JMenuItem();
@@ -101,8 +101,9 @@ public class GDesktop extends JFrame
   protected JCheckBoxMenuItem showConsole = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem showNews = new JCheckBoxMenuItem();
-  
+
   protected JMenuItem snapShotWindow = new JMenuItem();
+
   /**
    * Creates a new GDesktop object.
    */
@@ -353,7 +354,7 @@ public class GDesktop extends JFrame
         snapShotWindow_actionPerformed(e);
       }
     });
-    
+
     desktopMenubar.add(FileMenu);
     desktopMenubar.add(toolsMenu);
     VamsasMenu.setVisible(false);
@@ -394,7 +395,7 @@ public class GDesktop extends JFrame
   protected void snapShotWindow_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   protected void showConsole_actionPerformed(ActionEvent e)
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 0b2e6be..df09a61 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -90,7 +90,6 @@ public class GFinder extends JPanel
     }
   }
 
-
   private void jbInit() throws Exception
   {
     jLabelFind.setFont(new java.awt.Font("Verdana", 0, 12));
diff --git a/src/jalview/jbgui/GFontChooser.java b/src/jalview/jbgui/GFontChooser.java
index f379de8..8c893a2 100755
--- a/src/jalview/jbgui/GFontChooser.java
+++ b/src/jalview/jbgui/GFontChooser.java
@@ -20,6 +20,9 @@
  */
 package jalview.jbgui;
 
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -35,9 +38,6 @@ import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.SwingConstants;
 
-import jalview.gui.JvSwingUtils;
-import jalview.util.MessageManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -46,7 +46,8 @@ import jalview.util.MessageManager;
  */
 public class GFontChooser extends JPanel
 {
-  private static final Font VERDANA_11PT = new java.awt.Font("Verdana", 0, 11);
+  private static final Font VERDANA_11PT = new java.awt.Font("Verdana", 0,
+          11);
 
   protected JComboBox fontSize = new JComboBox();
 
diff --git a/src/jalview/jbgui/GPDBSearchPanel.java b/src/jalview/jbgui/GPDBSearchPanel.java
index 6f6f1aa..64095d0 100644
--- a/src/jalview/jbgui/GPDBSearchPanel.java
+++ b/src/jalview/jbgui/GPDBSearchPanel.java
@@ -72,11 +72,11 @@ public abstract class GPDBSearchPanel extends JPanel
   protected JButton btn_ok = new JButton();
 
   protected JButton btn_back = new JButton();
-  
+
   protected JButton btn_cancel = new JButton();
-  
+
   protected JTextField txt_search = new JTextField(20);
-  
+
   protected JTable tbl_summary = new JTable()
   {
     public String getToolTipText(MouseEvent evt)
@@ -95,10 +95,8 @@ public abstract class GPDBSearchPanel extends JPanel
       }
       toolTipText = (toolTipText == null ? null
               : (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(
-                      true, toolTipText.subSequence(0, 500)
- + "...")
-                      : JvSwingUtils.wrapTooltip(true,
-                      toolTipText)));
+                      true, toolTipText.subSequence(0, 500) + "...")
+                      : JvSwingUtils.wrapTooltip(true, toolTipText)));
 
       return toolTipText;
     }
@@ -106,14 +104,14 @@ public abstract class GPDBSearchPanel extends JPanel
 
   protected StringBuilder errorWarning = new StringBuilder();
 
-  protected JScrollPane scrl_searchResult = new JScrollPane(
-tbl_summary);
+  protected JScrollPane scrl_searchResult = new JScrollPane(tbl_summary);
 
   protected ImageIcon warningImage = new ImageIcon(getClass().getResource(
           "/images/warning.gif"));
 
   protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
           "/images/loading.gif"));
+
   protected JLabel lbl_warning = new JLabel(warningImage);
 
   protected JLabel lbl_loading = new JLabel(loadingImage);
@@ -166,6 +164,7 @@ tbl_summary);
       {
         validateSelection();
       }
+
       public void mouseReleased(MouseEvent e)
       {
         validateSelection();
@@ -202,7 +201,6 @@ tbl_summary);
       }
     });
 
-
     scrl_searchResult.setPreferredSize(new Dimension(500, 300));
     scrl_searchResult
             .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
@@ -228,8 +226,9 @@ tbl_summary);
         else
         {
           tooltipText = MessageManager.formatMessage(
-                  "label.separate_multiple_query_values", new Object[]
-                  { getCmbSearchTarget().getSelectedItem().toString() });
+                  "label.separate_multiple_query_values",
+                  new Object[] { getCmbSearchTarget().getSelectedItem()
+                          .toString() });
         }
         txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
                 tooltipText));
@@ -239,7 +238,6 @@ tbl_summary);
 
     populateCmbSearchTargetOptions();
 
-
     txt_search.setFont(new java.awt.Font("Verdana", 0, 12));
 
     txt_search.addKeyListener(new KeyAdapter()
@@ -286,7 +284,8 @@ tbl_summary);
 
     final String searchTabTitle = MessageManager
             .getString("label.search_result");
-    final String configureCols = MessageManager.getString("label.configure_displayed_columns");
+    final String configureCols = MessageManager
+            .getString("label.configure_displayed_columns");
     ChangeListener changeListener = new ChangeListener()
     {
       public void stateChanged(ChangeEvent changeEvent)
@@ -354,6 +353,7 @@ tbl_summary);
             : true;
 
   }
+
   public void validateSelection()
   {
     if (tbl_summary.getSelectedRows().length > 0)
@@ -365,6 +365,7 @@ tbl_summary);
       btn_ok.setEnabled(false);
     }
   }
+
   public JComboBox getCmbSearchTarget()
   {
     return cmb_searchTarget;
diff --git a/src/jalview/jbgui/GPairwiseAlignPanel.java b/src/jalview/jbgui/GPairwiseAlignPanel.java
index 5875e2d..b064551 100755
--- a/src/jalview/jbgui/GPairwiseAlignPanel.java
+++ b/src/jalview/jbgui/GPairwiseAlignPanel.java
@@ -22,9 +22,13 @@ package jalview.jbgui;
 
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+
+import javax.swing.JButton;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 4f4afb0..b12355a 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -76,8 +76,8 @@ public class GPreferences extends JPanel
 {
   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
 
-  private static final Font LABEL_FONT_ITALIC = JvSwingUtils
-          .getLabelFont(false, true);
+  private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
+          false, true);
 
   /*
    * Visual tab components
@@ -156,7 +156,6 @@ public class GPreferences extends JPanel
 
   protected JTextField chimeraPath = new JTextField();
 
-
   /*
    * Colours tab components
    */
@@ -276,16 +275,17 @@ public class GPreferences extends JPanel
     tabbedPane.add(initConnectionsTab(),
             MessageManager.getString("label.connections"));
 
-    tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
+    tabbedPane.add(initOutputTab(),
+            MessageManager.getString("label.output"));
 
-    tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
+    tabbedPane.add(initEditingTab(),
+            MessageManager.getString("label.editing"));
 
     /*
      * See DasSourceBrowser for the real work of configuring this tab.
      */
     dasTab.setLayout(new BorderLayout());
-    tabbedPane
-            .add(dasTab, MessageManager.getString("label.das_settings"));
+    tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 
     /*
      * See WsPreferences for the real work of configuring this tab.
@@ -402,8 +402,9 @@ public class GPreferences extends JPanel
     autoIdWidth.setFont(LABEL_FONT);
     autoIdWidth.setText(MessageManager
             .getString("label.automatically_set_id_width"));
-    autoIdWidth
-            .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
+    autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager
+                    .getString("label.adjusts_width_generated_eps_png")));
     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
     autoIdWidth.addActionListener(new ActionListener()
     {
@@ -418,9 +419,11 @@ public class GPreferences extends JPanel
     userIdWidthlabel.setText(MessageManager
             .getString("label.figure_id_column_width"));
     userIdWidth
-            .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
+            .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+                    .getString("label.manually_specify_width_left_column")));
     userIdWidthlabel
-            .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
+            .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+                    .getString("label.manually_specify_width_left_column")));
     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
     userIdWidth.setText("");
@@ -727,8 +730,7 @@ public class GPreferences extends JPanel
     nucColourLabel.setFont(LABEL_FONT);
     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
     nucColourLabel.setText(MessageManager
-            .getString("label.nuc_alignment_colour")
-            + " ");
+            .getString("label.nuc_alignment_colour") + " ");
     JvSwingUtils.addtoLayout(coloursTab, MessageManager
             .getString("label.default_colour_scheme_for_alignment"),
             nucColourLabel, nucColour);
@@ -765,7 +767,8 @@ public class GPreferences extends JPanel
     int ypos = 30;
 
     structFromPdb.setFont(LABEL_FONT);
-    structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
+    structFromPdb
+            .setText(MessageManager.getString("label.struct_from_pdb"));
     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
     structFromPdb.addActionListener(new ActionListener()
     {
@@ -865,13 +868,9 @@ public class GPreferences extends JPanel
     docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
     structureTab.add(docFieldPref);
 
-
-
-
     return structureTab;
   }
 
-
   /**
    * Action on choosing a structure viewer from combobox options.
    * 
@@ -1121,7 +1120,7 @@ public class GPreferences extends JPanel
         }
       }
     });
- 
+
     sortby.setFont(LABEL_FONT);
     sortby.setBounds(new Rectangle(172, 260, 155, 21));
     JLabel sortLabel = new JLabel();
diff --git a/src/jalview/jbgui/GRestInputParamEditDialog.java b/src/jalview/jbgui/GRestInputParamEditDialog.java
index 74ebcad..eb1a348 100644
--- a/src/jalview/jbgui/GRestInputParamEditDialog.java
+++ b/src/jalview/jbgui/GRestInputParamEditDialog.java
@@ -20,15 +20,20 @@
  */
 package jalview.jbgui;
 
-import java.awt.Dimension;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-
 import jalview.gui.JvSwingUtils;
 import jalview.gui.OptsAndParamsPage;
 import jalview.util.MessageManager;
 
-import javax.swing.*;
+import java.awt.Dimension;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
 import javax.swing.border.TitledBorder;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
diff --git a/src/jalview/jbgui/GRestServiceEditorPane.java b/src/jalview/jbgui/GRestServiceEditorPane.java
index a8ac912..3329780 100644
--- a/src/jalview/jbgui/GRestServiceEditorPane.java
+++ b/src/jalview/jbgui/GRestServiceEditorPane.java
@@ -146,9 +146,8 @@ public class GRestServiceEditorPane extends JPanel
     // details.add(cpanel = new JPanel(), BorderLayout.CENTER);
     // cpanel.setLayout(new FlowLayout());
     hSeparable = new JCheckBox(MessageManager.getString("label.per_seq"));
-    hSeparable
-            .setToolTipText(JvSwingUtils
-                            .wrapTooltip(true, MessageManager.getString("label.job_created_when_checked")));
+    hSeparable.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.job_created_when_checked")));
     hSeparable.addActionListener(new ActionListener()
     {
 
@@ -162,7 +161,10 @@ public class GRestServiceEditorPane extends JPanel
     vSeparable = new JCheckBox(
             MessageManager.getString("label.result_vertically_separable"));
     vSeparable
-            .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.when_checked_job_visible_region_and_results")));
+            .setToolTipText(JvSwingUtils.wrapTooltip(
+                    true,
+                    MessageManager
+                            .getString("label.when_checked_job_visible_region_and_results")));
     vSeparable.addActionListener(new ActionListener()
     {
 
@@ -392,8 +394,8 @@ public class GRestServiceEditorPane extends JPanel
             .getString("label.rsbs_encoded_service")));
     urldescPane.add(urldescVp, "span");
     paste.add(urldescPane, "span");
-    urldescPane
-            .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.flat_file_representation")));
+    urldescPane.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.flat_file_representation")));
 
     parseRes = new JTextArea();
     parseResVp = new JScrollPane();
@@ -404,8 +406,8 @@ public class GRestServiceEditorPane extends JPanel
             "[grow 100, fill]"));
     parseWarnings.setBorder(new TitledBorder(MessageManager
             .getString("label.parsing_errors")));
-    parseWarnings
-            .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.result_of_parsing_rsbs")));
+    parseWarnings.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.result_of_parsing_rsbs")));
     parseWarnings.add(parseResVp, "center");
     parseRes.setEditable(false);
     paste.add(parseWarnings, "span");
diff --git a/src/jalview/jbgui/GRnaStructureViewer.java b/src/jalview/jbgui/GRnaStructureViewer.java
index 95c9a1c..60f5436 100644
--- a/src/jalview/jbgui/GRnaStructureViewer.java
+++ b/src/jalview/jbgui/GRnaStructureViewer.java
@@ -20,7 +20,7 @@
  */
 package jalview.jbgui;
 
-import javax.swing.*;
+import javax.swing.JInternalFrame;
 
 public class GRnaStructureViewer extends JInternalFrame
 {
diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java
index ed74f02..46580a2 100755
--- a/src/jalview/jbgui/GSequenceLink.java
+++ b/src/jalview/jbgui/GSequenceLink.java
@@ -24,9 +24,21 @@ import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
 
 public class GSequenceLink extends Panel
 {
@@ -118,11 +130,10 @@ public class GSequenceLink extends Panel
       return true;
     }
 
-    JOptionPane
-            .showInternalMessageDialog(
-                    jalview.gui.Desktop.desktop,
-                    MessageManager.getString("warn.url_must_contain"),
-                    MessageManager.getString("label.invalid_url"), JOptionPane.WARNING_MESSAGE);
+    JOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
+            MessageManager.getString("warn.url_must_contain"),
+            MessageManager.getString("label.invalid_url"),
+            JOptionPane.WARNING_MESSAGE);
     return false;
   }
 
diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java
index 93f7040..1362007 100755
--- a/src/jalview/jbgui/GSliderPanel.java
+++ b/src/jalview/jbgui/GSliderPanel.java
@@ -22,9 +22,22 @@ package jalview.jbgui;
 
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/jbgui/GSplitFrame.java b/src/jalview/jbgui/GSplitFrame.java
index bcd5f64..b9f07db 100644
--- a/src/jalview/jbgui/GSplitFrame.java
+++ b/src/jalview/jbgui/GSplitFrame.java
@@ -1,5 +1,7 @@
 package jalview.jbgui;
 
+import jalview.util.Platform;
+
 import java.awt.Component;
 import java.awt.MouseInfo;
 import java.awt.Point;
@@ -9,8 +11,6 @@ import javax.swing.JInternalFrame;
 import javax.swing.JSplitPane;
 import javax.swing.plaf.basic.BasicInternalFrameUI;
 
-import jalview.util.Platform;
-
 public class GSplitFrame extends JInternalFrame
 {
   private static final long serialVersionUID = 1L;
@@ -95,7 +95,7 @@ public class GSplitFrame extends JInternalFrame
   protected GAlignFrame getFrameAtMouse()
   {
     Point loc = MouseInfo.getPointerInfo().getLocation();
-    
+
     if (isIn(loc, splitPane.getTopComponent()))
     {
       return getTopFrame();
diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java
index 2c51b3d..c4043c4 100644
--- a/src/jalview/jbgui/GStructureChooser.java
+++ b/src/jalview/jbgui/GStructureChooser.java
@@ -75,7 +75,7 @@ public abstract class GStructureChooser extends JPanel implements
   protected JComboBox cmb_filterOption = new JComboBox();
 
   protected AlignmentPanel ap;
-  
+
   protected StringBuilder errorWarning = new StringBuilder();
 
   protected JLabel lbl_result = new JLabel(
@@ -136,7 +136,6 @@ public abstract class GStructureChooser extends JPanel implements
 
   protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
 
-
   protected AssciateSeqPanel idInputAssSeqPanel = new AssciateSeqPanel();
 
   protected AssciateSeqPanel fileChooserAssSeqPanel = new AssciateSeqPanel();
@@ -174,8 +173,7 @@ public abstract class GStructureChooser extends JPanel implements
     }
   };
 
-  protected JScrollPane scrl_foundStructures = new JScrollPane(
-          tbl_summary);
+  protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
 
   protected JTable tbl_local_pdb = new JTable();
 
@@ -187,6 +185,7 @@ public abstract class GStructureChooser extends JPanel implements
           PreferenceSource.STRUCTURE_CHOOSER);
 
   protected PDBDocField[] previousWantedFields;
+
   public GStructureChooser()
   {
     try
@@ -306,7 +305,6 @@ public abstract class GStructureChooser extends JPanel implements
     pnl_main.add(chk_invertFilter);
     lbl_loading.setVisible(false);
 
-
     pnl_fileChooser.add(btn_pdbFromFile);
     pnl_fileChooser.add(lbl_fromFileStatus);
     pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
@@ -316,7 +314,7 @@ public abstract class GStructureChooser extends JPanel implements
     pnl_idInput.add(lbl_pdbManualFetchStatus);
     pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
     pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
-    
+
     final String foundStructureSummary = MessageManager
             .getString("label.found_structures_summary");
     final String configureCols = MessageManager
@@ -328,8 +326,7 @@ public abstract class GStructureChooser extends JPanel implements
         JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
                 .getSource();
         int index = sourceTabbedPane.getSelectedIndex();
-        if (sourceTabbedPane.getTitleAt(index)
-.equals(configureCols))
+        if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
         {
           btn_view.setEnabled(false);
           btn_cancel.setEnabled(false);
@@ -356,14 +353,14 @@ public abstract class GStructureChooser extends JPanel implements
     pnl_filter.setPreferredSize(new Dimension(500, 300));
     pnl_filter.add(foundStructureSummary, scrl_foundStructures);
     pnl_filter.add(configureCols, pdbDocFieldPrefs);
-    
+
     pnl_locPDB.add(scrl_localPDB);
 
     pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
     pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
     pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
     pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
-    
+
     this.setLayout(mainLayout);
     this.add(pnl_main, java.awt.BorderLayout.NORTH);
     this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
@@ -387,7 +384,7 @@ public abstract class GStructureChooser extends JPanel implements
             previousWantedFields) ? false : true;
 
   }
-  
+
   @Override
   /**
    * Event listener for the 'filter' combo-box and 'invert' check-box
@@ -464,6 +461,7 @@ public abstract class GStructureChooser extends JPanel implements
   public class AssociateSeqOptions
   {
     private SequenceI sequence;
+
     private String name;
 
     public AssociateSeqOptions(SequenceI seq)
diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 982036d..943aa8c 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -20,6 +20,9 @@
  */
 package jalview.jbgui;
 
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.util.MessageManager;
+
 import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -33,9 +36,6 @@ import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JRadioButtonMenuItem;
 
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.util.MessageManager;
-
 public abstract class GStructureViewer extends JInternalFrame implements
         JalviewStructureDisplayI
 {
@@ -166,7 +166,8 @@ public abstract class GStructureViewer extends JInternalFrame implements
     colourMenu.setText(MessageManager.getString("label.colours"));
 
     JMenuItem backGround = new JMenuItem();
-    backGround.setText(MessageManager.getString("action.background_colour"));
+    backGround
+            .setText(MessageManager.getString("action.background_colour"));
     backGround.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 8b20939..b5695b2 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -23,10 +23,23 @@ package jalview.jbgui;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
 import javax.swing.colorchooser.AbstractColorChooserPanel;
 
 /**
@@ -185,11 +198,11 @@ public class GUserDefinedColours extends JPanel
     label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
     label.setOpaque(false);
     label.setPreferredSize(new Dimension(260, 34));
-    label.setText(MessageManager.formatMessage(
-            "label.html_content",
-            new String[]
-            { MessageManager
-                    .getString("label.save_colour_scheme_with_unique_name_added_to_colour_menu") }));
+    label.setText(MessageManager
+            .formatMessage(
+                    "label.html_content",
+                    new String[] { MessageManager
+                            .getString("label.save_colour_scheme_with_unique_name_added_to_colour_menu") }));
     caseSensitive.setText(MessageManager.getString("label.case_sensitive"));
     caseSensitive.addActionListener(new ActionListener()
     {
@@ -229,12 +242,16 @@ public class GUserDefinedColours extends JPanel
     jPanel4.add(panel1, java.awt.BorderLayout.CENTER);
     this.add(jPanel4, java.awt.BorderLayout.CENTER);
     this.add(colorChooser, java.awt.BorderLayout.EAST);
-    
+
     AbstractColorChooserPanel[] choosers = colorChooser.getChooserPanels();
-    // JAL-1360 larger JColorChooser in Java 7 overwrites AA panel; restrict to swatch picker only
-    if (choosers.length > 3) {
-    	// Java 7 default has 5 options rather than 3 for choosing colours; keep the first only
-    	colorChooser.setChooserPanels(new AbstractColorChooserPanel[]{choosers[0]});
+    // JAL-1360 larger JColorChooser in Java 7 overwrites AA panel; restrict to
+    // swatch picker only
+    if (choosers.length > 3)
+    {
+      // Java 7 default has 5 options rather than 3 for choosing colours; keep
+      // the first only
+      colorChooser
+              .setChooserPanels(new AbstractColorChooserPanel[] { choosers[0] });
     }
   }
 
diff --git a/src/jalview/jbgui/GWebserviceInfo.java b/src/jalview/jbgui/GWebserviceInfo.java
index 624f2e0..9169e63 100755
--- a/src/jalview/jbgui/GWebserviceInfo.java
+++ b/src/jalview/jbgui/GWebserviceInfo.java
@@ -22,10 +22,20 @@ package jalview.jbgui;
 
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/jbgui/PDBDocFieldPreferences.java b/src/jalview/jbgui/PDBDocFieldPreferences.java
index 4ec649a..4b400a3 100644
--- a/src/jalview/jbgui/PDBDocFieldPreferences.java
+++ b/src/jalview/jbgui/PDBDocFieldPreferences.java
@@ -50,16 +50,14 @@ public class PDBDocFieldPreferences extends JScrollPane
     switch (source)
     {
     case SEARCH_SUMMARY:
-      columnNames = new String[]
-      { "PDB Field", "Show in search summary" };
+      columnNames = new String[] { "PDB Field", "Show in search summary" };
       break;
     case STRUCTURE_CHOOSER:
-      columnNames = new String[]
-      { "PDB Field", "Show in structure summary" };
+      columnNames = new String[] { "PDB Field", "Show in structure summary" };
       break;
     case PREFERENCES:
-      columnNames = new String[]
-      { "PDB Field", "Show in search summary", "Show in structure summary" };
+      columnNames = new String[] { "PDB Field", "Show in search summary",
+          "Show in structure summary" };
       break;
     default:
       break;
@@ -77,16 +75,16 @@ public class PDBDocFieldPreferences extends JScrollPane
       switch (source)
       {
       case SEARCH_SUMMARY:
-        data[x++] = new Object[]
-        { field.getName(), searchSummaryFields.contains(field) };
+        data[x++] = new Object[] { field.getName(),
+            searchSummaryFields.contains(field) };
         break;
       case STRUCTURE_CHOOSER:
-        data[x++] = new Object[]
-        { field.getName(), structureSummaryFields.contains(field) };
+        data[x++] = new Object[] { field.getName(),
+            structureSummaryFields.contains(field) };
         break;
       case PREFERENCES:
-        data[x++] = new Object[]
-        { field.getName(), searchSummaryFields.contains(field),
+        data[x++] = new Object[] { field.getName(),
+            searchSummaryFields.contains(field),
             structureSummaryFields.contains(field) };
         break;
       default:
@@ -232,8 +230,7 @@ public class PDBDocFieldPreferences extends JScrollPane
     }
 
     private void updatePrefs(Collection prefConfig,
-            PDBDocField pdbField,
-            boolean selected)
+            PDBDocField pdbField, boolean selected)
     {
       if (prefConfig.contains(pdbField) && !selected)
       {
diff --git a/src/jalview/json/binding/biojs/BioJSRepositoryPojo.java b/src/jalview/json/binding/biojs/BioJSRepositoryPojo.java
index 46b4ab8..5c79e51 100644
--- a/src/jalview/json/binding/biojs/BioJSRepositoryPojo.java
+++ b/src/jalview/json/binding/biojs/BioJSRepositoryPojo.java
@@ -45,8 +45,7 @@ public class BioJSRepositoryPojo
     this.latestReleaseVersion = (String) JsonObj
             .get("latestReleaseVersion");
 
-    JSONArray repositoriesJsonArray = (JSONArray) JsonObj
-.get("releases");
+    JSONArray repositoriesJsonArray = (JSONArray) JsonObj.get("releases");
     for (Iterator repoIter = repositoriesJsonArray.iterator(); repoIter
             .hasNext();)
     {
@@ -69,7 +68,6 @@ public class BioJSRepositoryPojo
     this.description = description;
   }
 
-
   public String getLatestReleaseVersion()
   {
     return latestReleaseVersion;
diff --git a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
index 9fd712f..6b9cf42 100644
--- a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
@@ -8,10 +8,14 @@ import com.github.reinert.jjschema.Attributes;
 public class AlignmentAnnotationPojo
 {
 
-  @Attributes(required = false, description = "Label for the Alignment Annotation")
+  @Attributes(
+    required = false,
+    description = "Label for the Alignment Annotation")
   private String label;
 
-  @Attributes(required = false, description = "Description for the Alignment Annotation")
+  @Attributes(
+    required = false,
+    description = "Description for the Alignment Annotation")
   private String description;
 
   @Attributes(required = false)
@@ -47,6 +51,4 @@ public class AlignmentAnnotationPojo
     this.annotations = annotations;
   }
 
-
-
 }
diff --git a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
index 9021a73..bd2ebe7 100644
--- a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
@@ -1,6 +1,5 @@
 package jalview.json.binding.biojson.v1;
 
-
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -8,16 +7,20 @@ import java.util.Map;
 
 import com.github.reinert.jjschema.Attributes;
 
-@Attributes(title="BioJSON", description="A specification for the representation and exchange of bioinformatics data")
+@Attributes(
+  title = "BioJSON",
+  description = "A specification for the representation and exchange of bioinformatics data")
 public class AlignmentPojo
 {
-  @Attributes(required = true, description = "Serial version identifier for BioJSON schema")
+  @Attributes(
+    required = true,
+    description = "Serial version identifier for BioJSON schema")
   private String svid = "1.0";
 
   @Attributes(
     required = true,
     minItems = 1,
-    	    description = "An array of Sequences which makes up the Alignment")
+    description = "An array of Sequences which makes up the Alignment")
   private List seqs = new ArrayList();
 
   @Attributes(
@@ -48,12 +51,13 @@ public class AlignmentPojo
         "Blosum62", "RNA Helices", "% Identity" },
     description = "The Colour Scheme applied to the alignment")
   private String colourScheme;
-  
+
   @Attributes(
-	required = true, 
-	maxItems = 0, description = "AppSettings stores key=value pairs of custom application specific 
"
-			                  + "settings (i.e visualisation settings, etc) for different applications
"
-			                  + "that consume or generate BioJSON")
+    required = true,
+    maxItems = 0,
+    description = "AppSettings stores key=value pairs of custom application specific 
"
+            + "settings (i.e visualisation settings, etc) for different applications
"
+            + "that consume or generate BioJSON")
   Map appSettings = new HashMap();
 
   public AlignmentPojo()
diff --git a/src/jalview/json/binding/biojson/v1/AnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
index 919f6ab..9b693fa 100644
--- a/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
@@ -4,19 +4,25 @@ import com.github.reinert.jjschema.Attributes;
 
 public class AnnotationPojo
 {
-  @Attributes(required = false, description = "Display character for the given annotation")
+  @Attributes(
+    required = false,
+    description = "Display character for the given annotation")
   private String displayCharacter;
 
-  @Attributes(required = false, description = "Description for the annotation")
+  @Attributes(
+    required = false,
+    description = "Description for the annotation")
   private String description;
 
-  @Attributes(required = true, enums = {"E", "H", "\u0000", ")", "("}, description = "Determines what is rendered for the secondary 
structure 
  • ’E’ - indicates Beta Sheet/Strand 
  • ’H’ - indicates alpha helix 
  •  ‘\\u0000’ - indicates blank

For RNA Helix (only shown when working with
 nucleotide sequences): 
  •  ‘(’ - indicates bases pair with columns upstream
     (to right) 
  •  ’(’ - indicate region pairs with bases to the left
")
+  @Attributes(
+    required = true,
+    enums = { "E", "H", "\u0000", ")", "(" },
+    description = "Determines what is rendered for the secondary 
structure 
  • ’E’ - indicates Beta Sheet/Strand 
  • ’H’ - indicates alpha helix 
  •  ‘\\u0000’ - indicates blank

For RNA Helix (only shown when working with
 nucleotide sequences): 
  •  ‘(’ - indicates bases pair with columns upstream
     (to right) 
  •  ’(’ - indicate region pairs with bases to the left
")
   private char secondaryStructure;
 
   @Attributes(required = false, description = "Value of the annotation")
   private float value;
 
-
   public String getDisplayCharacter()
   {
     return displayCharacter;
diff --git a/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java b/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
index 64fee65..6729139 100644
--- a/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
@@ -7,10 +7,14 @@ import com.github.reinert.jjschema.Attributes;
 
 public class SequenceFeaturesPojo
 {
-  @Attributes(required = true, description = "Start residue position for the sequence feature")
+  @Attributes(
+    required = true,
+    description = "Start residue position for the sequence feature")
   private int xStart;
 
-  @Attributes(required = true, description = "End residue position for the sequence feature")
+  @Attributes(
+    required = true,
+    description = "End residue position for the sequence feature")
   private int xEnd;
 
   @Attributes(
@@ -20,7 +24,9 @@ public class SequenceFeaturesPojo
     description = "Reference to the sequence in the alignment
 (more like a foreign key)")
   private String sequenceRef;
 
-  @Attributes(required = true, description = "The name or type of the SequenceFeature")
+  @Attributes(
+    required = true,
+    description = "The name or type of the SequenceFeature")
   private String type;
 
   @Attributes(required = false, description = "Score")
@@ -28,8 +34,10 @@ public class SequenceFeaturesPojo
 
   @Attributes(required = false, description = "Description for the feature")
   private String description;
-  
-  @Attributes(required = false, description = "Additional metadata for the feature")
+
+  @Attributes(
+    required = false,
+    description = "Additional metadata for the feature")
   private Map otherDetails;
 
   @Attributes(required = false, description = "Fill colour")
@@ -38,7 +46,9 @@ public class SequenceFeaturesPojo
   @Attributes(required = true, description = "Feature group")
   private String featureGroup;
 
-  @Attributes(required = false, description = "URL links associated to the feature")
+  @Attributes(
+    required = false,
+    description = "URL links associated to the feature")
   private Vector links;
 
   public SequenceFeaturesPojo()
diff --git a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
index e5c4395..41dec70 100644
--- a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
@@ -11,30 +11,46 @@ public class SequenceGrpPojo
     description = "The Colour Scheme applied to the Sequence Group")
   private String colourScheme;
 
-  @Attributes(required = true, description = "The name assigned to the seqGroup")
+  @Attributes(
+    required = true,
+    description = "The name assigned to the seqGroup")
   private String groupName;
 
-  @Attributes(required = false, description = "Serial version identifier for the seqGroup object model")
+  @Attributes(
+    required = false,
+    description = "Serial version identifier for the seqGroup object model")
   private String description;
 
-  @Attributes(required = false, description = "Determines if the seqGroup border should be visible or not")
+  @Attributes(
+    required = false,
+    description = "Determines if the seqGroup border should be visible or not")
   private boolean displayBoxes;
 
-  @Attributes(required = false, description = "Determines if the texts of the group is displayed or not")
+  @Attributes(
+    required = false,
+    description = "Determines if the texts of the group is displayed or not")
   private boolean displayText;
 
-  @Attributes(required = false, description = "Determines if the residues text for the group is coloured")
+  @Attributes(
+    required = false,
+    description = "Determines if the residues text for the group is coloured")
   private boolean colourText;
 
-  @Attributes(required = false, description = "Boolean value indicating whether residues should only be shown 
that are different from current reference or consensus sequence")
+  @Attributes(
+    required = false,
+    description = "Boolean value indicating whether residues should only be shown 
that are different from current reference or consensus sequence")
   private boolean showNonconserved;
 
-  @Attributes(required = true, description = "The index of the group’s first residue in the alignment space")
+  @Attributes(
+    required = true,
+    description = "The index of the group’s first residue in the alignment space")
   private int startRes;
 
-  @Attributes(required = true, description = "The index of the group’s last residue in the alignment space")
+  @Attributes(
+    required = true,
+    description = "The index of the group’s last residue in the alignment space")
   private int endRes;
-  
+
   @Attributes(
     required = true,
     minItems = 1,
@@ -142,5 +158,4 @@ public class SequenceGrpPojo
     this.sequenceRefs = sequenceRefs;
   }
 
-
 }
diff --git a/src/jalview/json/binding/biojson/v1/SequencePojo.java b/src/jalview/json/binding/biojson/v1/SequencePojo.java
index 9d39d42..069832a 100644
--- a/src/jalview/json/binding/biojson/v1/SequencePojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequencePojo.java
@@ -2,8 +2,6 @@ package jalview.json.binding.biojson.v1;
 
 import com.github.reinert.jjschema.Attributes;
 
-
-
 public class SequencePojo
 {
   @Attributes(
@@ -16,22 +14,30 @@ public class SequencePojo
   @Attributes(required = true, description = "Sequence name")
   private String name;
 
-  @Attributes(required = false, description = "Sequence type", enums = {"DNA", "RNA", "Protein"})
+  @Attributes(required = false, description = "Sequence type", enums = {
+      "DNA", "RNA", "Protein" })
   private String type;
 
-  @Attributes(required = true, description = "Unique identifier for a given Sequence")
+  @Attributes(
+    required = true,
+    description = "Unique identifier for a given Sequence")
   private String id;
-  
-  @Attributes(required = false, description = "The order/position of a sequence in the alignment space")
+
+  @Attributes(
+    required = false,
+    description = "The order/position of a sequence in the alignment space")
   private int order;
-  
-  @Attributes(required = true, description = "The index of the sequence’s first residue in its source database, 
using a one-based numbering index system")
+
+  @Attributes(
+    required = true,
+    description = "The index of the sequence’s first residue in its source database, 
using a one-based numbering index system")
   private int start;
 
-  @Attributes(required = true, description = "The index of the sequence’s last residue in its source database, 
using a one-based numbering index system")
+  @Attributes(
+    required = true,
+    description = "The index of the sequence’s last residue in its source database, 
using a one-based numbering index system")
   private int end;
 
-
   public SequencePojo()
   {
   }
@@ -42,6 +48,7 @@ public class SequencePojo
     this.name = name;
     this.seq = seq;
   }
+
   public String getSeq()
   {
     return seq;
@@ -103,7 +110,6 @@ public class SequencePojo
     this.order = order;
   }
 
-
   public String getType()
   {
     return type;
diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 9ac75d2..bb7ed37 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -20,9 +20,10 @@
  */
 package jalview.math;
 
-import java.io.*;
+import jalview.util.Format;
+import jalview.util.MessageManager;
 
-import jalview.util.*;
+import java.io.PrintStream;
 
 /**
  * DOCUMENT ME!
@@ -403,7 +404,9 @@ public class Matrix
 
           if (iter == maxIter)
           {
-            throw new Exception(MessageManager.formatMessage("exception.matrix_too_many_iteration", new String[]{"tqli", Integer.valueOf(maxIter).toString()}));
+            throw new Exception(MessageManager.formatMessage(
+                    "exception.matrix_too_many_iteration", new String[] {
+                        "tqli", Integer.valueOf(maxIter).toString() }));
           }
           else
           {
@@ -652,7 +655,9 @@ public class Matrix
 
           if (iter == maxIter)
           {
-              throw new Exception(MessageManager.formatMessage("exception.matrix_too_many_iteration", new String[]{"tqli2", Integer.valueOf(maxIter).toString()}));
+            throw new Exception(MessageManager.formatMessage(
+                    "exception.matrix_too_many_iteration", new String[] {
+                        "tqli2", Integer.valueOf(maxIter).toString() }));
           }
           else
           {
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 61194ce..e5c2218 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -102,9 +102,9 @@ public class AnnotationRenderer
       // if (validRes && column>1 && row_annotations[column-2]!=null &&
       // dc.equals(row_annotations[column-2].displayCharacter))
       {
-        g.fillPolygon(new int[]
-        { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
-        { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+        g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+                new int[] { y + iconOffset, y + 14 + iconOffset,
+                    y + 8 + iconOffset }, 3);
         x1 += 5;
       }
       if (diffdownstream)
@@ -118,9 +118,8 @@ public class AnnotationRenderer
       // display a forward arrow
       if (diffdownstream)
       {
-        g.fillPolygon(new int[]
-        { x2 - 5, x2 - 5, x2 }, new int[]
-        { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+        g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
+            y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
         x2 -= 5;
       }
       if (diffupstream)
@@ -227,9 +226,9 @@ public class AnnotationRenderer
       // if (validRes && column>1 && row_annotations[column-2]!=null &&
       // dc.equals(row_annotations[column-2].displayCharacter))
       {
-        g.fillPolygon(new int[]
-        { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
-        { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+        g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+                new int[] { y + iconOffset, y + 14 + iconOffset,
+                    y + 8 + iconOffset }, 3);
         x1 += 5;
       }
       if (diffdownstream)
@@ -243,9 +242,8 @@ public class AnnotationRenderer
       // display a forward arrow
       if (diffdownstream)
       {
-        g.fillPolygon(new int[]
-        { x2 - 5, x2 - 5, x2 }, new int[]
-        { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+        g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
+            y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
         x2 -= 5;
       }
       if (diffupstream)
@@ -634,17 +632,17 @@ public class AnnotationRenderer
                 //
                 // if (scaleColLabel)
                 // {
-                  // justify the label and scale to fit in column
-                  if (fmWidth > charWidth)
-                  {
-                    // scale only if the current font isn't already small enough
-                    fmScaling = charWidth;
-                    fmScaling /= fmWidth;
-                    g.setFont(ofont.deriveFont(AffineTransform
-                            .getScaleInstance(fmScaling, 1.0)));
-                    // and update the label's width to reflect the scaling.
-                    fmWidth = charWidth;
-                  }
+                // justify the label and scale to fit in column
+                if (fmWidth > charWidth)
+                {
+                  // scale only if the current font isn't already small enough
+                  fmScaling = charWidth;
+                  fmScaling /= fmWidth;
+                  g.setFont(ofont.deriveFont(AffineTransform
+                          .getScaleInstance(fmScaling, 1.0)));
+                  // and update the label's width to reflect the scaling.
+                  fmWidth = charWidth;
+                }
                 // }
               }
               // TODO is it ok to use width of / show all characters here?
@@ -1096,11 +1094,9 @@ public class AnnotationRenderer
     {
       g.fillRect(lastSSX, y + 4 + iconOffset,
               (x * charWidth) - lastSSX - 4, 7);
-      g.fillPolygon(new int[]
-      { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
-              new int[]
-              { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
-              3);
+      g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
+          (x * charWidth) }, new int[] { y + iconOffset,
+          y + 14 + iconOffset, y + 7 + iconOffset }, 3);
     }
     else
     {
@@ -1255,8 +1251,7 @@ public class AnnotationRenderer
       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));
+              BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
 
       y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
       g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
@@ -1439,8 +1434,7 @@ public class AnnotationRenderer
       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));
+              BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
 
       y2 = (int) (y - ((_aa.threshold.value - min) / range)
               * _aa.graphHeight);
diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 0f2a49c..2957e49 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -157,8 +157,8 @@ public class FeatureRenderer extends
    * This is used by the Molecule Viewer and Overview to get the accurate
    * colourof the rendered sequence
    */
-  public synchronized int findFeatureColour(int initialCol, final SequenceI seq,
-          int column)
+  public synchronized int findFeatureColour(int initialCol,
+          final SequenceI seq, int column)
   {
     if (!av.isShowSequenceFeatures())
     {
@@ -316,7 +316,7 @@ public class FeatureRenderer extends
         }
 
         if (offscreenRender && offscreenImage == null)
-        {      
+        {
           if (sequenceFeature.begin <= start
                   && sequenceFeature.end >= start)
           {
diff --git a/src/jalview/rest/RestHandler.java b/src/jalview/rest/RestHandler.java
index 3f00c07..488e9f0 100644
--- a/src/jalview/rest/RestHandler.java
+++ b/src/jalview/rest/RestHandler.java
@@ -1,5 +1,7 @@
 package jalview.rest;
 
+import jalview.httpserver.AbstractRequestHandler;
+
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.net.BindException;
@@ -7,8 +9,6 @@ import java.net.BindException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import jalview.httpserver.AbstractRequestHandler;
-
 /**
  * A simple handler to process (or delegate) HTTP requests on /jalview/rest
  */
diff --git a/src/jalview/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java
index 61866aa..e2522a1 100644
--- a/src/jalview/schemabinding/version2/AlcodMap.java
+++ b/src/jalview/schemabinding/version2/AlcodMap.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,166 +19,174 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodMap implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * internal jalview id for the dnasq for this mapping.
-     *  
-     */
-    private java.lang.String _dnasq;
-
-    /**
-     * a Mapping entry and an associated protein sequence
-     *  
-     */
-    private jalview.schemabinding.version2.Mapping _mapping;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlcodMap() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'dnasq'. The field 'dnasq' has
-     * the following description: internal jalview id for the dnasq
-     * for this mapping.
-     *  
-     * 
-     * @return the value of field 'Dnasq'.
-     */
-    public java.lang.String getDnasq(
-    ) {
-        return this._dnasq;
-    }
-
-    /**
-     * Returns the value of field 'mapping'. The field 'mapping'
-     * has the following description: a Mapping entry and an
-     * associated protein sequence
-     *  
-     * 
-     * @return the value of field 'Mapping'.
-     */
-    public jalview.schemabinding.version2.Mapping getMapping(
-    ) {
-        return this._mapping;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'dnasq'. The field 'dnasq' has the
-     * following description: internal jalview id for the dnasq for
-     * this mapping.
-     *  
-     * 
-     * @param dnasq the value of field 'dnasq'.
-     */
-    public void setDnasq(
-            final java.lang.String dnasq) {
-        this._dnasq = dnasq;
-    }
-
-    /**
-     * Sets the value of field 'mapping'. The field 'mapping' has
-     * the following description: a Mapping entry and an associated
-     * protein sequence
-     *  
-     * 
-     * @param mapping the value of field 'mapping'.
-     */
-    public void setMapping(
-            final jalview.schemabinding.version2.Mapping mapping) {
-        this._mapping = mapping;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.AlcodMap
-     */
-    public static jalview.schemabinding.version2.AlcodMap unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.AlcodMap) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodMap.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class AlcodMap implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * internal jalview id for the dnasq for this mapping.
+   * 
+   */
+  private java.lang.String _dnasq;
+
+  /**
+   * a Mapping entry and an associated protein sequence
+   * 
+   */
+  private jalview.schemabinding.version2.Mapping _mapping;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodMap()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'dnasq'. The field 'dnasq' has the following
+   * description: internal jalview id for the dnasq for this mapping.
+   * 
+   * 
+   * @return the value of field 'Dnasq'.
+   */
+  public java.lang.String getDnasq()
+  {
+    return this._dnasq;
+  }
+
+  /**
+   * Returns the value of field 'mapping'. The field 'mapping' has the following
+   * description: a Mapping entry and an associated protein sequence
+   * 
+   * 
+   * @return the value of field 'Mapping'.
+   */
+  public jalview.schemabinding.version2.Mapping getMapping()
+  {
+    return this._mapping;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'dnasq'. The field 'dnasq' has the following
+   * description: internal jalview id for the dnasq for this mapping.
+   * 
+   * 
+   * @param dnasq
+   *          the value of field 'dnasq'.
+   */
+  public void setDnasq(final java.lang.String dnasq)
+  {
+    this._dnasq = dnasq;
+  }
+
+  /**
+   * Sets the value of field 'mapping'. The field 'mapping' has the following
+   * description: a Mapping entry and an associated protein sequence
+   * 
+   * 
+   * @param mapping
+   *          the value of field 'mapping'.
+   */
+  public void setMapping(
+          final jalview.schemabinding.version2.Mapping mapping)
+  {
+    this._mapping = mapping;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.AlcodMap
+   */
+  public static jalview.schemabinding.version2.AlcodMap unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AlcodMap) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.AlcodMap.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Alcodon.java b/src/jalview/schemabinding/version2/Alcodon.java
index 1732401..3bd1cbb 100644
--- a/src/jalview/schemabinding/version2/Alcodon.java
+++ b/src/jalview/schemabinding/version2/Alcodon.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,245 +19,257 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Alcodon implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _pos1.
-     */
-    private long _pos1;
-
-    /**
-     * keeps track of state for field: _pos1
-     */
-    private boolean _has_pos1;
-
-    /**
-     * Field _pos2.
-     */
-    private long _pos2;
-
-    /**
-     * keeps track of state for field: _pos2
-     */
-    private boolean _has_pos2;
-
-    /**
-     * Field _pos3.
-     */
-    private long _pos3;
-
-    /**
-     * keeps track of state for field: _pos3
-     */
-    private boolean _has_pos3;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Alcodon() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deletePos1(
-    ) {
-        this._has_pos1= false;
-    }
-
-    /**
-     */
-    public void deletePos2(
-    ) {
-        this._has_pos2= false;
-    }
-
-    /**
-     */
-    public void deletePos3(
-    ) {
-        this._has_pos3= false;
-    }
-
-    /**
-     * Returns the value of field 'pos1'.
-     * 
-     * @return the value of field 'Pos1'.
-     */
-    public long getPos1(
-    ) {
-        return this._pos1;
-    }
-
-    /**
-     * Returns the value of field 'pos2'.
-     * 
-     * @return the value of field 'Pos2'.
+public class Alcodon implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _pos1.
+   */
+  private long _pos1;
+
+  /**
+   * keeps track of state for field: _pos1
+   */
+  private boolean _has_pos1;
+
+  /**
+   * Field _pos2.
+   */
+  private long _pos2;
+
+  /**
+   * keeps track of state for field: _pos2
+   */
+  private boolean _has_pos2;
+
+  /**
+   * Field _pos3.
+   */
+  private long _pos3;
+
+  /**
+   * keeps track of state for field: _pos3
+   */
+  private boolean _has_pos3;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Alcodon()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
      */
-    public long getPos2(
-    ) {
-        return this._pos2;
-    }
-
-    /**
-     * Returns the value of field 'pos3'.
-     * 
-     * @return the value of field 'Pos3'.
-     */
-    public long getPos3(
-    ) {
-        return this._pos3;
-    }
-
-    /**
-     * Method hasPos1.
-     * 
-     * @return true if at least one Pos1 has been added
-     */
-    public boolean hasPos1(
-    ) {
-        return this._has_pos1;
-    }
-
-    /**
-     * Method hasPos2.
-     * 
-     * @return true if at least one Pos2 has been added
-     */
-    public boolean hasPos2(
-    ) {
-        return this._has_pos2;
-    }
-
-    /**
-     * Method hasPos3.
-     * 
-     * @return true if at least one Pos3 has been added
-     */
-    public boolean hasPos3(
-    ) {
-        return this._has_pos3;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
+  public void deletePos1()
+  {
+    this._has_pos1 = false;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+  /**
      */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'pos1'.
-     * 
-     * @param pos1 the value of field 'pos1'.
-     */
-    public void setPos1(
-            final long pos1) {
-        this._pos1 = pos1;
-        this._has_pos1 = true;
-    }
-
-    /**
-     * Sets the value of field 'pos2'.
-     * 
-     * @param pos2 the value of field 'pos2'.
-     */
-    public void setPos2(
-            final long pos2) {
-        this._pos2 = pos2;
-        this._has_pos2 = true;
-    }
-
-    /**
-     * Sets the value of field 'pos3'.
-     * 
-     * @param pos3 the value of field 'pos3'.
-     */
-    public void setPos3(
-            final long pos3) {
-        this._pos3 = pos3;
-        this._has_pos3 = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Alcodo
-     */
-    public static jalview.schemabinding.version2.Alcodon unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alcodon.class, reader);
-    }
+  public void deletePos2()
+  {
+    this._has_pos2 = false;
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+  /**
      */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+  public void deletePos3()
+  {
+    this._has_pos3 = false;
+  }
+
+  /**
+   * Returns the value of field 'pos1'.
+   * 
+   * @return the value of field 'Pos1'.
+   */
+  public long getPos1()
+  {
+    return this._pos1;
+  }
+
+  /**
+   * Returns the value of field 'pos2'.
+   * 
+   * @return the value of field 'Pos2'.
+   */
+  public long getPos2()
+  {
+    return this._pos2;
+  }
+
+  /**
+   * Returns the value of field 'pos3'.
+   * 
+   * @return the value of field 'Pos3'.
+   */
+  public long getPos3()
+  {
+    return this._pos3;
+  }
+
+  /**
+   * Method hasPos1.
+   * 
+   * @return true if at least one Pos1 has been added
+   */
+  public boolean hasPos1()
+  {
+    return this._has_pos1;
+  }
+
+  /**
+   * Method hasPos2.
+   * 
+   * @return true if at least one Pos2 has been added
+   */
+  public boolean hasPos2()
+  {
+    return this._has_pos2;
+  }
+
+  /**
+   * Method hasPos3.
+   * 
+   * @return true if at least one Pos3 has been added
+   */
+  public boolean hasPos3()
+  {
+    return this._has_pos3;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'pos1'.
+   * 
+   * @param pos1
+   *          the value of field 'pos1'.
+   */
+  public void setPos1(final long pos1)
+  {
+    this._pos1 = pos1;
+    this._has_pos1 = true;
+  }
+
+  /**
+   * Sets the value of field 'pos2'.
+   * 
+   * @param pos2
+   *          the value of field 'pos2'.
+   */
+  public void setPos2(final long pos2)
+  {
+    this._pos2 = pos2;
+    this._has_pos2 = true;
+  }
+
+  /**
+   * Sets the value of field 'pos3'.
+   * 
+   * @param pos3
+   *          the value of field 'pos3'.
+   */
+  public void setPos3(final long pos3)
+  {
+    this._pos3 = pos3;
+    this._has_pos3 = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Alcodo
+   */
+  public static jalview.schemabinding.version2.Alcodon unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Alcodon.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java
index 76db239..218e07e 100644
--- a/src/jalview/schemabinding/version2/AlcodonFrame.java
+++ b/src/jalview/schemabinding/version2/AlcodonFrame.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,414 +19,448 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodonFrame implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _alcodonList.
-     */
-    private java.util.Vector _alcodonList;
-
-    /**
-     * Field _alcodMapList.
-     */
-    private java.util.Vector _alcodMapList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlcodonFrame() {
-        super();
-        this._alcodonList = new java.util.Vector();
-        this._alcodMapList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAlcodMap
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodMap(
-            final jalview.schemabinding.version2.AlcodMap vAlcodMap)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodMapList.addElement(vAlcodMap);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodMap
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodMap(
-            final int index,
-            final jalview.schemabinding.version2.AlcodMap vAlcodMap)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodMapList.add(index, vAlcodMap);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAlcodon
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodon(
-            final jalview.schemabinding.version2.Alcodon vAlcodon)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodonList.addElement(vAlcodon);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodon
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodon(
-            final int index,
-            final jalview.schemabinding.version2.Alcodon vAlcodon)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodonList.add(index, vAlcodon);
-    }
-
-    /**
-     * Method enumerateAlcodMap.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.AlcodMap elements
-     */
-    public java.util.Enumeration enumerateAlcodMap(
-    ) {
-        return this._alcodMapList.elements();
-    }
-
-    /**
-     * Method enumerateAlcodon.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Alcodon elements
-     */
-    public java.util.Enumeration enumerateAlcodon(
-    ) {
-        return this._alcodonList.elements();
-    }
-
-    /**
-     * Method getAlcodMap.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.AlcodMap at the given index
-     */
-    public jalview.schemabinding.version2.AlcodMap getAlcodMap(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodMapList.size()) {
-            throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index);
-    }
-
-    /**
-     * Method getAlcodMap.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.AlcodMap[] getAlcodMap(
-    ) {
-        jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];
-        return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array);
-    }
-
-    /**
-     * Method getAlcodMapCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAlcodMapCount(
-    ) {
-        return this._alcodMapList.size();
-    }
-
-    /**
-     * Method getAlcodon.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Alcodon at the given index
-     */
-    public jalview.schemabinding.version2.Alcodon getAlcodon(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodonList.size()) {
-            throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);
-    }
-
-    /**
-     * Method getAlcodon.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Alcodon[] getAlcodon(
-    ) {
-        jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
-        return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array);
-    }
-
-    /**
-     * Method getAlcodonCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAlcodonCount(
-    ) {
-        return this._alcodonList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Method removeAlcodMap.
-     * 
-     * @param vAlcodMap
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAlcodMap(
-            final jalview.schemabinding.version2.AlcodMap vAlcodMap) {
-        boolean removed = _alcodMapList.remove(vAlcodMap);
-        return removed;
+public class AlcodonFrame implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _alcodonList.
+   */
+  private java.util.Vector _alcodonList;
+
+  /**
+   * Field _alcodMapList.
+   */
+  private java.util.Vector _alcodMapList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodonFrame()
+  {
+    super();
+    this._alcodonList = new java.util.Vector();
+    this._alcodMapList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAlcodMap
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlcodMap(
+          final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodMapList.addElement(vAlcodMap);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodMap
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlcodMap(final int index,
+          final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodMapList.add(index, vAlcodMap);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlcodon
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlcodon(
+          final jalview.schemabinding.version2.Alcodon vAlcodon)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodonList.addElement(vAlcodon);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodon
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlcodon(final int index,
+          final jalview.schemabinding.version2.Alcodon vAlcodon)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodonList.add(index, vAlcodon);
+  }
+
+  /**
+   * Method enumerateAlcodMap.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.AlcodMap
+   *         elements
+   */
+  public java.util.Enumeration enumerateAlcodMap()
+  {
+    return this._alcodMapList.elements();
+  }
+
+  /**
+   * Method enumerateAlcodon.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Alcodon
+   *         elements
+   */
+  public java.util.Enumeration enumerateAlcodon()
+  {
+    return this._alcodonList.elements();
+  }
+
+  /**
+   * Method getAlcodMap.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.AlcodMap at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.AlcodMap getAlcodMap(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodMapList.size())
+    {
+      throw new IndexOutOfBoundsException("getAlcodMap: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodMapList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeAlcodMapAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(
-            final int index) {
-        java.lang.Object obj = this._alcodMapList.remove(index);
-        return (jalview.schemabinding.version2.AlcodMap) obj;
-    }
-
-    /**
-     * Method removeAlcodon.
-     * 
-     * @param vAlcodon
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAlcodon(
-            final jalview.schemabinding.version2.Alcodon vAlcodon) {
-        boolean removed = _alcodonList.remove(vAlcodon);
-        return removed;
-    }
-
-    /**
-     * Method removeAlcodonAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Alcodon removeAlcodonAt(
-            final int index) {
-        java.lang.Object obj = this._alcodonList.remove(index);
-        return (jalview.schemabinding.version2.Alcodon) obj;
-    }
-
-    /**
-     */
-    public void removeAllAlcodMap(
-    ) {
-        this._alcodMapList.clear();
+    return (jalview.schemabinding.version2.AlcodMap) _alcodMapList
+            .get(index);
+  }
+
+  /**
+   * Method getAlcodMap.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.AlcodMap[] getAlcodMap()
+  {
+    jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];
+    return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAlcodMapCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAlcodMapCount()
+  {
+    return this._alcodMapList.size();
+  }
+
+  /**
+   * Method getAlcodon.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Alcodon at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Alcodon getAlcodon(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodonList.size())
+    {
+      throw new IndexOutOfBoundsException("getAlcodon: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonList.size() - 1) + "]");
     }
 
-    /**
-     */
-    public void removeAllAlcodon(
-    ) {
-        this._alcodonList.clear();
+    return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);
+  }
+
+  /**
+   * Method getAlcodon.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Alcodon[] getAlcodon()
+  {
+    jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
+    return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAlcodonCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAlcodonCount()
+  {
+    return this._alcodonList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodMap
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAlcodMap(
-            final int index,
-            final jalview.schemabinding.version2.AlcodMap vAlcodMap)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodMapList.size()) {
-            throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");
-        }
-        
-        this._alcodMapList.set(index, vAlcodMap);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAlcodMapArray
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method removeAlcodMap.
+   * 
+   * @param vAlcodMap
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAlcodMap(
+          final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+  {
+    boolean removed = _alcodMapList.remove(vAlcodMap);
+    return removed;
+  }
+
+  /**
+   * Method removeAlcodMapAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(
+          final int index)
+  {
+    java.lang.Object obj = this._alcodMapList.remove(index);
+    return (jalview.schemabinding.version2.AlcodMap) obj;
+  }
+
+  /**
+   * Method removeAlcodon.
+   * 
+   * @param vAlcodon
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAlcodon(
+          final jalview.schemabinding.version2.Alcodon vAlcodon)
+  {
+    boolean removed = _alcodonList.remove(vAlcodon);
+    return removed;
+  }
+
+  /**
+   * Method removeAlcodonAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Alcodon removeAlcodonAt(
+          final int index)
+  {
+    java.lang.Object obj = this._alcodonList.remove(index);
+    return (jalview.schemabinding.version2.Alcodon) obj;
+  }
+
+  /**
      */
-    public void setAlcodMap(
-            final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) {
-        //-- copy array
-        _alcodMapList.clear();
-        
-        for (int i = 0; i < vAlcodMapArray.length; i++) {
-                this._alcodMapList.add(vAlcodMapArray[i]);
-        }
-    }
+  public void removeAllAlcodMap()
+  {
+    this._alcodMapList.clear();
+  }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodon
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
+  /**
      */
-    public void setAlcodon(
-            final int index,
-            final jalview.schemabinding.version2.Alcodon vAlcodon)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodonList.size()) {
-            throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
-        }
-        
-        this._alcodonList.set(index, vAlcodon);
+  public void removeAllAlcodon()
+  {
+    this._alcodonList.clear();
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodMap
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAlcodMap(final int index,
+          final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodMapList.size())
+    {
+      throw new IndexOutOfBoundsException("setAlcodMap: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodMapList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param vAlcodonArray
-     */
-    public void setAlcodon(
-            final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) {
-        //-- copy array
-        _alcodonList.clear();
-        
-        for (int i = 0; i < vAlcodonArray.length; i++) {
-                this._alcodonList.add(vAlcodonArray[i]);
-        }
+    this._alcodMapList.set(index, vAlcodMap);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlcodMapArray
+   */
+  public void setAlcodMap(
+          final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray)
+  {
+    // -- copy array
+    _alcodMapList.clear();
+
+    for (int i = 0; i < vAlcodMapArray.length; i++)
+    {
+      this._alcodMapList.add(vAlcodMapArray[i]);
     }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.AlcodonFrame
-     */
-    public static jalview.schemabinding.version2.AlcodonFrame unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodon
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAlcodon(final int index,
+          final jalview.schemabinding.version2.Alcodon vAlcodon)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodonList.size())
+    {
+      throw new IndexOutOfBoundsException("setAlcodon: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._alcodonList.set(index, vAlcodon);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlcodonArray
+   */
+  public void setAlcodon(
+          final jalview.schemabinding.version2.Alcodon[] vAlcodonArray)
+  {
+    // -- copy array
+    _alcodonList.clear();
+
+    for (int i = 0; i < vAlcodonArray.length; i++)
+    {
+      this._alcodonList.add(vAlcodonArray[i]);
     }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.AlcodonFrame
+   */
+  public static jalview.schemabinding.version2.AlcodonFrame unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.AlcodonFrame.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 3da8552..2fead37 100644
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,1329 +19,1378 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Annotation implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _graph.
-     */
-    private boolean _graph;
-
-    /**
-     * keeps track of state for field: _graph
-     */
-    private boolean _has_graph;
-
-    /**
-     * Field _graphType.
-     */
-    private int _graphType;
-
-    /**
-     * keeps track of state for field: _graphType
-     */
-    private boolean _has_graphType;
-
-    /**
-     * Field _sequenceRef.
-     */
-    private java.lang.String _sequenceRef;
-
-    /**
-     * Field _groupRef.
-     */
-    private java.lang.String _groupRef;
-
-    /**
-     * 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;
-
-    /**
-     * height in pixels for the graph if this is a graph-type
-     * annotation.
-     */
-    private int _graphHeight;
-
-    /**
-     * keeps track of state for field: _graphHeight
-     */
-    private boolean _has_graphHeight;
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _scoreOnly.
-     */
-    private boolean _scoreOnly = false;
-
-    /**
-     * keeps track of state for field: _scoreOnly
-     */
-    private boolean _has_scoreOnly;
-
-    /**
-     * Field _score.
-     */
-    private double _score;
-
-    /**
-     * keeps track of state for field: _score
-     */
-    private boolean _has_score;
-
-    /**
-     * Field _visible.
-     */
-    private boolean _visible;
-
-    /**
-     * keeps track of state for field: _visible
-     */
-    private boolean _has_visible;
-
-    /**
-     * Field _centreColLabels.
-     */
-    private boolean _centreColLabels;
-
-    /**
-     * keeps track of state for field: _centreColLabels
-     */
-    private boolean _has_centreColLabels;
-
-    /**
-     * Field _scaleColLabels.
-     */
-    private boolean _scaleColLabels;
-
-    /**
-     * keeps track of state for field: _scaleColLabels
-     */
-    private boolean _has_scaleColLabels;
-
-    /**
-     * Field _showAllColLabels.
-     */
-    private boolean _showAllColLabels;
-
-    /**
-     * keeps track of state for field: _showAllColLabels
-     */
-    private boolean _has_showAllColLabels;
-
-    /**
-     * is an autocalculated annotation row
-     */
-    private boolean _autoCalculated = false;
-
-    /**
-     * keeps track of state for field: _autoCalculated
-     */
-    private boolean _has_autoCalculated;
-
-    /**
-     * is to be shown below the alignment - introduced in Jalview
-     * 2.8 for visualizing T-COFFEE alignment scores
-     */
-    private boolean _belowAlignment = true;
-
-    /**
-     * keeps track of state for field: _belowAlignment
-     */
-    private boolean _has_belowAlignment;
-
-    /**
-     * Optional string identifier used to group sets of annotation
-     * produced by a particular calculation. Values are opaque
-     * strings but have semantic meaning to Jalview's renderer,
-     * data importer and calculation system.
-     */
-    private java.lang.String _calcId;
-
-    /**
-     * 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;
-
-    /**
-     * Field _propertyList.
-     */
-    private java.util.Vector _propertyList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Annotation() {
-        super();
-        this._annotationElementList = new java.util.Vector();
-        this._propertyList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotationElement(
-            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationElementList.addElement(vAnnotationElement);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotationElement(
-            final int index,
-            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationElementList.add(index, vAnnotationElement);
-    }
-
-    /**
-     * 
-     * 
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addProperty(
-            final jalview.schemabinding.version2.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.addElement(vProperty);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addProperty(
-            final int index,
-            final jalview.schemabinding.version2.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.add(index, vProperty);
-    }
-
-    /**
-     */
-    public void deleteAutoCalculated(
-    ) {
-        this._has_autoCalculated= false;
-    }
-
-    /**
-     */
-    public void deleteBelowAlignment(
-    ) {
-        this._has_belowAlignment= false;
-    }
-
-    /**
-     */
-    public void deleteCentreColLabels(
-    ) {
-        this._has_centreColLabels= false;
-    }
-
-    /**
-     */
-    public void deleteGraph(
-    ) {
-        this._has_graph= false;
-    }
-
-    /**
-     */
-    public void deleteGraphColour(
-    ) {
-        this._has_graphColour= false;
-    }
-
-    /**
-     */
-    public void deleteGraphGroup(
-    ) {
-        this._has_graphGroup= false;
-    }
-
-    /**
-     */
-    public void deleteGraphHeight(
-    ) {
-        this._has_graphHeight= false;
-    }
-
-    /**
-     */
-    public void deleteGraphType(
-    ) {
-        this._has_graphType= false;
-    }
-
-    /**
-     */
-    public void deleteScaleColLabels(
-    ) {
-        this._has_scaleColLabels= false;
-    }
-
-    /**
-     */
-    public void deleteScore(
-    ) {
-        this._has_score= false;
-    }
-
-    /**
-     */
-    public void deleteScoreOnly(
-    ) {
-        this._has_scoreOnly= false;
-    }
-
-    /**
-     */
-    public void deleteShowAllColLabels(
-    ) {
-        this._has_showAllColLabels= false;
-    }
-
-    /**
-     */
-    public void deleteVisible(
-    ) {
-        this._has_visible= false;
-    }
-
-    /**
-     * Method enumerateAnnotationElement.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.AnnotationElement elements
-     */
-    public java.util.Enumeration enumerateAnnotationElement(
-    ) {
-        return this._annotationElementList.elements();
-    }
-
-    /**
-     * Method enumerateProperty.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Property elements
-     */
-    public java.util.Enumeration enumerateProperty(
-    ) {
-        return this._propertyList.elements();
-    }
-
-    /**
-     * Method getAnnotationElement.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.AnnotationElement at the
-     * given index
-     */
-    public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationElementList.size()) {
-            throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index);
-    }
-
-    /**
-     * Method getAnnotationElement.Returns the contents of the
-     * collection in an Array.  
Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we know that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement(
-    ) {
-        jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
-        return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array);
-    }
-
-    /**
-     * Method getAnnotationElementCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAnnotationElementCount(
-    ) {
-        return this._annotationElementList.size();
-    }
-
-    /**
-     * Returns the value of field 'autoCalculated'. The field
-     * 'autoCalculated' has the following description: is an
-     * autocalculated annotation row
-     * 
-     * @return the value of field 'AutoCalculated'.
-     */
-    public boolean getAutoCalculated(
-    ) {
-        return this._autoCalculated;
-    }
-
-    /**
-     * Returns the value of field 'belowAlignment'. The field
-     * 'belowAlignment' has the following description: is to be
-     * shown below the alignment - introduced in Jalview 2.8 for
-     * visualizing T-COFFEE alignment scores
-     * 
-     * @return the value of field 'BelowAlignment'.
-     */
-    public boolean getBelowAlignment(
-    ) {
-        return this._belowAlignment;
-    }
-
-    /**
-     * Returns the value of field 'calcId'. The field 'calcId' has
-     * the following description: Optional string identifier used
-     * to group sets of annotation produced by a particular
-     * calculation. Values are opaque strings but have semantic
-     * meaning to Jalview's renderer, data importer and calculation
-     * system.
-     * 
-     * @return the value of field 'CalcId'.
-     */
-    public java.lang.String getCalcId(
-    ) {
-        return this._calcId;
-    }
-
-    /**
-     * Returns the value of field 'centreColLabels'.
-     * 
-     * @return the value of field 'CentreColLabels'.
-     */
-    public boolean getCentreColLabels(
-    ) {
-        return this._centreColLabels;
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return the value of field 'Graph'.
-     */
-    public boolean getGraph(
-    ) {
-        return this._graph;
-    }
-
-    /**
-     * Returns the value of field 'graphColour'.
-     * 
-     * @return the value of field 'GraphColour'.
-     */
-    public int getGraphColour(
-    ) {
-        return this._graphColour;
-    }
-
-    /**
-     * Returns the value of field 'graphGroup'.
-     * 
-     * @return the value of field 'GraphGroup'.
-     */
-    public int getGraphGroup(
-    ) {
-        return this._graphGroup;
-    }
-
-    /**
-     * Returns the value of field 'graphHeight'. The field
-     * 'graphHeight' has the following description: height in
-     * pixels for the graph if this is a graph-type annotation.
-     * 
-     * @return the value of field 'GraphHeight'.
-     */
-    public int getGraphHeight(
-    ) {
-        return this._graphHeight;
-    }
-
-    /**
-     * Returns the value of field 'graphType'.
-     * 
-     * @return the value of field 'GraphType'.
-     */
-    public int getGraphType(
-    ) {
-        return this._graphType;
-    }
-
-    /**
-     * Returns the value of field 'groupRef'.
-     * 
-     * @return the value of field 'GroupRef'.
-     */
-    public java.lang.String getGroupRef(
-    ) {
-        return this._groupRef;
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'label'.
-     * 
-     * @return the value of field 'Label'.
-     */
-    public java.lang.String getLabel(
-    ) {
-        return this._label;
-    }
-
-    /**
-     * Method getProperty.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Property at the given index
-     */
-    public jalview.schemabinding.version2.Property getProperty(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Property) _propertyList.get(index);
-    }
-
-    /**
-     * Method getProperty.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Property[] getProperty(
-    ) {
-        jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
-        return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array);
-    }
-
-    /**
-     * Method getPropertyCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPropertyCount(
-    ) {
-        return this._propertyList.size();
-    }
-
-    /**
-     * Returns the value of field 'scaleColLabels'.
-     * 
-     * @return the value of field 'ScaleColLabels'.
-     */
-    public boolean getScaleColLabels(
-    ) {
-        return this._scaleColLabels;
-    }
-
-    /**
-     * Returns the value of field 'score'.
-     * 
-     * @return the value of field 'Score'.
-     */
-    public double getScore(
-    ) {
-        return this._score;
-    }
-
-    /**
-     * Returns the value of field 'scoreOnly'.
-     * 
-     * @return the value of field 'ScoreOnly'.
-     */
-    public boolean getScoreOnly(
-    ) {
-        return this._scoreOnly;
-    }
-
-    /**
-     * Returns the value of field 'sequenceRef'.
-     * 
-     * @return the value of field 'SequenceRef'.
-     */
-    public java.lang.String getSequenceRef(
-    ) {
-        return this._sequenceRef;
-    }
-
-    /**
-     * Returns the value of field 'showAllColLabels'.
-     * 
-     * @return the value of field 'ShowAllColLabels'.
-     */
-    public boolean getShowAllColLabels(
-    ) {
-        return this._showAllColLabels;
-    }
-
-    /**
-     * Returns the value of field 'thresholdLine'.
-     * 
-     * @return the value of field 'ThresholdLine'.
-     */
-    public jalview.schemabinding.version2.ThresholdLine getThresholdLine(
-    ) {
-        return this._thresholdLine;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean getVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * Method hasAutoCalculated.
-     * 
-     * @return true if at least one AutoCalculated has been added
-     */
-    public boolean hasAutoCalculated(
-    ) {
-        return this._has_autoCalculated;
-    }
-
-    /**
-     * Method hasBelowAlignment.
-     * 
-     * @return true if at least one BelowAlignment has been added
-     */
-    public boolean hasBelowAlignment(
-    ) {
-        return this._has_belowAlignment;
-    }
-
-    /**
-     * Method hasCentreColLabels.
-     * 
-     * @return true if at least one CentreColLabels has been added
-     */
-    public boolean hasCentreColLabels(
-    ) {
-        return this._has_centreColLabels;
-    }
-
-    /**
-     * Method hasGraph.
-     * 
-     * @return true if at least one Graph has been added
-     */
-    public boolean hasGraph(
-    ) {
-        return this._has_graph;
-    }
-
-    /**
-     * Method hasGraphColour.
-     * 
-     * @return true if at least one GraphColour has been added
-     */
-    public boolean hasGraphColour(
-    ) {
-        return this._has_graphColour;
-    }
-
-    /**
-     * Method hasGraphGroup.
-     * 
-     * @return true if at least one GraphGroup has been added
-     */
-    public boolean hasGraphGroup(
-    ) {
-        return this._has_graphGroup;
-    }
-
-    /**
-     * Method hasGraphHeight.
-     * 
-     * @return true if at least one GraphHeight has been added
-     */
-    public boolean hasGraphHeight(
-    ) {
-        return this._has_graphHeight;
-    }
-
-    /**
-     * Method hasGraphType.
-     * 
-     * @return true if at least one GraphType has been added
-     */
-    public boolean hasGraphType(
-    ) {
-        return this._has_graphType;
-    }
-
-    /**
-     * Method hasScaleColLabels.
-     * 
-     * @return true if at least one ScaleColLabels has been added
-     */
-    public boolean hasScaleColLabels(
-    ) {
-        return this._has_scaleColLabels;
-    }
-
-    /**
-     * Method hasScore.
-     * 
-     * @return true if at least one Score has been added
-     */
-    public boolean hasScore(
-    ) {
-        return this._has_score;
-    }
-
-    /**
-     * Method hasScoreOnly.
-     * 
-     * @return true if at least one ScoreOnly has been added
-     */
-    public boolean hasScoreOnly(
-    ) {
-        return this._has_scoreOnly;
-    }
-
-    /**
-     * Method hasShowAllColLabels.
-     * 
-     * @return true if at least one ShowAllColLabels has been added
-     */
-    public boolean hasShowAllColLabels(
-    ) {
-        return this._has_showAllColLabels;
-    }
-
-    /**
-     * Method hasVisible.
-     * 
-     * @return true if at least one Visible has been added
-     */
-    public boolean hasVisible(
-    ) {
-        return this._has_visible;
-    }
-
-    /**
-     * Returns the value of field 'autoCalculated'. The field
-     * 'autoCalculated' has the following description: is an
-     * autocalculated annotation row
-     * 
-     * @return the value of field 'AutoCalculated'.
-     */
-    public boolean isAutoCalculated(
-    ) {
-        return this._autoCalculated;
-    }
-
-    /**
-     * Returns the value of field 'belowAlignment'. The field
-     * 'belowAlignment' has the following description: is to be
-     * shown below the alignment - introduced in Jalview 2.8 for
-     * visualizing T-COFFEE alignment scores
-     * 
-     * @return the value of field 'BelowAlignment'.
-     */
-    public boolean isBelowAlignment(
-    ) {
-        return this._belowAlignment;
-    }
-
-    /**
-     * Returns the value of field 'centreColLabels'.
-     * 
-     * @return the value of field 'CentreColLabels'.
-     */
-    public boolean isCentreColLabels(
-    ) {
-        return this._centreColLabels;
-    }
-
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return the value of field 'Graph'.
-     */
-    public boolean isGraph(
-    ) {
-        return this._graph;
-    }
-
-    /**
-     * Returns the value of field 'scaleColLabels'.
-     * 
-     * @return the value of field 'ScaleColLabels'.
-     */
-    public boolean isScaleColLabels(
-    ) {
-        return this._scaleColLabels;
-    }
-
-    /**
-     * Returns the value of field 'scoreOnly'.
-     * 
-     * @return the value of field 'ScoreOnly'.
-     */
-    public boolean isScoreOnly(
-    ) {
-        return this._scoreOnly;
-    }
-
-    /**
-     * Returns the value of field 'showAllColLabels'.
-     * 
-     * @return the value of field 'ShowAllColLabels'.
-     */
-    public boolean isShowAllColLabels(
-    ) {
-        return this._showAllColLabels;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean isVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllAnnotationElement(
-    ) {
-        this._annotationElementList.clear();
-    }
-
-    /**
-     */
-    public void removeAllProperty(
-    ) {
-        this._propertyList.clear();
-    }
-
-    /**
-     * Method removeAnnotationElement.
-     * 
-     * @param vAnnotationElement
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAnnotationElement(
-            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) {
-        boolean removed = _annotationElementList.remove(vAnnotationElement);
-        return removed;
-    }
-
-    /**
-     * Method removeAnnotationElementAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
-            final int index) {
-        java.lang.Object obj = this._annotationElementList.remove(index);
-        return (jalview.schemabinding.version2.AnnotationElement) obj;
-    }
-
-    /**
-     * Method removeProperty.
-     * 
-     * @param vProperty
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeProperty(
-            final jalview.schemabinding.version2.Property vProperty) {
-        boolean removed = _propertyList.remove(vProperty);
-        return removed;
-    }
-
-    /**
-     * Method removePropertyAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Property removePropertyAt(
-            final int index) {
-        java.lang.Object obj = this._propertyList.remove(index);
-        return (jalview.schemabinding.version2.Property) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAnnotationElement(
-            final int index,
-            final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationElementList.size()) {
-            throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
-        }
-        
-        this._annotationElementList.set(index, vAnnotationElement);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotationElementArray
-     */
-    public void setAnnotationElement(
-            final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) {
-        //-- copy array
-        _annotationElementList.clear();
-        
-        for (int i = 0; i < vAnnotationElementArray.length; i++) {
-                this._annotationElementList.add(vAnnotationElementArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'autoCalculated'. The field
-     * 'autoCalculated' has the following description: is an
-     * autocalculated annotation row
-     * 
-     * @param autoCalculated the value of field 'autoCalculated'.
-     */
-    public void setAutoCalculated(
-            final boolean autoCalculated) {
-        this._autoCalculated = autoCalculated;
-        this._has_autoCalculated = true;
-    }
-
-    /**
-     * Sets the value of field 'belowAlignment'. The field
-     * 'belowAlignment' has the following description: is to be
-     * shown below the alignment - introduced in Jalview 2.8 for
-     * visualizing T-COFFEE alignment scores
-     * 
-     * @param belowAlignment the value of field 'belowAlignment'.
-     */
-    public void setBelowAlignment(
-            final boolean belowAlignment) {
-        this._belowAlignment = belowAlignment;
-        this._has_belowAlignment = true;
-    }
-
-    /**
-     * Sets the value of field 'calcId'. The field 'calcId' has the
-     * following description: Optional string identifier used to
-     * group sets of annotation produced by a particular
-     * calculation. Values are opaque strings but have semantic
-     * meaning to Jalview's renderer, data importer and calculation
-     * system.
-     * 
-     * @param calcId the value of field 'calcId'.
-     */
-    public void setCalcId(
-            final java.lang.String calcId) {
-        this._calcId = calcId;
-    }
-
-    /**
-     * Sets the value of field 'centreColLabels'.
-     * 
-     * @param centreColLabels the value of field 'centreColLabels'.
-     */
-    public void setCentreColLabels(
-            final boolean centreColLabels) {
-        this._centreColLabels = centreColLabels;
-        this._has_centreColLabels = true;
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'graph'.
-     * 
-     * @param graph the value of field 'graph'.
-     */
-    public void setGraph(
-            final boolean graph) {
-        this._graph = graph;
-        this._has_graph = true;
-    }
-
-    /**
-     * Sets the value of field 'graphColour'.
-     * 
-     * @param graphColour the value of field 'graphColour'.
-     */
-    public void setGraphColour(
-            final int graphColour) {
-        this._graphColour = graphColour;
-        this._has_graphColour = true;
-    }
-
-    /**
-     * Sets the value of field 'graphGroup'.
-     * 
-     * @param graphGroup the value of field 'graphGroup'.
-     */
-    public void setGraphGroup(
-            final int graphGroup) {
-        this._graphGroup = graphGroup;
-        this._has_graphGroup = true;
-    }
-
-    /**
-     * Sets the value of field 'graphHeight'. The field
-     * 'graphHeight' has the following description: height in
-     * pixels for the graph if this is a graph-type annotation.
-     * 
-     * @param graphHeight the value of field 'graphHeight'.
-     */
-    public void setGraphHeight(
-            final int graphHeight) {
-        this._graphHeight = graphHeight;
-        this._has_graphHeight = true;
-    }
-
-    /**
-     * Sets the value of field 'graphType'.
-     * 
-     * @param graphType the value of field 'graphType'.
-     */
-    public void setGraphType(
-            final int graphType) {
-        this._graphType = graphType;
-        this._has_graphType = true;
-    }
-
-    /**
-     * Sets the value of field 'groupRef'.
-     * 
-     * @param groupRef the value of field 'groupRef'.
-     */
-    public void setGroupRef(
-            final java.lang.String groupRef) {
-        this._groupRef = groupRef;
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'label'.
-     * 
-     * @param label the value of field 'label'.
-     */
-    public void setLabel(
-            final java.lang.String label) {
-        this._label = label;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setProperty(
-            final int index,
-            final jalview.schemabinding.version2.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        this._propertyList.set(index, vProperty);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPropertyArray
-     */
-    public void setProperty(
-            final jalview.schemabinding.version2.Property[] vPropertyArray) {
-        //-- copy array
-        _propertyList.clear();
-        
-        for (int i = 0; i < vPropertyArray.length; i++) {
-                this._propertyList.add(vPropertyArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'scaleColLabels'.
-     * 
-     * @param scaleColLabels the value of field 'scaleColLabels'.
-     */
-    public void setScaleColLabels(
-            final boolean scaleColLabels) {
-        this._scaleColLabels = scaleColLabels;
-        this._has_scaleColLabels = true;
-    }
-
-    /**
-     * Sets the value of field 'score'.
-     * 
-     * @param score the value of field 'score'.
-     */
-    public void setScore(
-            final double score) {
-        this._score = score;
-        this._has_score = true;
-    }
-
-    /**
-     * Sets the value of field 'scoreOnly'.
-     * 
-     * @param scoreOnly the value of field 'scoreOnly'.
-     */
-    public void setScoreOnly(
-            final boolean scoreOnly) {
-        this._scoreOnly = scoreOnly;
-        this._has_scoreOnly = true;
-    }
-
-    /**
-     * Sets the value of field 'sequenceRef'.
-     * 
-     * @param sequenceRef the value of field 'sequenceRef'.
-     */
-    public void setSequenceRef(
-            final java.lang.String sequenceRef) {
-        this._sequenceRef = sequenceRef;
-    }
-
-    /**
-     * Sets the value of field 'showAllColLabels'.
-     * 
-     * @param showAllColLabels the value of field 'showAllColLabels'
-     */
-    public void setShowAllColLabels(
-            final boolean showAllColLabels) {
-        this._showAllColLabels = showAllColLabels;
-        this._has_showAllColLabels = true;
-    }
-
-    /**
-     * Sets the value of field 'thresholdLine'.
-     * 
-     * @param thresholdLine the value of field 'thresholdLine'.
-     */
-    public void setThresholdLine(
-            final jalview.schemabinding.version2.ThresholdLine thresholdLine) {
-        this._thresholdLine = thresholdLine;
-    }
-
-    /**
-     * Sets the value of field 'visible'.
-     * 
-     * @param visible the value of field 'visible'.
-     */
-    public void setVisible(
-            final boolean visible) {
-        this._visible = visible;
-        this._has_visible = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Annotation
-     */
-    public static jalview.schemabinding.version2.Annotation unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Annotation implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _graph.
+   */
+  private boolean _graph;
+
+  /**
+   * keeps track of state for field: _graph
+   */
+  private boolean _has_graph;
+
+  /**
+   * Field _graphType.
+   */
+  private int _graphType;
+
+  /**
+   * keeps track of state for field: _graphType
+   */
+  private boolean _has_graphType;
+
+  /**
+   * Field _sequenceRef.
+   */
+  private java.lang.String _sequenceRef;
+
+  /**
+   * Field _groupRef.
+   */
+  private java.lang.String _groupRef;
+
+  /**
+   * 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;
+
+  /**
+   * height in pixels for the graph if this is a graph-type annotation.
+   */
+  private int _graphHeight;
+
+  /**
+   * keeps track of state for field: _graphHeight
+   */
+  private boolean _has_graphHeight;
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _scoreOnly.
+   */
+  private boolean _scoreOnly = false;
+
+  /**
+   * keeps track of state for field: _scoreOnly
+   */
+  private boolean _has_scoreOnly;
+
+  /**
+   * Field _score.
+   */
+  private double _score;
+
+  /**
+   * keeps track of state for field: _score
+   */
+  private boolean _has_score;
+
+  /**
+   * Field _visible.
+   */
+  private boolean _visible;
+
+  /**
+   * keeps track of state for field: _visible
+   */
+  private boolean _has_visible;
+
+  /**
+   * Field _centreColLabels.
+   */
+  private boolean _centreColLabels;
+
+  /**
+   * keeps track of state for field: _centreColLabels
+   */
+  private boolean _has_centreColLabels;
+
+  /**
+   * Field _scaleColLabels.
+   */
+  private boolean _scaleColLabels;
+
+  /**
+   * keeps track of state for field: _scaleColLabels
+   */
+  private boolean _has_scaleColLabels;
+
+  /**
+   * Field _showAllColLabels.
+   */
+  private boolean _showAllColLabels;
+
+  /**
+   * keeps track of state for field: _showAllColLabels
+   */
+  private boolean _has_showAllColLabels;
+
+  /**
+   * is an autocalculated annotation row
+   */
+  private boolean _autoCalculated = false;
+
+  /**
+   * keeps track of state for field: _autoCalculated
+   */
+  private boolean _has_autoCalculated;
+
+  /**
+   * is to be shown below the alignment - introduced in Jalview 2.8 for
+   * visualizing T-COFFEE alignment scores
+   */
+  private boolean _belowAlignment = true;
+
+  /**
+   * keeps track of state for field: _belowAlignment
+   */
+  private boolean _has_belowAlignment;
+
+  /**
+   * Optional string identifier used to group sets of annotation produced by a
+   * particular calculation. Values are opaque strings but have semantic meaning
+   * to Jalview's renderer, data importer and calculation system.
+   */
+  private java.lang.String _calcId;
+
+  /**
+   * 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;
+
+  /**
+   * Field _propertyList.
+   */
+  private java.util.Vector _propertyList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Annotation()
+  {
+    super();
+    this._annotationElementList = new java.util.Vector();
+    this._propertyList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAnnotationElement(
+          final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationElementList.addElement(vAnnotationElement);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAnnotationElement(
+          final int index,
+          final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationElementList.add(index, vAnnotationElement);
+  }
+
+  /**
+   * 
+   * 
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addProperty(
+          final jalview.schemabinding.version2.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.addElement(vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addProperty(final int index,
+          final jalview.schemabinding.version2.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.add(index, vProperty);
+  }
+
+  /**
+     */
+  public void deleteAutoCalculated()
+  {
+    this._has_autoCalculated = false;
+  }
+
+  /**
+     */
+  public void deleteBelowAlignment()
+  {
+    this._has_belowAlignment = false;
+  }
+
+  /**
+     */
+  public void deleteCentreColLabels()
+  {
+    this._has_centreColLabels = false;
+  }
+
+  /**
+     */
+  public void deleteGraph()
+  {
+    this._has_graph = false;
+  }
+
+  /**
+     */
+  public void deleteGraphColour()
+  {
+    this._has_graphColour = false;
+  }
+
+  /**
+     */
+  public void deleteGraphGroup()
+  {
+    this._has_graphGroup = false;
+  }
+
+  /**
+     */
+  public void deleteGraphHeight()
+  {
+    this._has_graphHeight = false;
+  }
+
+  /**
+     */
+  public void deleteGraphType()
+  {
+    this._has_graphType = false;
+  }
+
+  /**
+     */
+  public void deleteScaleColLabels()
+  {
+    this._has_scaleColLabels = false;
+  }
+
+  /**
+     */
+  public void deleteScore()
+  {
+    this._has_score = false;
+  }
+
+  /**
+     */
+  public void deleteScoreOnly()
+  {
+    this._has_scoreOnly = false;
+  }
+
+  /**
+     */
+  public void deleteShowAllColLabels()
+  {
+    this._has_showAllColLabels = false;
+  }
+
+  /**
+     */
+  public void deleteVisible()
+  {
+    this._has_visible = false;
+  }
+
+  /**
+   * Method enumerateAnnotationElement.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.AnnotationElement elements
+   */
+  public java.util.Enumeration enumerateAnnotationElement()
+  {
+    return this._annotationElementList.elements();
+  }
+
+  /**
+   * Method enumerateProperty.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Property
+   *         elements
+   */
+  public java.util.Enumeration enumerateProperty()
+  {
+    return this._propertyList.elements();
+  }
+
+  /**
+   * Method getAnnotationElement.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.AnnotationElement
+   *         at the given index
+   */
+  public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationElementList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getAnnotationElement: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._annotationElementList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList
+            .get(index);
+  }
+
+  /**
+   * Method getAnnotationElement.Returns the contents of the collection in an
+   * Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()
+  {
+    jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
+    return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAnnotationElementCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAnnotationElementCount()
+  {
+    return this._annotationElementList.size();
+  }
+
+  /**
+   * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has
+   * the following description: is an autocalculated annotation row
+   * 
+   * @return the value of field 'AutoCalculated'.
+   */
+  public boolean getAutoCalculated()
+  {
+    return this._autoCalculated;
+  }
+
+  /**
+   * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has
+   * the following description: is to be shown below the alignment - introduced
+   * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+   * 
+   * @return the value of field 'BelowAlignment'.
+   */
+  public boolean getBelowAlignment()
+  {
+    return this._belowAlignment;
+  }
+
+  /**
+   * Returns the value of field 'calcId'. The field 'calcId' has the following
+   * description: Optional string identifier used to group sets of annotation
+   * produced by a particular calculation. Values are opaque strings but have
+   * semantic meaning to Jalview's renderer, data importer and calculation
+   * system.
+   * 
+   * @return the value of field 'CalcId'.
+   */
+  public java.lang.String getCalcId()
+  {
+    return this._calcId;
+  }
+
+  /**
+   * Returns the value of field 'centreColLabels'.
+   * 
+   * @return the value of field 'CentreColLabels'.
+   */
+  public boolean getCentreColLabels()
+  {
+    return this._centreColLabels;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'graph'.
+   * 
+   * @return the value of field 'Graph'.
+   */
+  public boolean getGraph()
+  {
+    return this._graph;
+  }
+
+  /**
+   * Returns the value of field 'graphColour'.
+   * 
+   * @return the value of field 'GraphColour'.
+   */
+  public int getGraphColour()
+  {
+    return this._graphColour;
+  }
+
+  /**
+   * Returns the value of field 'graphGroup'.
+   * 
+   * @return the value of field 'GraphGroup'.
+   */
+  public int getGraphGroup()
+  {
+    return this._graphGroup;
+  }
+
+  /**
+   * Returns the value of field 'graphHeight'. The field 'graphHeight' has the
+   * following description: height in pixels for the graph if this is a
+   * graph-type annotation.
+   * 
+   * @return the value of field 'GraphHeight'.
+   */
+  public int getGraphHeight()
+  {
+    return this._graphHeight;
+  }
+
+  /**
+   * Returns the value of field 'graphType'.
+   * 
+   * @return the value of field 'GraphType'.
+   */
+  public int getGraphType()
+  {
+    return this._graphType;
+  }
+
+  /**
+   * Returns the value of field 'groupRef'.
+   * 
+   * @return the value of field 'GroupRef'.
+   */
+  public java.lang.String getGroupRef()
+  {
+    return this._groupRef;
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'label'.
+   * 
+   * @return the value of field 'Label'.
+   */
+  public java.lang.String getLabel()
+  {
+    return this._label;
+  }
+
+  /**
+   * Method getProperty.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Property at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Property getProperty(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("getProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Property) _propertyList
+            .get(index);
+  }
+
+  /**
+   * Method getProperty.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Property[] getProperty()
+  {
+    jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
+    return (jalview.schemabinding.version2.Property[]) this._propertyList
+            .toArray(array);
+  }
+
+  /**
+   * Method getPropertyCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPropertyCount()
+  {
+    return this._propertyList.size();
+  }
+
+  /**
+   * Returns the value of field 'scaleColLabels'.
+   * 
+   * @return the value of field 'ScaleColLabels'.
+   */
+  public boolean getScaleColLabels()
+  {
+    return this._scaleColLabels;
+  }
+
+  /**
+   * Returns the value of field 'score'.
+   * 
+   * @return the value of field 'Score'.
+   */
+  public double getScore()
+  {
+    return this._score;
+  }
+
+  /**
+   * Returns the value of field 'scoreOnly'.
+   * 
+   * @return the value of field 'ScoreOnly'.
+   */
+  public boolean getScoreOnly()
+  {
+    return this._scoreOnly;
+  }
+
+  /**
+   * Returns the value of field 'sequenceRef'.
+   * 
+   * @return the value of field 'SequenceRef'.
+   */
+  public java.lang.String getSequenceRef()
+  {
+    return this._sequenceRef;
+  }
+
+  /**
+   * Returns the value of field 'showAllColLabels'.
+   * 
+   * @return the value of field 'ShowAllColLabels'.
+   */
+  public boolean getShowAllColLabels()
+  {
+    return this._showAllColLabels;
+  }
+
+  /**
+   * Returns the value of field 'thresholdLine'.
+   * 
+   * @return the value of field 'ThresholdLine'.
+   */
+  public jalview.schemabinding.version2.ThresholdLine getThresholdLine()
+  {
+    return this._thresholdLine;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean getVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * Method hasAutoCalculated.
+   * 
+   * @return true if at least one AutoCalculated has been added
+   */
+  public boolean hasAutoCalculated()
+  {
+    return this._has_autoCalculated;
+  }
+
+  /**
+   * Method hasBelowAlignment.
+   * 
+   * @return true if at least one BelowAlignment has been added
+   */
+  public boolean hasBelowAlignment()
+  {
+    return this._has_belowAlignment;
+  }
+
+  /**
+   * Method hasCentreColLabels.
+   * 
+   * @return true if at least one CentreColLabels has been added
+   */
+  public boolean hasCentreColLabels()
+  {
+    return this._has_centreColLabels;
+  }
+
+  /**
+   * Method hasGraph.
+   * 
+   * @return true if at least one Graph has been added
+   */
+  public boolean hasGraph()
+  {
+    return this._has_graph;
+  }
+
+  /**
+   * Method hasGraphColour.
+   * 
+   * @return true if at least one GraphColour has been added
+   */
+  public boolean hasGraphColour()
+  {
+    return this._has_graphColour;
+  }
+
+  /**
+   * Method hasGraphGroup.
+   * 
+   * @return true if at least one GraphGroup has been added
+   */
+  public boolean hasGraphGroup()
+  {
+    return this._has_graphGroup;
+  }
+
+  /**
+   * Method hasGraphHeight.
+   * 
+   * @return true if at least one GraphHeight has been added
+   */
+  public boolean hasGraphHeight()
+  {
+    return this._has_graphHeight;
+  }
+
+  /**
+   * Method hasGraphType.
+   * 
+   * @return true if at least one GraphType has been added
+   */
+  public boolean hasGraphType()
+  {
+    return this._has_graphType;
+  }
+
+  /**
+   * Method hasScaleColLabels.
+   * 
+   * @return true if at least one ScaleColLabels has been added
+   */
+  public boolean hasScaleColLabels()
+  {
+    return this._has_scaleColLabels;
+  }
+
+  /**
+   * Method hasScore.
+   * 
+   * @return true if at least one Score has been added
+   */
+  public boolean hasScore()
+  {
+    return this._has_score;
+  }
+
+  /**
+   * Method hasScoreOnly.
+   * 
+   * @return true if at least one ScoreOnly has been added
+   */
+  public boolean hasScoreOnly()
+  {
+    return this._has_scoreOnly;
+  }
+
+  /**
+   * Method hasShowAllColLabels.
+   * 
+   * @return true if at least one ShowAllColLabels has been added
+   */
+  public boolean hasShowAllColLabels()
+  {
+    return this._has_showAllColLabels;
+  }
+
+  /**
+   * Method hasVisible.
+   * 
+   * @return true if at least one Visible has been added
+   */
+  public boolean hasVisible()
+  {
+    return this._has_visible;
+  }
+
+  /**
+   * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has
+   * the following description: is an autocalculated annotation row
+   * 
+   * @return the value of field 'AutoCalculated'.
+   */
+  public boolean isAutoCalculated()
+  {
+    return this._autoCalculated;
+  }
+
+  /**
+   * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has
+   * the following description: is to be shown below the alignment - introduced
+   * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+   * 
+   * @return the value of field 'BelowAlignment'.
+   */
+  public boolean isBelowAlignment()
+  {
+    return this._belowAlignment;
+  }
+
+  /**
+   * Returns the value of field 'centreColLabels'.
+   * 
+   * @return the value of field 'CentreColLabels'.
+   */
+  public boolean isCentreColLabels()
+  {
+    return this._centreColLabels;
+  }
+
+  /**
+   * Returns the value of field 'graph'.
+   * 
+   * @return the value of field 'Graph'.
+   */
+  public boolean isGraph()
+  {
+    return this._graph;
+  }
+
+  /**
+   * Returns the value of field 'scaleColLabels'.
+   * 
+   * @return the value of field 'ScaleColLabels'.
+   */
+  public boolean isScaleColLabels()
+  {
+    return this._scaleColLabels;
+  }
+
+  /**
+   * Returns the value of field 'scoreOnly'.
+   * 
+   * @return the value of field 'ScoreOnly'.
+   */
+  public boolean isScoreOnly()
+  {
+    return this._scoreOnly;
+  }
+
+  /**
+   * Returns the value of field 'showAllColLabels'.
+   * 
+   * @return the value of field 'ShowAllColLabels'.
+   */
+  public boolean isShowAllColLabels()
+  {
+    return this._showAllColLabels;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean isVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllAnnotationElement()
+  {
+    this._annotationElementList.clear();
+  }
+
+  /**
+     */
+  public void removeAllProperty()
+  {
+    this._propertyList.clear();
+  }
+
+  /**
+   * Method removeAnnotationElement.
+   * 
+   * @param vAnnotationElement
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAnnotationElement(
+          final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+  {
+    boolean removed = _annotationElementList.remove(vAnnotationElement);
+    return removed;
+  }
+
+  /**
+   * Method removeAnnotationElementAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
+          final int index)
+  {
+    java.lang.Object obj = this._annotationElementList.remove(index);
+    return (jalview.schemabinding.version2.AnnotationElement) obj;
+  }
+
+  /**
+   * Method removeProperty.
+   * 
+   * @param vProperty
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeProperty(
+          final jalview.schemabinding.version2.Property vProperty)
+  {
+    boolean removed = _propertyList.remove(vProperty);
+    return removed;
+  }
+
+  /**
+   * Method removePropertyAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Property removePropertyAt(
+          final int index)
+  {
+    java.lang.Object obj = this._propertyList.remove(index);
+    return (jalview.schemabinding.version2.Property) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotationElement
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAnnotationElement(
+          final int index,
+          final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationElementList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setAnnotationElement: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._annotationElementList.size() - 1) + "]");
+    }
+
+    this._annotationElementList.set(index, vAnnotationElement);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotationElementArray
+   */
+  public void setAnnotationElement(
+          final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray)
+  {
+    // -- copy array
+    _annotationElementList.clear();
+
+    for (int i = 0; i < vAnnotationElementArray.length; i++)
+    {
+      this._annotationElementList.add(vAnnotationElementArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'autoCalculated'. The field 'autoCalculated' has
+   * the following description: is an autocalculated annotation row
+   * 
+   * @param autoCalculated
+   *          the value of field 'autoCalculated'.
+   */
+  public void setAutoCalculated(final boolean autoCalculated)
+  {
+    this._autoCalculated = autoCalculated;
+    this._has_autoCalculated = true;
+  }
+
+  /**
+   * Sets the value of field 'belowAlignment'. The field 'belowAlignment' has
+   * the following description: is to be shown below the alignment - introduced
+   * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+   * 
+   * @param belowAlignment
+   *          the value of field 'belowAlignment'.
+   */
+  public void setBelowAlignment(final boolean belowAlignment)
+  {
+    this._belowAlignment = belowAlignment;
+    this._has_belowAlignment = true;
+  }
+
+  /**
+   * Sets the value of field 'calcId'. The field 'calcId' has the following
+   * description: Optional string identifier used to group sets of annotation
+   * produced by a particular calculation. Values are opaque strings but have
+   * semantic meaning to Jalview's renderer, data importer and calculation
+   * system.
+   * 
+   * @param calcId
+   *          the value of field 'calcId'.
+   */
+  public void setCalcId(final java.lang.String calcId)
+  {
+    this._calcId = calcId;
+  }
+
+  /**
+   * Sets the value of field 'centreColLabels'.
+   * 
+   * @param centreColLabels
+   *          the value of field 'centreColLabels'.
+   */
+  public void setCentreColLabels(final boolean centreColLabels)
+  {
+    this._centreColLabels = centreColLabels;
+    this._has_centreColLabels = true;
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *          the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'graph'.
+   * 
+   * @param graph
+   *          the value of field 'graph'.
+   */
+  public void setGraph(final boolean graph)
+  {
+    this._graph = graph;
+    this._has_graph = true;
+  }
+
+  /**
+   * Sets the value of field 'graphColour'.
+   * 
+   * @param graphColour
+   *          the value of field 'graphColour'.
+   */
+  public void setGraphColour(final int graphColour)
+  {
+    this._graphColour = graphColour;
+    this._has_graphColour = true;
+  }
+
+  /**
+   * Sets the value of field 'graphGroup'.
+   * 
+   * @param graphGroup
+   *          the value of field 'graphGroup'.
+   */
+  public void setGraphGroup(final int graphGroup)
+  {
+    this._graphGroup = graphGroup;
+    this._has_graphGroup = true;
+  }
+
+  /**
+   * Sets the value of field 'graphHeight'. The field 'graphHeight' has the
+   * following description: height in pixels for the graph if this is a
+   * graph-type annotation.
+   * 
+   * @param graphHeight
+   *          the value of field 'graphHeight'.
+   */
+  public void setGraphHeight(final int graphHeight)
+  {
+    this._graphHeight = graphHeight;
+    this._has_graphHeight = true;
+  }
+
+  /**
+   * Sets the value of field 'graphType'.
+   * 
+   * @param graphType
+   *          the value of field 'graphType'.
+   */
+  public void setGraphType(final int graphType)
+  {
+    this._graphType = graphType;
+    this._has_graphType = true;
+  }
+
+  /**
+   * Sets the value of field 'groupRef'.
+   * 
+   * @param groupRef
+   *          the value of field 'groupRef'.
+   */
+  public void setGroupRef(final java.lang.String groupRef)
+  {
+    this._groupRef = groupRef;
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'label'.
+   * 
+   * @param label
+   *          the value of field 'label'.
+   */
+  public void setLabel(final java.lang.String label)
+  {
+    this._label = label;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setProperty(final int index,
+          final jalview.schemabinding.version2.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("setProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
+    }
+
+    this._propertyList.set(index, vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPropertyArray
+   */
+  public void setProperty(
+          final jalview.schemabinding.version2.Property[] vPropertyArray)
+  {
+    // -- copy array
+    _propertyList.clear();
+
+    for (int i = 0; i < vPropertyArray.length; i++)
+    {
+      this._propertyList.add(vPropertyArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'scaleColLabels'.
+   * 
+   * @param scaleColLabels
+   *          the value of field 'scaleColLabels'.
+   */
+  public void setScaleColLabels(final boolean scaleColLabels)
+  {
+    this._scaleColLabels = scaleColLabels;
+    this._has_scaleColLabels = true;
+  }
+
+  /**
+   * Sets the value of field 'score'.
+   * 
+   * @param score
+   *          the value of field 'score'.
+   */
+  public void setScore(final double score)
+  {
+    this._score = score;
+    this._has_score = true;
+  }
+
+  /**
+   * Sets the value of field 'scoreOnly'.
+   * 
+   * @param scoreOnly
+   *          the value of field 'scoreOnly'.
+   */
+  public void setScoreOnly(final boolean scoreOnly)
+  {
+    this._scoreOnly = scoreOnly;
+    this._has_scoreOnly = true;
+  }
+
+  /**
+   * Sets the value of field 'sequenceRef'.
+   * 
+   * @param sequenceRef
+   *          the value of field 'sequenceRef'.
+   */
+  public void setSequenceRef(final java.lang.String sequenceRef)
+  {
+    this._sequenceRef = sequenceRef;
+  }
+
+  /**
+   * Sets the value of field 'showAllColLabels'.
+   * 
+   * @param showAllColLabels
+   *          the value of field 'showAllColLabels'
+   */
+  public void setShowAllColLabels(final boolean showAllColLabels)
+  {
+    this._showAllColLabels = showAllColLabels;
+    this._has_showAllColLabels = true;
+  }
+
+  /**
+   * Sets the value of field 'thresholdLine'.
+   * 
+   * @param thresholdLine
+   *          the value of field 'thresholdLine'.
+   */
+  public void setThresholdLine(
+          final jalview.schemabinding.version2.ThresholdLine thresholdLine)
+  {
+    this._thresholdLine = thresholdLine;
+  }
+
+  /**
+   * Sets the value of field 'visible'.
+   * 
+   * @param visible
+   *          the value of field 'visible'.
+   */
+  public void setVisible(final boolean visible)
+  {
+    this._visible = visible;
+    this._has_visible = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Annotation
+   */
+  public static jalview.schemabinding.version2.Annotation unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Annotation) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Annotation.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationColourScheme.java b/src/jalview/schemabinding/version2/AnnotationColourScheme.java
index 91222f1..2f76e76 100644
--- a/src/jalview/schemabinding/version2/AnnotationColourScheme.java
+++ b/src/jalview/schemabinding/version2/AnnotationColourScheme.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,461 +19,479 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationColourScheme 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;
-
-    /**
-     * Field _perSequence.
-     */
-    private boolean _perSequence;
-
-    /**
-     * keeps track of state for field: _perSequence
-     */
-    private boolean _has_perSequence;
-
-    /**
-     * Field _predefinedColours.
-     */
-    private boolean _predefinedColours;
-
-    /**
-     * keeps track of state for field: _predefinedColours
-     */
-    private boolean _has_predefinedColours;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationColourScheme() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteAboveThreshold(
-    ) {
-        this._has_aboveThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteMaxColour(
-    ) {
-        this._has_maxColour= false;
-    }
-
-    /**
-     */
-    public void deleteMinColour(
-    ) {
-        this._has_minColour= false;
-    }
-
-    /**
-     */
-    public void deletePerSequence(
-    ) {
-        this._has_perSequence= false;
-    }
-
-    /**
-     */
-    public void deletePredefinedColours(
-    ) {
-        this._has_predefinedColours= false;
-    }
-
-    /**
-     */
-    public void deleteThreshold(
-    ) {
-        this._has_threshold= false;
-    }
-
-    /**
-     * Returns the value of field 'aboveThreshold'.
-     * 
-     * @return the value of field 'AboveThreshold'.
-     */
-    public int getAboveThreshold(
-    ) {
-        return this._aboveThreshold;
-    }
-
-    /**
-     * Returns the value of field 'annotation'.
-     * 
-     * @return the value of field 'Annotation'.
-     */
-    public java.lang.String getAnnotation(
-    ) {
-        return this._annotation;
-    }
-
-    /**
-     * Returns the value of field 'colourScheme'.
-     * 
-     * @return the value of field 'ColourScheme'.
-     */
-    public java.lang.String getColourScheme(
-    ) {
-        return this._colourScheme;
-    }
-
-    /**
-     * Returns the value of field 'maxColour'.
-     * 
-     * @return the value of field 'MaxColour'.
-     */
-    public int getMaxColour(
-    ) {
-        return this._maxColour;
-    }
-
-    /**
-     * Returns the value of field 'minColour'.
-     * 
-     * @return the value of field 'MinColour'.
-     */
-    public int getMinColour(
-    ) {
-        return this._minColour;
-    }
-
-    /**
-     * Returns the value of field 'perSequence'.
-     * 
-     * @return the value of field 'PerSequence'.
-     */
-    public boolean getPerSequence(
-    ) {
-        return this._perSequence;
-    }
-
-    /**
-     * Returns the value of field 'predefinedColours'.
-     * 
-     * @return the value of field 'PredefinedColours'.
-     */
-    public boolean getPredefinedColours(
-    ) {
-        return this._predefinedColours;
-    }
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return the value of field 'Threshold'.
-     */
-    public float getThreshold(
-    ) {
-        return this._threshold;
-    }
-
-    /**
-     * Method hasAboveThreshold.
-     * 
-     * @return true if at least one AboveThreshold has been added
-     */
-    public boolean hasAboveThreshold(
-    ) {
-        return this._has_aboveThreshold;
-    }
-
-    /**
-     * Method hasMaxColour.
-     * 
-     * @return true if at least one MaxColour has been added
-     */
-    public boolean hasMaxColour(
-    ) {
-        return this._has_maxColour;
-    }
-
-    /**
-     * Method hasMinColour.
-     * 
-     * @return true if at least one MinColour has been added
-     */
-    public boolean hasMinColour(
-    ) {
-        return this._has_minColour;
-    }
-
-    /**
-     * Method hasPerSequence.
-     * 
-     * @return true if at least one PerSequence has been added
-     */
-    public boolean hasPerSequence(
-    ) {
-        return this._has_perSequence;
-    }
-
-    /**
-     * Method hasPredefinedColours.
-     * 
-     * @return true if at least one PredefinedColours has been added
-     */
-    public boolean hasPredefinedColours(
-    ) {
-        return this._has_predefinedColours;
-    }
-
-    /**
-     * Method hasThreshold.
-     * 
-     * @return true if at least one Threshold has been added
-     */
-    public boolean hasThreshold(
-    ) {
-        return this._has_threshold;
-    }
-
-    /**
-     * Returns the value of field 'perSequence'.
-     * 
-     * @return the value of field 'PerSequence'.
-     */
-    public boolean isPerSequence(
-    ) {
-        return this._perSequence;
-    }
-
-    /**
-     * Returns the value of field 'predefinedColours'.
-     * 
-     * @return the value of field 'PredefinedColours'.
-     */
-    public boolean isPredefinedColours(
-    ) {
-        return this._predefinedColours;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'aboveThreshold'.
-     * 
-     * @param aboveThreshold the value of field 'aboveThreshold'.
-     */
-    public void setAboveThreshold(
-            final int aboveThreshold) {
-        this._aboveThreshold = aboveThreshold;
-        this._has_aboveThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'annotation'.
-     * 
-     * @param annotation the value of field 'annotation'.
-     */
-    public void setAnnotation(
-            final java.lang.String annotation) {
-        this._annotation = annotation;
-    }
-
-    /**
-     * Sets the value of field 'colourScheme'.
-     * 
-     * @param colourScheme the value of field 'colourScheme'.
-     */
-    public void setColourScheme(
-            final java.lang.String colourScheme) {
-        this._colourScheme = colourScheme;
-    }
-
-    /**
-     * Sets the value of field 'maxColour'.
-     * 
-     * @param maxColour the value of field 'maxColour'.
-     */
-    public void setMaxColour(
-            final int maxColour) {
-        this._maxColour = maxColour;
-        this._has_maxColour = true;
-    }
-
-    /**
-     * Sets the value of field 'minColour'.
-     * 
-     * @param minColour the value of field 'minColour'.
-     */
-    public void setMinColour(
-            final int minColour) {
-        this._minColour = minColour;
-        this._has_minColour = true;
-    }
-
-    /**
-     * Sets the value of field 'perSequence'.
-     * 
-     * @param perSequence the value of field 'perSequence'.
-     */
-    public void setPerSequence(
-            final boolean perSequence) {
-        this._perSequence = perSequence;
-        this._has_perSequence = true;
-    }
-
-    /**
-     * Sets the value of field 'predefinedColours'.
-     * 
-     * @param predefinedColours the value of field
-     * 'predefinedColours'.
-     */
-    public void setPredefinedColours(
-            final boolean predefinedColours) {
-        this._predefinedColours = predefinedColours;
-        this._has_predefinedColours = true;
-    }
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(
-            final float threshold) {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.AnnotationColourScheme
-     */
-    public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColourScheme.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class AnnotationColourScheme 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;
+
+  /**
+   * Field _perSequence.
+   */
+  private boolean _perSequence;
+
+  /**
+   * keeps track of state for field: _perSequence
+   */
+  private boolean _has_perSequence;
+
+  /**
+   * Field _predefinedColours.
+   */
+  private boolean _predefinedColours;
+
+  /**
+   * keeps track of state for field: _predefinedColours
+   */
+  private boolean _has_predefinedColours;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationColourScheme()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteAboveThreshold()
+  {
+    this._has_aboveThreshold = false;
+  }
+
+  /**
+     */
+  public void deleteMaxColour()
+  {
+    this._has_maxColour = false;
+  }
+
+  /**
+     */
+  public void deleteMinColour()
+  {
+    this._has_minColour = false;
+  }
+
+  /**
+     */
+  public void deletePerSequence()
+  {
+    this._has_perSequence = false;
+  }
+
+  /**
+     */
+  public void deletePredefinedColours()
+  {
+    this._has_predefinedColours = false;
+  }
+
+  /**
+     */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  }
+
+  /**
+   * Returns the value of field 'aboveThreshold'.
+   * 
+   * @return the value of field 'AboveThreshold'.
+   */
+  public int getAboveThreshold()
+  {
+    return this._aboveThreshold;
+  }
+
+  /**
+   * Returns the value of field 'annotation'.
+   * 
+   * @return the value of field 'Annotation'.
+   */
+  public java.lang.String getAnnotation()
+  {
+    return this._annotation;
+  }
+
+  /**
+   * Returns the value of field 'colourScheme'.
+   * 
+   * @return the value of field 'ColourScheme'.
+   */
+  public java.lang.String getColourScheme()
+  {
+    return this._colourScheme;
+  }
+
+  /**
+   * Returns the value of field 'maxColour'.
+   * 
+   * @return the value of field 'MaxColour'.
+   */
+  public int getMaxColour()
+  {
+    return this._maxColour;
+  }
+
+  /**
+   * Returns the value of field 'minColour'.
+   * 
+   * @return the value of field 'MinColour'.
+   */
+  public int getMinColour()
+  {
+    return this._minColour;
+  }
+
+  /**
+   * Returns the value of field 'perSequence'.
+   * 
+   * @return the value of field 'PerSequence'.
+   */
+  public boolean getPerSequence()
+  {
+    return this._perSequence;
+  }
+
+  /**
+   * Returns the value of field 'predefinedColours'.
+   * 
+   * @return the value of field 'PredefinedColours'.
+   */
+  public boolean getPredefinedColours()
+  {
+    return this._predefinedColours;
+  }
+
+  /**
+   * Returns the value of field 'threshold'.
+   * 
+   * @return the value of field 'Threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  }
+
+  /**
+   * Method hasAboveThreshold.
+   * 
+   * @return true if at least one AboveThreshold has been added
+   */
+  public boolean hasAboveThreshold()
+  {
+    return this._has_aboveThreshold;
+  }
+
+  /**
+   * Method hasMaxColour.
+   * 
+   * @return true if at least one MaxColour has been added
+   */
+  public boolean hasMaxColour()
+  {
+    return this._has_maxColour;
+  }
+
+  /**
+   * Method hasMinColour.
+   * 
+   * @return true if at least one MinColour has been added
+   */
+  public boolean hasMinColour()
+  {
+    return this._has_minColour;
+  }
+
+  /**
+   * Method hasPerSequence.
+   * 
+   * @return true if at least one PerSequence has been added
+   */
+  public boolean hasPerSequence()
+  {
+    return this._has_perSequence;
+  }
+
+  /**
+   * Method hasPredefinedColours.
+   * 
+   * @return true if at least one PredefinedColours has been added
+   */
+  public boolean hasPredefinedColours()
+  {
+    return this._has_predefinedColours;
+  }
+
+  /**
+   * Method hasThreshold.
+   * 
+   * @return true if at least one Threshold has been added
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  }
+
+  /**
+   * Returns the value of field 'perSequence'.
+   * 
+   * @return the value of field 'PerSequence'.
+   */
+  public boolean isPerSequence()
+  {
+    return this._perSequence;
+  }
+
+  /**
+   * Returns the value of field 'predefinedColours'.
+   * 
+   * @return the value of field 'PredefinedColours'.
+   */
+  public boolean isPredefinedColours()
+  {
+    return this._predefinedColours;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'aboveThreshold'.
+   * 
+   * @param aboveThreshold
+   *          the value of field 'aboveThreshold'.
+   */
+  public void setAboveThreshold(final int aboveThreshold)
+  {
+    this._aboveThreshold = aboveThreshold;
+    this._has_aboveThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'annotation'.
+   * 
+   * @param annotation
+   *          the value of field 'annotation'.
+   */
+  public void setAnnotation(final java.lang.String annotation)
+  {
+    this._annotation = annotation;
+  }
+
+  /**
+   * Sets the value of field 'colourScheme'.
+   * 
+   * @param colourScheme
+   *          the value of field 'colourScheme'.
+   */
+  public void setColourScheme(final java.lang.String colourScheme)
+  {
+    this._colourScheme = colourScheme;
+  }
+
+  /**
+   * Sets the value of field 'maxColour'.
+   * 
+   * @param maxColour
+   *          the value of field 'maxColour'.
+   */
+  public void setMaxColour(final int maxColour)
+  {
+    this._maxColour = maxColour;
+    this._has_maxColour = true;
+  }
+
+  /**
+   * Sets the value of field 'minColour'.
+   * 
+   * @param minColour
+   *          the value of field 'minColour'.
+   */
+  public void setMinColour(final int minColour)
+  {
+    this._minColour = minColour;
+    this._has_minColour = true;
+  }
+
+  /**
+   * Sets the value of field 'perSequence'.
+   * 
+   * @param perSequence
+   *          the value of field 'perSequence'.
+   */
+  public void setPerSequence(final boolean perSequence)
+  {
+    this._perSequence = perSequence;
+    this._has_perSequence = true;
+  }
+
+  /**
+   * Sets the value of field 'predefinedColours'.
+   * 
+   * @param predefinedColours
+   *          the value of field 'predefinedColours'.
+   */
+  public void setPredefinedColours(final boolean predefinedColours)
+  {
+    this._predefinedColours = predefinedColours;
+    this._has_predefinedColours = true;
+  }
+
+  /**
+   * Sets the value of field 'threshold'.
+   * 
+   * @param threshold
+   *          the value of field 'threshold'.
+   */
+  public void setThreshold(final float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled
+   *         jalview.schemabinding.version2.AnnotationColourScheme
+   */
+  public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.AnnotationColourScheme.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java
index 965fc07..350ebce 100644
--- a/src/jalview/schemabinding/version2/AnnotationColours.java
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,99 +19,110 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationColours extends AnnotationColourScheme 
-implements java.io.Serializable
+public class AnnotationColours extends AnnotationColourScheme implements
+        java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationColours() {
-        super();
-    }
-
+  public AnnotationColours()
+  {
+    super();
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.AnnotationColourScheme
-     */
-    public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled
+   *         jalview.schemabinding.version2.AnnotationColourScheme
+   */
+  public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.AnnotationColours.class,
+                    reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java
index 6df737f..2a765ea 100644
--- a/src/jalview/schemabinding/version2/AnnotationElement.java
+++ b/src/jalview/schemabinding/version2/AnnotationElement.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,322 +19,338 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationElement implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _position.
-     */
-    private int _position;
-
-    /**
-     * keeps track of state for field: _position
-     */
-    private boolean _has_position;
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _displayCharacter.
-     */
-    private java.lang.String _displayCharacter;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _secondaryStructure.
-     */
-    private java.lang.String _secondaryStructure;
-
-    /**
-     * Field _value.
-     */
-    private float _value;
-
-    /**
-     * keeps track of state for field: _value
-     */
-    private boolean _has_value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationElement() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deletePosition(
-    ) {
-        this._has_position= false;
-    }
-
-    /**
-     */
-    public void deleteValue(
-    ) {
-        this._has_value= false;
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'displayCharacter'.
-     * 
-     * @return the value of field 'DisplayCharacter'.
-     */
-    public java.lang.String getDisplayCharacter(
-    ) {
-        return this._displayCharacter;
-    }
-
-    /**
-     * Returns the value of field 'position'.
-     * 
-     * @return the value of field 'Position'.
-     */
-    public int getPosition(
-    ) {
-        return this._position;
-    }
-
-    /**
-     * Returns the value of field 'secondaryStructure'.
-     * 
-     * @return the value of field 'SecondaryStructure'.
-     */
-    public java.lang.String getSecondaryStructure(
-    ) {
-        return this._secondaryStructure;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public float getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasPosition.
-     * 
-     * @return true if at least one Position has been added
-     */
-    public boolean hasPosition(
-    ) {
-        return this._has_position;
-    }
-
-    /**
-     * Method hasValue.
-     * 
-     * @return true if at least one Value has been added
-     */
-    public boolean hasValue(
-    ) {
-        return this._has_value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'displayCharacter'.
-     * 
-     * @param displayCharacter the value of field 'displayCharacter'
-     */
-    public void setDisplayCharacter(
-            final java.lang.String displayCharacter) {
-        this._displayCharacter = displayCharacter;
-    }
-
-    /**
-     * Sets the value of field 'position'.
-     * 
-     * @param position the value of field 'position'.
-     */
-    public void setPosition(
-            final int position) {
-        this._position = position;
-        this._has_position = true;
-    }
-
-    /**
-     * Sets the value of field 'secondaryStructure'.
-     * 
-     * @param secondaryStructure the value of field
-     * 'secondaryStructure'.
-     */
-    public void setSecondaryStructure(
-            final java.lang.String secondaryStructure) {
-        this._secondaryStructure = secondaryStructure;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final float value) {
-        this._value = value;
-        this._has_value = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.AnnotationElement
-     */
-    public static jalview.schemabinding.version2.AnnotationElement unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class AnnotationElement implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _position.
+   */
+  private int _position;
+
+  /**
+   * keeps track of state for field: _position
+   */
+  private boolean _has_position;
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _displayCharacter.
+   */
+  private java.lang.String _displayCharacter;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _secondaryStructure.
+   */
+  private java.lang.String _secondaryStructure;
+
+  /**
+   * Field _value.
+   */
+  private float _value;
+
+  /**
+   * keeps track of state for field: _value
+   */
+  private boolean _has_value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationElement()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+     */
+  public void deletePosition()
+  {
+    this._has_position = false;
+  }
+
+  /**
+     */
+  public void deleteValue()
+  {
+    this._has_value = false;
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'displayCharacter'.
+   * 
+   * @return the value of field 'DisplayCharacter'.
+   */
+  public java.lang.String getDisplayCharacter()
+  {
+    return this._displayCharacter;
+  }
+
+  /**
+   * Returns the value of field 'position'.
+   * 
+   * @return the value of field 'Position'.
+   */
+  public int getPosition()
+  {
+    return this._position;
+  }
+
+  /**
+   * Returns the value of field 'secondaryStructure'.
+   * 
+   * @return the value of field 'SecondaryStructure'.
+   */
+  public java.lang.String getSecondaryStructure()
+  {
+    return this._secondaryStructure;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public float getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasPosition.
+   * 
+   * @return true if at least one Position has been added
+   */
+  public boolean hasPosition()
+  {
+    return this._has_position;
+  }
+
+  /**
+   * Method hasValue.
+   * 
+   * @return true if at least one Value has been added
+   */
+  public boolean hasValue()
+  {
+    return this._has_value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *          the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *          the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'displayCharacter'.
+   * 
+   * @param displayCharacter
+   *          the value of field 'displayCharacter'
+   */
+  public void setDisplayCharacter(final java.lang.String displayCharacter)
+  {
+    this._displayCharacter = displayCharacter;
+  }
+
+  /**
+   * Sets the value of field 'position'.
+   * 
+   * @param position
+   *          the value of field 'position'.
+   */
+  public void setPosition(final int position)
+  {
+    this._position = position;
+    this._has_position = true;
+  }
+
+  /**
+   * Sets the value of field 'secondaryStructure'.
+   * 
+   * @param secondaryStructure
+   *          the value of field 'secondaryStructure'.
+   */
+  public void setSecondaryStructure(
+          final java.lang.String secondaryStructure)
+  {
+    this._secondaryStructure = secondaryStructure;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *          the value of field 'value'.
+   */
+  public void setValue(final float value)
+  {
+    this._value = value;
+    this._has_value = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.AnnotationElement
+   */
+  public static jalview.schemabinding.version2.AnnotationElement unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.AnnotationElement.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/CalcIdParam.java b/src/jalview/schemabinding/version2/CalcIdParam.java
index cae3ec2..57d6986 100644
--- a/src/jalview/schemabinding/version2/CalcIdParam.java
+++ b/src/jalview/schemabinding/version2/CalcIdParam.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,282 +19,282 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class CalcIdParam extends WebServiceParameterSet 
-implements java.io.Serializable
+public class CalcIdParam extends WebServiceParameterSet implements
+        java.io.Serializable
 {
 
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * handle for the calculation which uses
-     *  this parameter set
-     *  
-     */
-    private java.lang.String _calcId;
-
-    /**
-     * should the calculation be performed
-     *  immediately after loading in order to refresh results
-     *  
-     */
-    private boolean _needsUpdate = false;
-
-    /**
-     * keeps track of state for field: _needsUpdate
-     */
-    private boolean _has_needsUpdate;
-
-    /**
-     * should the calculation be automatically
-     *  performed on edits
-     *  
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * handle for the calculation which uses this parameter set
+   * 
+   */
+  private java.lang.String _calcId;
+
+  /**
+   * should the calculation be performed immediately after loading in order to
+   * refresh results
+   * 
+   */
+  private boolean _needsUpdate = false;
+
+  /**
+   * keeps track of state for field: _needsUpdate
+   */
+  private boolean _has_needsUpdate;
+
+  /**
+   * should the calculation be automatically performed on edits
+   * 
+   */
+  private boolean _autoUpdate;
+
+  /**
+   * keeps track of state for field: _autoUpdate
+   */
+  private boolean _has_autoUpdate;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public CalcIdParam()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
      */
-    private boolean _autoUpdate;
-
-    /**
-     * keeps track of state for field: _autoUpdate
-     */
-    private boolean _has_autoUpdate;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public CalcIdParam() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteAutoUpdate(
-    ) {
-        this._has_autoUpdate= false;
-    }
-
-    /**
-     */
-    public void deleteNeedsUpdate(
-    ) {
-        this._has_needsUpdate= false;
-    }
-
-    /**
-     * Returns the value of field 'autoUpdate'. The field
-     * 'autoUpdate' has the following description: should the
-     * calculation be automatically
-     *  performed on edits
-     *  
-     * 
-     * @return the value of field 'AutoUpdate'.
-     */
-    public boolean getAutoUpdate(
-    ) {
-        return this._autoUpdate;
-    }
-
-    /**
-     * Returns the value of field 'calcId'. The field 'calcId' has
-     * the following description: handle for the calculation which
-     * uses
-     *  this parameter set
-     *  
-     * 
-     * @return the value of field 'CalcId'.
-     */
-    public java.lang.String getCalcId(
-    ) {
-        return this._calcId;
-    }
-
-    /**
-     * Returns the value of field 'needsUpdate'. The field
-     * 'needsUpdate' has the following description: should the
-     * calculation be performed
-     *  immediately after loading in order to refresh results
-     *  
-     * 
-     * @return the value of field 'NeedsUpdate'.
-     */
-    public boolean getNeedsUpdate(
-    ) {
-        return this._needsUpdate;
-    }
-
-    /**
-     * Method hasAutoUpdate.
-     * 
-     * @return true if at least one AutoUpdate has been added
-     */
-    public boolean hasAutoUpdate(
-    ) {
-        return this._has_autoUpdate;
-    }
-
-    /**
-     * Method hasNeedsUpdate.
-     * 
-     * @return true if at least one NeedsUpdate has been added
-     */
-    public boolean hasNeedsUpdate(
-    ) {
-        return this._has_needsUpdate;
-    }
-
-    /**
-     * Returns the value of field 'autoUpdate'. The field
-     * 'autoUpdate' has the following description: should the
-     * calculation be automatically
-     *  performed on edits
-     *  
-     * 
-     * @return the value of field 'AutoUpdate'.
-     */
-    public boolean isAutoUpdate(
-    ) {
-        return this._autoUpdate;
-    }
-
-    /**
-     * Returns the value of field 'needsUpdate'. The field
-     * 'needsUpdate' has the following description: should the
-     * calculation be performed
-     *  immediately after loading in order to refresh results
-     *  
-     * 
-     * @return the value of field 'NeedsUpdate'.
-     */
-    public boolean isNeedsUpdate(
-    ) {
-        return this._needsUpdate;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'autoUpdate'. The field 'autoUpdate'
-     * has the following description: should the calculation be
-     * automatically
-     *  performed on edits
-     *  
-     * 
-     * @param autoUpdate the value of field 'autoUpdate'.
-     */
-    public void setAutoUpdate(
-            final boolean autoUpdate) {
-        this._autoUpdate = autoUpdate;
-        this._has_autoUpdate = true;
-    }
-
-    /**
-     * Sets the value of field 'calcId'. The field 'calcId' has the
-     * following description: handle for the calculation which uses
-     *  this parameter set
-     *  
-     * 
-     * @param calcId the value of field 'calcId'.
-     */
-    public void setCalcId(
-            final java.lang.String calcId) {
-        this._calcId = calcId;
-    }
-
-    /**
-     * Sets the value of field 'needsUpdate'. The field
-     * 'needsUpdate' has the following description: should the
-     * calculation be performed
-     *  immediately after loading in order to refresh results
-     *  
-     * 
-     * @param needsUpdate the value of field 'needsUpdate'.
-     */
-    public void setNeedsUpdate(
-            final boolean needsUpdate) {
-        this._needsUpdate = needsUpdate;
-        this._has_needsUpdate = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.CalcIdParam
-     */
-    public static jalview.schemabinding.version2.CalcIdParam unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.CalcIdParam) Unmarshaller.unmarshal(jalview.schemabinding.version2.CalcIdParam.class, reader);
-    }
+  public void deleteAutoUpdate()
+  {
+    this._has_autoUpdate = false;
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+  /**
      */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+  public void deleteNeedsUpdate()
+  {
+    this._has_needsUpdate = false;
+  }
+
+  /**
+   * Returns the value of field 'autoUpdate'. The field 'autoUpdate' has the
+   * following description: should the calculation be automatically performed on
+   * edits
+   * 
+   * 
+   * @return the value of field 'AutoUpdate'.
+   */
+  public boolean getAutoUpdate()
+  {
+    return this._autoUpdate;
+  }
+
+  /**
+   * Returns the value of field 'calcId'. The field 'calcId' has the following
+   * description: handle for the calculation which uses this parameter set
+   * 
+   * 
+   * @return the value of field 'CalcId'.
+   */
+  public java.lang.String getCalcId()
+  {
+    return this._calcId;
+  }
+
+  /**
+   * Returns the value of field 'needsUpdate'. The field 'needsUpdate' has the
+   * following description: should the calculation be performed immediately
+   * after loading in order to refresh results
+   * 
+   * 
+   * @return the value of field 'NeedsUpdate'.
+   */
+  public boolean getNeedsUpdate()
+  {
+    return this._needsUpdate;
+  }
+
+  /**
+   * Method hasAutoUpdate.
+   * 
+   * @return true if at least one AutoUpdate has been added
+   */
+  public boolean hasAutoUpdate()
+  {
+    return this._has_autoUpdate;
+  }
+
+  /**
+   * Method hasNeedsUpdate.
+   * 
+   * @return true if at least one NeedsUpdate has been added
+   */
+  public boolean hasNeedsUpdate()
+  {
+    return this._has_needsUpdate;
+  }
+
+  /**
+   * Returns the value of field 'autoUpdate'. The field 'autoUpdate' has the
+   * following description: should the calculation be automatically performed on
+   * edits
+   * 
+   * 
+   * @return the value of field 'AutoUpdate'.
+   */
+  public boolean isAutoUpdate()
+  {
+    return this._autoUpdate;
+  }
+
+  /**
+   * Returns the value of field 'needsUpdate'. The field 'needsUpdate' has the
+   * following description: should the calculation be performed immediately
+   * after loading in order to refresh results
+   * 
+   * 
+   * @return the value of field 'NeedsUpdate'.
+   */
+  public boolean isNeedsUpdate()
+  {
+    return this._needsUpdate;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'autoUpdate'. The field 'autoUpdate' has the
+   * following description: should the calculation be automatically performed on
+   * edits
+   * 
+   * 
+   * @param autoUpdate
+   *          the value of field 'autoUpdate'.
+   */
+  public void setAutoUpdate(final boolean autoUpdate)
+  {
+    this._autoUpdate = autoUpdate;
+    this._has_autoUpdate = true;
+  }
+
+  /**
+   * Sets the value of field 'calcId'. The field 'calcId' has the following
+   * description: handle for the calculation which uses this parameter set
+   * 
+   * 
+   * @param calcId
+   *          the value of field 'calcId'.
+   */
+  public void setCalcId(final java.lang.String calcId)
+  {
+    this._calcId = calcId;
+  }
+
+  /**
+   * Sets the value of field 'needsUpdate'. The field 'needsUpdate' has the
+   * following description: should the calculation be performed immediately
+   * after loading in order to refresh results
+   * 
+   * 
+   * @param needsUpdate
+   *          the value of field 'needsUpdate'.
+   */
+  public void setNeedsUpdate(final boolean needsUpdate)
+  {
+    this._needsUpdate = needsUpdate;
+    this._has_needsUpdate = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.CalcIdParam
+   */
+  public static jalview.schemabinding.version2.CalcIdParam unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.CalcIdParam) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.CalcIdParam.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java
index d64263d..9d5a916 100644
--- a/src/jalview/schemabinding/version2/Colour.java
+++ b/src/jalview/schemabinding/version2/Colour.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,465 +19,481 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Colour implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _RGB.
-     */
-    private java.lang.String _RGB;
-
-    /**
-     * Field _minRGB.
-     */
-    private java.lang.String _minRGB;
-
-    /**
-     * loosely specified enumeration: NONE,ABOVE, or BELOW
-     */
-    private java.lang.String _threshType;
-
-    /**
-     * Field _threshold.
-     */
-    private float _threshold;
-
-    /**
-     * keeps track of state for field: _threshold
-     */
-    private boolean _has_threshold;
-
-    /**
-     * Field _max.
-     */
-    private float _max;
-
-    /**
-     * keeps track of state for field: _max
-     */
-    private boolean _has_max;
-
-    /**
-     * Field _min.
-     */
-    private float _min;
-
-    /**
-     * keeps track of state for field: _min
-     */
-    private boolean _has_min;
-
-    /**
-     * Field _colourByLabel.
-     */
-    private boolean _colourByLabel;
-
-    /**
-     * keeps track of state for field: _colourByLabel
-     */
-    private boolean _has_colourByLabel;
-
-    /**
-     * Field _autoScale.
-     */
-    private boolean _autoScale;
-
-    /**
-     * keeps track of state for field: _autoScale
-     */
-    private boolean _has_autoScale;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Colour() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteAutoScale(
-    ) {
-        this._has_autoScale= false;
-    }
-
-    /**
-     */
-    public void deleteColourByLabel(
-    ) {
-        this._has_colourByLabel= false;
-    }
-
-    /**
-     */
-    public void deleteMax(
-    ) {
-        this._has_max= false;
-    }
-
-    /**
-     */
-    public void deleteMin(
-    ) {
-        this._has_min= false;
-    }
-
-    /**
-     */
-    public void deleteThreshold(
-    ) {
-        this._has_threshold= false;
-    }
-
-    /**
-     * Returns the value of field 'autoScale'.
-     * 
-     * @return the value of field 'AutoScale'.
-     */
-    public boolean getAutoScale(
-    ) {
-        return this._autoScale;
-    }
-
-    /**
-     * Returns the value of field 'colourByLabel'.
-     * 
-     * @return the value of field 'ColourByLabel'.
-     */
-    public boolean getColourByLabel(
-    ) {
-        return this._colourByLabel;
-    }
-
-    /**
-     * Returns the value of field 'max'.
-     * 
-     * @return the value of field 'Max'.
-     */
-    public float getMax(
-    ) {
-        return this._max;
-    }
-
-    /**
-     * Returns the value of field 'min'.
-     * 
-     * @return the value of field 'Min'.
-     */
-    public float getMin(
-    ) {
-        return this._min;
-    }
-
-    /**
-     * Returns the value of field 'minRGB'.
-     * 
-     * @return the value of field 'MinRGB'.
-     */
-    public java.lang.String getMinRGB(
-    ) {
-        return this._minRGB;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'RGB'.
-     * 
-     * @return the value of field 'RGB'.
-     */
-    public java.lang.String getRGB(
-    ) {
-        return this._RGB;
-    }
-
-    /**
-     * Returns the value of field 'threshType'. The field
-     * 'threshType' has the following description: loosely
-     * specified enumeration: NONE,ABOVE, or BELOW
-     * 
-     * @return the value of field 'ThreshType'.
-     */
-    public java.lang.String getThreshType(
-    ) {
-        return this._threshType;
-    }
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return the value of field 'Threshold'.
-     */
-    public float getThreshold(
-    ) {
-        return this._threshold;
-    }
-
-    /**
-     * Method hasAutoScale.
-     * 
-     * @return true if at least one AutoScale has been added
-     */
-    public boolean hasAutoScale(
-    ) {
-        return this._has_autoScale;
-    }
-
-    /**
-     * Method hasColourByLabel.
-     * 
-     * @return true if at least one ColourByLabel has been added
-     */
-    public boolean hasColourByLabel(
-    ) {
-        return this._has_colourByLabel;
-    }
-
-    /**
-     * Method hasMax.
-     * 
-     * @return true if at least one Max has been added
-     */
-    public boolean hasMax(
-    ) {
-        return this._has_max;
-    }
-
-    /**
-     * Method hasMin.
-     * 
-     * @return true if at least one Min has been added
-     */
-    public boolean hasMin(
-    ) {
-        return this._has_min;
-    }
-
-    /**
-     * Method hasThreshold.
-     * 
-     * @return true if at least one Threshold has been added
-     */
-    public boolean hasThreshold(
-    ) {
-        return this._has_threshold;
-    }
-
-    /**
-     * Returns the value of field 'autoScale'.
-     * 
-     * @return the value of field 'AutoScale'.
-     */
-    public boolean isAutoScale(
-    ) {
-        return this._autoScale;
-    }
-
-    /**
-     * Returns the value of field 'colourByLabel'.
-     * 
-     * @return the value of field 'ColourByLabel'.
-     */
-    public boolean isColourByLabel(
-    ) {
-        return this._colourByLabel;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'autoScale'.
-     * 
-     * @param autoScale the value of field 'autoScale'.
-     */
-    public void setAutoScale(
-            final boolean autoScale) {
-        this._autoScale = autoScale;
-        this._has_autoScale = true;
-    }
-
-    /**
-     * Sets the value of field 'colourByLabel'.
-     * 
-     * @param colourByLabel the value of field 'colourByLabel'.
-     */
-    public void setColourByLabel(
-            final boolean colourByLabel) {
-        this._colourByLabel = colourByLabel;
-        this._has_colourByLabel = true;
-    }
-
-    /**
-     * Sets the value of field 'max'.
-     * 
-     * @param max the value of field 'max'.
-     */
-    public void setMax(
-            final float max) {
-        this._max = max;
-        this._has_max = true;
-    }
-
-    /**
-     * Sets the value of field 'min'.
-     * 
-     * @param min the value of field 'min'.
-     */
-    public void setMin(
-            final float min) {
-        this._min = min;
-        this._has_min = true;
-    }
-
-    /**
-     * Sets the value of field 'minRGB'.
-     * 
-     * @param minRGB the value of field 'minRGB'.
-     */
-    public void setMinRGB(
-            final java.lang.String minRGB) {
-        this._minRGB = minRGB;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'RGB'.
-     * 
-     * @param RGB the value of field 'RGB'.
-     */
-    public void setRGB(
-            final java.lang.String RGB) {
-        this._RGB = RGB;
-    }
-
-    /**
-     * Sets the value of field 'threshType'. The field 'threshType'
-     * has the following description: loosely specified
-     * enumeration: NONE,ABOVE, or BELOW
-     * 
-     * @param threshType the value of field 'threshType'.
-     */
-    public void setThreshType(
-            final java.lang.String threshType) {
-        this._threshType = threshType;
-    }
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(
-            final float threshold) {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Colour
-     */
-    public static jalview.schemabinding.version2.Colour unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Colour implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _RGB.
+   */
+  private java.lang.String _RGB;
+
+  /**
+   * Field _minRGB.
+   */
+  private java.lang.String _minRGB;
+
+  /**
+   * loosely specified enumeration: NONE,ABOVE, or BELOW
+   */
+  private java.lang.String _threshType;
+
+  /**
+   * Field _threshold.
+   */
+  private float _threshold;
+
+  /**
+   * keeps track of state for field: _threshold
+   */
+  private boolean _has_threshold;
+
+  /**
+   * Field _max.
+   */
+  private float _max;
+
+  /**
+   * keeps track of state for field: _max
+   */
+  private boolean _has_max;
+
+  /**
+   * Field _min.
+   */
+  private float _min;
+
+  /**
+   * keeps track of state for field: _min
+   */
+  private boolean _has_min;
+
+  /**
+   * Field _colourByLabel.
+   */
+  private boolean _colourByLabel;
+
+  /**
+   * keeps track of state for field: _colourByLabel
+   */
+  private boolean _has_colourByLabel;
+
+  /**
+   * Field _autoScale.
+   */
+  private boolean _autoScale;
+
+  /**
+   * keeps track of state for field: _autoScale
+   */
+  private boolean _has_autoScale;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Colour()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteAutoScale()
+  {
+    this._has_autoScale = false;
+  }
+
+  /**
+     */
+  public void deleteColourByLabel()
+  {
+    this._has_colourByLabel = false;
+  }
+
+  /**
+     */
+  public void deleteMax()
+  {
+    this._has_max = false;
+  }
+
+  /**
+     */
+  public void deleteMin()
+  {
+    this._has_min = false;
+  }
+
+  /**
+     */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  }
+
+  /**
+   * Returns the value of field 'autoScale'.
+   * 
+   * @return the value of field 'AutoScale'.
+   */
+  public boolean getAutoScale()
+  {
+    return this._autoScale;
+  }
+
+  /**
+   * Returns the value of field 'colourByLabel'.
+   * 
+   * @return the value of field 'ColourByLabel'.
+   */
+  public boolean getColourByLabel()
+  {
+    return this._colourByLabel;
+  }
+
+  /**
+   * Returns the value of field 'max'.
+   * 
+   * @return the value of field 'Max'.
+   */
+  public float getMax()
+  {
+    return this._max;
+  }
+
+  /**
+   * Returns the value of field 'min'.
+   * 
+   * @return the value of field 'Min'.
+   */
+  public float getMin()
+  {
+    return this._min;
+  }
+
+  /**
+   * Returns the value of field 'minRGB'.
+   * 
+   * @return the value of field 'MinRGB'.
+   */
+  public java.lang.String getMinRGB()
+  {
+    return this._minRGB;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'RGB'.
+   * 
+   * @return the value of field 'RGB'.
+   */
+  public java.lang.String getRGB()
+  {
+    return this._RGB;
+  }
+
+  /**
+   * Returns the value of field 'threshType'. The field 'threshType' has the
+   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * 
+   * @return the value of field 'ThreshType'.
+   */
+  public java.lang.String getThreshType()
+  {
+    return this._threshType;
+  }
+
+  /**
+   * Returns the value of field 'threshold'.
+   * 
+   * @return the value of field 'Threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  }
+
+  /**
+   * Method hasAutoScale.
+   * 
+   * @return true if at least one AutoScale has been added
+   */
+  public boolean hasAutoScale()
+  {
+    return this._has_autoScale;
+  }
+
+  /**
+   * Method hasColourByLabel.
+   * 
+   * @return true if at least one ColourByLabel has been added
+   */
+  public boolean hasColourByLabel()
+  {
+    return this._has_colourByLabel;
+  }
+
+  /**
+   * Method hasMax.
+   * 
+   * @return true if at least one Max has been added
+   */
+  public boolean hasMax()
+  {
+    return this._has_max;
+  }
+
+  /**
+   * Method hasMin.
+   * 
+   * @return true if at least one Min has been added
+   */
+  public boolean hasMin()
+  {
+    return this._has_min;
+  }
+
+  /**
+   * Method hasThreshold.
+   * 
+   * @return true if at least one Threshold has been added
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  }
+
+  /**
+   * Returns the value of field 'autoScale'.
+   * 
+   * @return the value of field 'AutoScale'.
+   */
+  public boolean isAutoScale()
+  {
+    return this._autoScale;
+  }
+
+  /**
+   * Returns the value of field 'colourByLabel'.
+   * 
+   * @return the value of field 'ColourByLabel'.
+   */
+  public boolean isColourByLabel()
+  {
+    return this._colourByLabel;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'autoScale'.
+   * 
+   * @param autoScale
+   *          the value of field 'autoScale'.
+   */
+  public void setAutoScale(final boolean autoScale)
+  {
+    this._autoScale = autoScale;
+    this._has_autoScale = true;
+  }
+
+  /**
+   * Sets the value of field 'colourByLabel'.
+   * 
+   * @param colourByLabel
+   *          the value of field 'colourByLabel'.
+   */
+  public void setColourByLabel(final boolean colourByLabel)
+  {
+    this._colourByLabel = colourByLabel;
+    this._has_colourByLabel = true;
+  }
+
+  /**
+   * Sets the value of field 'max'.
+   * 
+   * @param max
+   *          the value of field 'max'.
+   */
+  public void setMax(final float max)
+  {
+    this._max = max;
+    this._has_max = true;
+  }
+
+  /**
+   * Sets the value of field 'min'.
+   * 
+   * @param min
+   *          the value of field 'min'.
+   */
+  public void setMin(final float min)
+  {
+    this._min = min;
+    this._has_min = true;
+  }
+
+  /**
+   * Sets the value of field 'minRGB'.
+   * 
+   * @param minRGB
+   *          the value of field 'minRGB'.
+   */
+  public void setMinRGB(final java.lang.String minRGB)
+  {
+    this._minRGB = minRGB;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'RGB'.
+   * 
+   * @param RGB
+   *          the value of field 'RGB'.
+   */
+  public void setRGB(final java.lang.String RGB)
+  {
+    this._RGB = RGB;
+  }
+
+  /**
+   * Sets the value of field 'threshType'. The field 'threshType' has the
+   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * 
+   * @param threshType
+   *          the value of field 'threshType'.
+   */
+  public void setThreshType(final java.lang.String threshType)
+  {
+    this._threshType = threshType;
+  }
+
+  /**
+   * Sets the value of field 'threshold'.
+   * 
+   * @param threshold
+   *          the value of field 'threshold'.
+   */
+  public void setThreshold(final float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Colour
+   */
+  public static jalview.schemabinding.version2.Colour unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Colour.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java
index 3917e13..85997ff 100644
--- a/src/jalview/schemabinding/version2/DBRef.java
+++ b/src/jalview/schemabinding/version2/DBRef.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,201 +19,215 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class DBRef implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _source.
-     */
-    private java.lang.String _source;
-
-    /**
-     * Field _version.
-     */
-    private java.lang.String _version;
-
-    /**
-     * Field _accessionId.
-     */
-    private java.lang.String _accessionId;
-
-    /**
-     * Field _mapping.
-     */
-    private jalview.schemabinding.version2.Mapping _mapping;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public DBRef() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'accessionId'.
-     * 
-     * @return the value of field 'AccessionId'.
-     */
-    public java.lang.String getAccessionId(
-    ) {
-        return this._accessionId;
-    }
-
-    /**
-     * Returns the value of field 'mapping'.
-     * 
-     * @return the value of field 'Mapping'.
-     */
-    public jalview.schemabinding.version2.Mapping getMapping(
-    ) {
-        return this._mapping;
-    }
-
-    /**
-     * Returns the value of field 'source'.
-     * 
-     * @return the value of field 'Source'.
-     */
-    public java.lang.String getSource(
-    ) {
-        return this._source;
-    }
-
-    /**
-     * Returns the value of field 'version'.
-     * 
-     * @return the value of field 'Version'.
-     */
-    public java.lang.String getVersion(
-    ) {
-        return this._version;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'accessionId'.
-     * 
-     * @param accessionId the value of field 'accessionId'.
-     */
-    public void setAccessionId(
-            final java.lang.String accessionId) {
-        this._accessionId = accessionId;
-    }
-
-    /**
-     * Sets the value of field 'mapping'.
-     * 
-     * @param mapping the value of field 'mapping'.
-     */
-    public void setMapping(
-            final jalview.schemabinding.version2.Mapping mapping) {
-        this._mapping = mapping;
-    }
-
-    /**
-     * Sets the value of field 'source'.
-     * 
-     * @param source the value of field 'source'.
-     */
-    public void setSource(
-            final java.lang.String source) {
-        this._source = source;
-    }
-
-    /**
-     * Sets the value of field 'version'.
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(
-            final java.lang.String version) {
-        this._version = version;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.DBRef
-     */
-    public static jalview.schemabinding.version2.DBRef unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class DBRef implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _source.
+   */
+  private java.lang.String _source;
+
+  /**
+   * Field _version.
+   */
+  private java.lang.String _version;
+
+  /**
+   * Field _accessionId.
+   */
+  private java.lang.String _accessionId;
+
+  /**
+   * Field _mapping.
+   */
+  private jalview.schemabinding.version2.Mapping _mapping;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public DBRef()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'accessionId'.
+   * 
+   * @return the value of field 'AccessionId'.
+   */
+  public java.lang.String getAccessionId()
+  {
+    return this._accessionId;
+  }
+
+  /**
+   * Returns the value of field 'mapping'.
+   * 
+   * @return the value of field 'Mapping'.
+   */
+  public jalview.schemabinding.version2.Mapping getMapping()
+  {
+    return this._mapping;
+  }
+
+  /**
+   * Returns the value of field 'source'.
+   * 
+   * @return the value of field 'Source'.
+   */
+  public java.lang.String getSource()
+  {
+    return this._source;
+  }
+
+  /**
+   * Returns the value of field 'version'.
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'accessionId'.
+   * 
+   * @param accessionId
+   *          the value of field 'accessionId'.
+   */
+  public void setAccessionId(final java.lang.String accessionId)
+  {
+    this._accessionId = accessionId;
+  }
+
+  /**
+   * Sets the value of field 'mapping'.
+   * 
+   * @param mapping
+   *          the value of field 'mapping'.
+   */
+  public void setMapping(
+          final jalview.schemabinding.version2.Mapping mapping)
+  {
+    this._mapping = mapping;
+  }
+
+  /**
+   * Sets the value of field 'source'.
+   * 
+   * @param source
+   *          the value of field 'source'.
+   */
+  public void setSource(final java.lang.String source)
+  {
+    this._source = source;
+  }
+
+  /**
+   * Sets the value of field 'version'.
+   * 
+   * @param version
+   *          the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.DBRef
+   */
+  public static jalview.schemabinding.version2.DBRef unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.DBRef.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java
index c1bbb25..9e484d5 100644
--- a/src/jalview/schemabinding/version2/Feature.java
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,501 +19,530 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Feature implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _begin.
-     */
-    private int _begin;
-
-    /**
-     * keeps track of state for field: _begin
-     */
-    private boolean _has_begin;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _status.
-     */
-    private java.lang.String _status;
-
-    /**
-     * Field _featureGroup.
-     */
-    private java.lang.String _featureGroup;
-
-    /**
-     * Field _score.
-     */
-    private float _score;
-
-    /**
-     * keeps track of state for field: _score
-     */
-    private boolean _has_score;
-
-    /**
-     * Field _otherDataList.
-     */
-    private java.util.Vector _otherDataList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Feature() {
-        super();
-        this._otherDataList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vOtherData
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addOtherData(
-            final jalview.schemabinding.version2.OtherData vOtherData)
-    throws java.lang.IndexOutOfBoundsException {
-        this._otherDataList.addElement(vOtherData);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vOtherData
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addOtherData(
-            final int index,
-            final jalview.schemabinding.version2.OtherData vOtherData)
-    throws java.lang.IndexOutOfBoundsException {
-        this._otherDataList.add(index, vOtherData);
-    }
-
-    /**
-     */
-    public void deleteBegin(
-    ) {
-        this._has_begin= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteScore(
-    ) {
-        this._has_score= false;
-    }
-
-    /**
-     * Method enumerateOtherData.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.OtherData elements
-     */
-    public java.util.Enumeration enumerateOtherData(
-    ) {
-        return this._otherDataList.elements();
-    }
-
-    /**
-     * Returns the value of field 'begin'.
-     * 
-     * @return the value of field 'Begin'.
-     */
-    public int getBegin(
-    ) {
-        return this._begin;
-    }
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'featureGroup'.
-     * 
-     * @return the value of field 'FeatureGroup'.
-     */
-    public java.lang.String getFeatureGroup(
-    ) {
-        return this._featureGroup;
-    }
-
-    /**
-     * Method getOtherData.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.OtherData at the given index
-     */
-    public jalview.schemabinding.version2.OtherData getOtherData(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._otherDataList.size()) {
-            throw new IndexOutOfBoundsException("getOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.OtherData) _otherDataList.get(index);
-    }
-
-    /**
-     * Method getOtherData.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.OtherData[] getOtherData(
-    ) {
-        jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];
-        return (jalview.schemabinding.version2.OtherData[]) this._otherDataList.toArray(array);
-    }
-
-    /**
-     * Method getOtherDataCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getOtherDataCount(
-    ) {
-        return this._otherDataList.size();
-    }
-
-    /**
-     * Returns the value of field 'score'.
-     * 
-     * @return the value of field 'Score'.
-     */
-    public float getScore(
-    ) {
-        return this._score;
-    }
-
-    /**
-     * Returns the value of field 'status'.
-     * 
-     * @return the value of field 'Status'.
-     */
-    public java.lang.String getStatus(
-    ) {
-        return this._status;
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method hasBegin.
-     * 
-     * @return true if at least one Begin has been added
-     */
-    public boolean hasBegin(
-    ) {
-        return this._has_begin;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasScore.
-     * 
-     * @return true if at least one Score has been added
-     */
-    public boolean hasScore(
-    ) {
-        return this._has_score;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllOtherData(
-    ) {
-        this._otherDataList.clear();
-    }
-
-    /**
-     * Method removeOtherData.
-     * 
-     * @param vOtherData
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeOtherData(
-            final jalview.schemabinding.version2.OtherData vOtherData) {
-        boolean removed = _otherDataList.remove(vOtherData);
-        return removed;
-    }
-
-    /**
-     * Method removeOtherDataAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.OtherData removeOtherDataAt(
-            final int index) {
-        java.lang.Object obj = this._otherDataList.remove(index);
-        return (jalview.schemabinding.version2.OtherData) obj;
-    }
-
-    /**
-     * Sets the value of field 'begin'.
-     * 
-     * @param begin the value of field 'begin'.
-     */
-    public void setBegin(
-            final int begin) {
-        this._begin = begin;
-        this._has_begin = true;
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'featureGroup'.
-     * 
-     * @param featureGroup the value of field 'featureGroup'.
-     */
-    public void setFeatureGroup(
-            final java.lang.String featureGroup) {
-        this._featureGroup = featureGroup;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vOtherData
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setOtherData(
-            final int index,
-            final jalview.schemabinding.version2.OtherData vOtherData)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._otherDataList.size()) {
-            throw new IndexOutOfBoundsException("setOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");
-        }
-        
-        this._otherDataList.set(index, vOtherData);
-    }
-
-    /**
-     * 
-     * 
-     * @param vOtherDataArray
-     */
-    public void setOtherData(
-            final jalview.schemabinding.version2.OtherData[] vOtherDataArray) {
-        //-- copy array
-        _otherDataList.clear();
-        
-        for (int i = 0; i < vOtherDataArray.length; i++) {
-                this._otherDataList.add(vOtherDataArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'score'.
-     * 
-     * @param score the value of field 'score'.
-     */
-    public void setScore(
-            final float score) {
-        this._score = score;
-        this._has_score = true;
-    }
-
-    /**
-     * Sets the value of field 'status'.
-     * 
-     * @param status the value of field 'status'.
-     */
-    public void setStatus(
-            final java.lang.String status) {
-        this._status = status;
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Featur
-     */
-    public static jalview.schemabinding.version2.Feature unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Feature implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _begin.
+   */
+  private int _begin;
+
+  /**
+   * keeps track of state for field: _begin
+   */
+  private boolean _has_begin;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _status.
+   */
+  private java.lang.String _status;
+
+  /**
+   * Field _featureGroup.
+   */
+  private java.lang.String _featureGroup;
+
+  /**
+   * Field _score.
+   */
+  private float _score;
+
+  /**
+   * keeps track of state for field: _score
+   */
+  private boolean _has_score;
+
+  /**
+   * Field _otherDataList.
+   */
+  private java.util.Vector _otherDataList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Feature()
+  {
+    super();
+    this._otherDataList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vOtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addOtherData(
+          final jalview.schemabinding.version2.OtherData vOtherData)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._otherDataList.addElement(vOtherData);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vOtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addOtherData(final int index,
+          final jalview.schemabinding.version2.OtherData vOtherData)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._otherDataList.add(index, vOtherData);
+  }
+
+  /**
+     */
+  public void deleteBegin()
+  {
+    this._has_begin = false;
+  }
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+     */
+  public void deleteScore()
+  {
+    this._has_score = false;
+  }
+
+  /**
+   * Method enumerateOtherData.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.OtherData
+   *         elements
+   */
+  public java.util.Enumeration enumerateOtherData()
+  {
+    return this._otherDataList.elements();
+  }
+
+  /**
+   * Returns the value of field 'begin'.
+   * 
+   * @return the value of field 'Begin'.
+   */
+  public int getBegin()
+  {
+    return this._begin;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'featureGroup'.
+   * 
+   * @return the value of field 'FeatureGroup'.
+   */
+  public java.lang.String getFeatureGroup()
+  {
+    return this._featureGroup;
+  }
+
+  /**
+   * Method getOtherData.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.OtherData at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.OtherData getOtherData(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._otherDataList.size())
+    {
+      throw new IndexOutOfBoundsException("getOtherData: Index value '"
+              + index + "' not in range [0.."
+              + (this._otherDataList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.OtherData) _otherDataList
+            .get(index);
+  }
+
+  /**
+   * Method getOtherData.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.OtherData[] getOtherData()
+  {
+    jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];
+    return (jalview.schemabinding.version2.OtherData[]) this._otherDataList
+            .toArray(array);
+  }
+
+  /**
+   * Method getOtherDataCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getOtherDataCount()
+  {
+    return this._otherDataList.size();
+  }
+
+  /**
+   * Returns the value of field 'score'.
+   * 
+   * @return the value of field 'Score'.
+   */
+  public float getScore()
+  {
+    return this._score;
+  }
+
+  /**
+   * Returns the value of field 'status'.
+   * 
+   * @return the value of field 'Status'.
+   */
+  public java.lang.String getStatus()
+  {
+    return this._status;
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method hasBegin.
+   * 
+   * @return true if at least one Begin has been added
+   */
+  public boolean hasBegin()
+  {
+    return this._has_begin;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasScore.
+   * 
+   * @return true if at least one Score has been added
+   */
+  public boolean hasScore()
+  {
+    return this._has_score;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllOtherData()
+  {
+    this._otherDataList.clear();
+  }
+
+  /**
+   * Method removeOtherData.
+   * 
+   * @param vOtherData
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeOtherData(
+          final jalview.schemabinding.version2.OtherData vOtherData)
+  {
+    boolean removed = _otherDataList.remove(vOtherData);
+    return removed;
+  }
+
+  /**
+   * Method removeOtherDataAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.OtherData removeOtherDataAt(
+          final int index)
+  {
+    java.lang.Object obj = this._otherDataList.remove(index);
+    return (jalview.schemabinding.version2.OtherData) obj;
+  }
+
+  /**
+   * Sets the value of field 'begin'.
+   * 
+   * @param begin
+   *          the value of field 'begin'.
+   */
+  public void setBegin(final int begin)
+  {
+    this._begin = begin;
+    this._has_begin = true;
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *          the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'featureGroup'.
+   * 
+   * @param featureGroup
+   *          the value of field 'featureGroup'.
+   */
+  public void setFeatureGroup(final java.lang.String featureGroup)
+  {
+    this._featureGroup = featureGroup;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vOtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setOtherData(final int index,
+          final jalview.schemabinding.version2.OtherData vOtherData)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._otherDataList.size())
+    {
+      throw new IndexOutOfBoundsException("setOtherData: Index value '"
+              + index + "' not in range [0.."
+              + (this._otherDataList.size() - 1) + "]");
+    }
+
+    this._otherDataList.set(index, vOtherData);
+  }
+
+  /**
+   * 
+   * 
+   * @param vOtherDataArray
+   */
+  public void setOtherData(
+          final jalview.schemabinding.version2.OtherData[] vOtherDataArray)
+  {
+    // -- copy array
+    _otherDataList.clear();
+
+    for (int i = 0; i < vOtherDataArray.length; i++)
+    {
+      this._otherDataList.add(vOtherDataArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'score'.
+   * 
+   * @param score
+   *          the value of field 'score'.
+   */
+  public void setScore(final float score)
+  {
+    this._score = score;
+    this._has_score = true;
+  }
+
+  /**
+   * Sets the value of field 'status'.
+   * 
+   * @param status
+   *          the value of field 'status'.
+   */
+  public void setStatus(final java.lang.String status)
+  {
+    this._status = status;
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *          the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Featur
+   */
+  public static jalview.schemabinding.version2.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Feature.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java
index 19c567c..fa75e76 100644
--- a/src/jalview/schemabinding/version2/FeatureSettings.java
+++ b/src/jalview/schemabinding/version2/FeatureSettings.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,414 +19,444 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class FeatureSettings implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _settingList.
-     */
-    private java.util.Vector _settingList;
-
-    /**
-     * Field _groupList.
-     */
-    private java.util.Vector _groupList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeatureSettings() {
-        super();
-        this._settingList = new java.util.Vector();
-        this._groupList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addGroup(
-            final jalview.schemabinding.version2.Group vGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._groupList.addElement(vGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addGroup(
-            final int index,
-            final jalview.schemabinding.version2.Group vGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._groupList.add(index, vGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final jalview.schemabinding.version2.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.addElement(vSetting);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final int index,
-            final jalview.schemabinding.version2.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.add(index, vSetting);
-    }
-
-    /**
-     * Method enumerateGroup.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Group elements
-     */
-    public java.util.Enumeration enumerateGroup(
-    ) {
-        return this._groupList.elements();
-    }
-
-    /**
-     * Method enumerateSetting.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Setting elements
-     */
-    public java.util.Enumeration enumerateSetting(
-    ) {
-        return this._settingList.elements();
-    }
-
-    /**
-     * Method getGroup.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Group at the given index
-     */
-    public jalview.schemabinding.version2.Group getGroup(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._groupList.size()) {
-            throw new IndexOutOfBoundsException("getGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Group) _groupList.get(index);
-    }
-
-    /**
-     * Method getGroup.Returns the contents of the collection in an
-     * Array.  
Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Group[] getGroup(
-    ) {
-        jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];
-        return (jalview.schemabinding.version2.Group[]) this._groupList.toArray(array);
-    }
-
-    /**
-     * Method getGroupCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getGroupCount(
-    ) {
-        return this._groupList.size();
-    }
-
-    /**
-     * Method getSetting.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Setting at the given index
-     */
-    public jalview.schemabinding.version2.Setting getSetting(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Setting) _settingList.get(index);
-    }
-
-    /**
-     * Method getSetting.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Setting[] getSetting(
-    ) {
-        jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];
-        return (jalview.schemabinding.version2.Setting[]) this._settingList.toArray(array);
-    }
-
-    /**
-     * Method getSettingCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSettingCount(
-    ) {
-        return this._settingList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllGroup(
-    ) {
-        this._groupList.clear();
+public class FeatureSettings implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _settingList.
+   */
+  private java.util.Vector _settingList;
+
+  /**
+   * Field _groupList.
+   */
+  private java.util.Vector _groupList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureSettings()
+  {
+    super();
+    this._settingList = new java.util.Vector();
+    this._groupList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addGroup(final jalview.schemabinding.version2.Group vGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._groupList.addElement(vGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addGroup(final int index,
+          final jalview.schemabinding.version2.Group vGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._groupList.add(index, vGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSetting(
+          final jalview.schemabinding.version2.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.addElement(vSetting);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSetting(final int index,
+          final jalview.schemabinding.version2.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.add(index, vSetting);
+  }
+
+  /**
+   * Method enumerateGroup.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Group
+   *         elements
+   */
+  public java.util.Enumeration enumerateGroup()
+  {
+    return this._groupList.elements();
+  }
+
+  /**
+   * Method enumerateSetting.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Setting
+   *         elements
+   */
+  public java.util.Enumeration enumerateSetting()
+  {
+    return this._settingList.elements();
+  }
+
+  /**
+   * Method getGroup.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Group at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.Group getGroup(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._groupList.size())
+    {
+      throw new IndexOutOfBoundsException("getGroup: Index value '" + index
+              + "' not in range [0.." + (this._groupList.size() - 1) + "]");
     }
 
-    /**
-     */
-    public void removeAllSetting(
-    ) {
-        this._settingList.clear();
-    }
-
-    /**
-     * Method removeGroup.
-     * 
-     * @param vGroup
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeGroup(
-            final jalview.schemabinding.version2.Group vGroup) {
-        boolean removed = _groupList.remove(vGroup);
-        return removed;
-    }
-
-    /**
-     * Method removeGroupAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Group removeGroupAt(
-            final int index) {
-        java.lang.Object obj = this._groupList.remove(index);
-        return (jalview.schemabinding.version2.Group) obj;
-    }
-
-    /**
-     * Method removeSetting.
-     * 
-     * @param vSetting
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSetting(
-            final jalview.schemabinding.version2.Setting vSetting) {
-        boolean removed = _settingList.remove(vSetting);
-        return removed;
+    return (jalview.schemabinding.version2.Group) _groupList.get(index);
+  }
+
+  /**
+   * Method getGroup.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Group[] getGroup()
+  {
+    jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];
+    return (jalview.schemabinding.version2.Group[]) this._groupList
+            .toArray(array);
+  }
+
+  /**
+   * Method getGroupCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getGroupCount()
+  {
+    return this._groupList.size();
+  }
+
+  /**
+   * Method getSetting.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Setting at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Setting getSetting(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("getSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeSettingAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Setting removeSettingAt(
-            final int index) {
-        java.lang.Object obj = this._settingList.remove(index);
-        return (jalview.schemabinding.version2.Setting) obj;
+    return (jalview.schemabinding.version2.Setting) _settingList.get(index);
+  }
+
+  /**
+   * Method getSetting.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Setting[] getSetting()
+  {
+    jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];
+    return (jalview.schemabinding.version2.Setting[]) this._settingList
+            .toArray(array);
+  }
+
+  /**
+   * Method getSettingCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSettingCount()
+  {
+    return this._settingList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setGroup(
-            final int index,
-            final jalview.schemabinding.version2.Group vGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._groupList.size()) {
-            throw new IndexOutOfBoundsException("setGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]");
-        }
-        
-        this._groupList.set(index, vGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vGroupArray
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
      */
-    public void setGroup(
-            final jalview.schemabinding.version2.Group[] vGroupArray) {
-        //-- copy array
-        _groupList.clear();
-        
-        for (int i = 0; i < vGroupArray.length; i++) {
-                this._groupList.add(vGroupArray[i]);
-        }
-    }
+  public void removeAllGroup()
+  {
+    this._groupList.clear();
+  }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
+  /**
      */
-    public void setSetting(
-            final int index,
-            final jalview.schemabinding.version2.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        this._settingList.set(index, vSetting);
+  public void removeAllSetting()
+  {
+    this._settingList.clear();
+  }
+
+  /**
+   * Method removeGroup.
+   * 
+   * @param vGroup
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeGroup(
+          final jalview.schemabinding.version2.Group vGroup)
+  {
+    boolean removed = _groupList.remove(vGroup);
+    return removed;
+  }
+
+  /**
+   * Method removeGroupAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Group removeGroupAt(final int index)
+  {
+    java.lang.Object obj = this._groupList.remove(index);
+    return (jalview.schemabinding.version2.Group) obj;
+  }
+
+  /**
+   * Method removeSetting.
+   * 
+   * @param vSetting
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSetting(
+          final jalview.schemabinding.version2.Setting vSetting)
+  {
+    boolean removed = _settingList.remove(vSetting);
+    return removed;
+  }
+
+  /**
+   * Method removeSettingAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Setting removeSettingAt(
+          final int index)
+  {
+    java.lang.Object obj = this._settingList.remove(index);
+    return (jalview.schemabinding.version2.Setting) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setGroup(final int index,
+          final jalview.schemabinding.version2.Group vGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._groupList.size())
+    {
+      throw new IndexOutOfBoundsException("setGroup: Index value '" + index
+              + "' not in range [0.." + (this._groupList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param vSettingArray
-     */
-    public void setSetting(
-            final jalview.schemabinding.version2.Setting[] vSettingArray) {
-        //-- copy array
-        _settingList.clear();
-        
-        for (int i = 0; i < vSettingArray.length; i++) {
-                this._settingList.add(vSettingArray[i]);
-        }
+    this._groupList.set(index, vGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vGroupArray
+   */
+  public void setGroup(
+          final jalview.schemabinding.version2.Group[] vGroupArray)
+  {
+    // -- copy array
+    _groupList.clear();
+
+    for (int i = 0; i < vGroupArray.length; i++)
+    {
+      this._groupList.add(vGroupArray[i]);
     }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.FeatureSettings
-     */
-    public static jalview.schemabinding.version2.FeatureSettings unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSetting(final int index,
+          final jalview.schemabinding.version2.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("setSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._settingList.set(index, vSetting);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSettingArray
+   */
+  public void setSetting(
+          final jalview.schemabinding.version2.Setting[] vSettingArray)
+  {
+    // -- copy array
+    _settingList.clear();
+
+    for (int i = 0; i < vSettingArray.length; i++)
+    {
+      this._settingList.add(vSettingArray[i]);
     }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.FeatureSettings
+   */
+  public static jalview.schemabinding.version2.FeatureSettings unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.FeatureSettings.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java
index f0c5ad5..5d17512 100644
--- a/src/jalview/schemabinding/version2/Features.java
+++ b/src/jalview/schemabinding/version2/Features.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,98 +19,106 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Features extends Feature 
-implements java.io.Serializable
+public class Features extends Feature implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Features() {
-        super();
-    }
-
+  public Features()
+  {
+    super();
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Featur
-     */
-    public static jalview.schemabinding.version2.Feature unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Featur
+   */
+  public static jalview.schemabinding.version2.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Features.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Group.java b/src/jalview/schemabinding/version2/Group.java
index 774321b..ec1af95 100644
--- a/src/jalview/schemabinding/version2/Group.java
+++ b/src/jalview/schemabinding/version2/Group.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,184 +19,195 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Group implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _display.
-     */
-    private boolean _display;
-
-    /**
-     * keeps track of state for field: _display
-     */
-    private boolean _has_display;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Group() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteDisplay(
-    ) {
-        this._has_display= false;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean getDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Method hasDisplay.
-     * 
-     * @return true if at least one Display has been added
-     */
-    public boolean hasDisplay(
-    ) {
-        return this._has_display;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean isDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'display'.
-     * 
-     * @param display the value of field 'display'.
-     */
-    public void setDisplay(
-            final boolean display) {
-        this._display = display;
-        this._has_display = true;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Group
-     */
-    public static jalview.schemabinding.version2.Group unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(jalview.schemabinding.version2.Group.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+public class Group implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _display.
+   */
+  private boolean _display;
+
+  /**
+   * keeps track of state for field: _display
+   */
+  private boolean _has_display;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Group()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
      */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+  public void deleteDisplay()
+  {
+    this._has_display = false;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean getDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Method hasDisplay.
+   * 
+   * @return true if at least one Display has been added
+   */
+  public boolean hasDisplay()
+  {
+    return this._has_display;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean isDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'display'.
+   * 
+   * @param display
+   *          the value of field 'display'.
+   */
+  public void setDisplay(final boolean display)
+  {
+    this._display = display;
+    this._has_display = true;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Group
+   */
+  public static jalview.schemabinding.version2.Group unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Group.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java
index f65c9de..beac4e0 100644
--- a/src/jalview/schemabinding/version2/HiddenColumns.java
+++ b/src/jalview/schemabinding/version2/HiddenColumns.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,198 +19,209 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class HiddenColumns implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public HiddenColumns() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.HiddenColumns
-     */
-    public static jalview.schemabinding.version2.HiddenColumns unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class HiddenColumns implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public HiddenColumns()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+     */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *          the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.HiddenColumns
+   */
+  public static jalview.schemabinding.version2.HiddenColumns unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.HiddenColumns.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 602473f..962569f 100644
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,1224 +19,1242 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JGroup implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _colour.
-     */
-    private java.lang.String _colour;
-
-    /**
-     * Field _consThreshold.
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold.
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _outlineColour.
-     */
-    private int _outlineColour;
-
-    /**
-     * keeps track of state for field: _outlineColour
-     */
-    private boolean _has_outlineColour;
-
-    /**
-     * Field _displayBoxes.
-     */
-    private boolean _displayBoxes;
-
-    /**
-     * keeps track of state for field: _displayBoxes
-     */
-    private boolean _has_displayBoxes;
-
-    /**
-     * Field _displayText.
-     */
-    private boolean _displayText;
-
-    /**
-     * keeps track of state for field: _displayText
-     */
-    private boolean _has_displayText;
-
-    /**
-     * Field _colourText.
-     */
-    private boolean _colourText;
-
-    /**
-     * keeps track of state for field: _colourText
-     */
-    private boolean _has_colourText;
-
-    /**
-     * Field _textCol1.
-     */
-    private int _textCol1;
-
-    /**
-     * keeps track of state for field: _textCol1
-     */
-    private boolean _has_textCol1;
-
-    /**
-     * Field _textCol2.
-     */
-    private int _textCol2;
-
-    /**
-     * keeps track of state for field: _textCol2
-     */
-    private boolean _has_textCol2;
-
-    /**
-     * Field _textColThreshold.
-     */
-    private int _textColThreshold;
-
-    /**
-     * keeps track of state for field: _textColThreshold
-     */
-    private boolean _has_textColThreshold;
-
-    /**
-     * Field _showUnconserved.
-     */
-    private boolean _showUnconserved;
-
-    /**
-     * keeps track of state for field: _showUnconserved
-     */
-    private boolean _has_showUnconserved;
-
-    /**
-     * Field _ignoreGapsinConsensus.
-     */
-    private boolean _ignoreGapsinConsensus = true;
-
-    /**
-     * keeps track of state for field: _ignoreGapsinConsensus
-     */
-    private boolean _has_ignoreGapsinConsensus;
-
-    /**
-     * Field _showConsensusHistogram.
-     */
-    private boolean _showConsensusHistogram = true;
-
-    /**
-     * keeps track of state for field: _showConsensusHistogram
-     */
-    private boolean _has_showConsensusHistogram;
-
-    /**
-     * Field _showSequenceLogo.
-     */
-    private boolean _showSequenceLogo = false;
-
-    /**
-     * keeps track of state for field: _showSequenceLogo
-     */
-    private boolean _has_showSequenceLogo;
-
-    /**
-     * Field _normaliseSequenceLogo.
-     */
-    private boolean _normaliseSequenceLogo = false;
-
-    /**
-     * keeps track of state for field: _normaliseSequenceLogo
-     */
-    private boolean _has_normaliseSequenceLogo;
-
-    /**
-     * Optional sequence group ID (only
-     *  needs to be
-     *  unique for this
-     *  alignment)
-     *  
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _seqList.
-     */
-    private java.util.Vector _seqList;
-
-    /**
-     * Field _annotationColours.
-     */
-    private jalview.schemabinding.version2.AnnotationColours _annotationColours;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JGroup() {
-        super();
-        this._seqList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeq(
-            final java.lang.String vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._seqList.addElement(vSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSeq(
-            final int index,
-            final java.lang.String vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._seqList.add(index, vSeq);
-    }
-
-    /**
-     */
-    public void deleteColourText(
-    ) {
-        this._has_colourText= false;
-    }
-
-    /**
-     */
-    public void deleteConsThreshold(
-    ) {
-        this._has_consThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteDisplayBoxes(
-    ) {
-        this._has_displayBoxes= false;
-    }
-
-    /**
-     */
-    public void deleteDisplayText(
-    ) {
-        this._has_displayText= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteIgnoreGapsinConsensus(
-    ) {
-        this._has_ignoreGapsinConsensus= false;
-    }
-
-    /**
-     */
-    public void deleteNormaliseSequenceLogo(
-    ) {
-        this._has_normaliseSequenceLogo= false;
-    }
-
-    /**
-     */
-    public void deleteOutlineColour(
-    ) {
-        this._has_outlineColour= false;
-    }
-
-    /**
-     */
-    public void deletePidThreshold(
-    ) {
-        this._has_pidThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteShowConsensusHistogram(
-    ) {
-        this._has_showConsensusHistogram= false;
-    }
-
-    /**
-     */
-    public void deleteShowSequenceLogo(
-    ) {
-        this._has_showSequenceLogo= false;
-    }
-
-    /**
-     */
-    public void deleteShowUnconserved(
-    ) {
-        this._has_showUnconserved= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     */
-    public void deleteTextCol1(
-    ) {
-        this._has_textCol1= false;
-    }
-
-    /**
-     */
-    public void deleteTextCol2(
-    ) {
-        this._has_textCol2= false;
-    }
-
-    /**
-     */
-    public void deleteTextColThreshold(
-    ) {
-        this._has_textColThreshold= false;
-    }
-
-    /**
-     * Method enumerateSeq.
-     * 
-     * @return an Enumeration over all java.lang.String elements
-     */
-    public java.util.Enumeration enumerateSeq(
-    ) {
-        return this._seqList.elements();
-    }
-
-    /**
-     * Returns the value of field 'annotationColours'.
-     * 
-     * @return the value of field 'AnnotationColours'.
-     */
-    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
-    ) {
-        return this._annotationColours;
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public java.lang.String getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return the value of field 'ColourText'.
-     */
-    public boolean getColourText(
-    ) {
-        return this._colourText;
-    }
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return the value of field 'ConsThreshold'.
-     */
-    public int getConsThreshold(
-    ) {
-        return this._consThreshold;
-    }
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return the value of field 'DisplayBoxes'.
-     */
-    public boolean getDisplayBoxes(
-    ) {
-        return this._displayBoxes;
-    }
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return the value of field 'DisplayText'.
-     */
-    public boolean getDisplayText(
-    ) {
-        return this._displayText;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'id'. The field 'id' has the
-     * following description: Optional sequence group ID (only
-     *  needs to be
-     *  unique for this
-     *  alignment)
-     *  
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'ignoreGapsinConsensus'.
-     * 
-     * @return the value of field 'IgnoreGapsinConsensus'.
-     */
-    public boolean getIgnoreGapsinConsensus(
-    ) {
-        return this._ignoreGapsinConsensus;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'normaliseSequenceLogo'.
-     * 
-     * @return the value of field 'NormaliseSequenceLogo'.
-     */
-    public boolean getNormaliseSequenceLogo(
-    ) {
-        return this._normaliseSequenceLogo;
-    }
-
-    /**
-     * Returns the value of field 'outlineColour'.
-     * 
-     * @return the value of field 'OutlineColour'.
-     */
-    public int getOutlineColour(
-    ) {
-        return this._outlineColour;
-    }
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return the value of field 'PidThreshold'.
-     */
-    public int getPidThreshold(
-    ) {
-        return this._pidThreshold;
-    }
-
-    /**
-     * Method getSeq.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the java.lang.String at the given index
-     */
-    public java.lang.String getSeq(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._seqList.size()) {
-            throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
-        }
-        
-        return (java.lang.String) _seqList.get(index);
-    }
-
-    /**
-     * Method getSeq.Returns the contents of the collection in an
-     * Array.  
Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public java.lang.String[] getSeq(
-    ) {
-        java.lang.String[] array = new java.lang.String[0];
-        return (java.lang.String[]) this._seqList.toArray(array);
-    }
-
-    /**
-     * Method getSeqCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSeqCount(
-    ) {
-        return this._seqList.size();
-    }
-
-    /**
-     * Returns the value of field 'showConsensusHistogram'.
-     * 
-     * @return the value of field 'ShowConsensusHistogram'.
-     */
-    public boolean getShowConsensusHistogram(
-    ) {
-        return this._showConsensusHistogram;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceLogo'.
-     * 
-     * @return the value of field 'ShowSequenceLogo'.
-     */
-    public boolean getShowSequenceLogo(
-    ) {
-        return this._showSequenceLogo;
-    }
-
-    /**
-     * Returns the value of field 'showUnconserved'.
-     * 
-     * @return the value of field 'ShowUnconserved'.
-     */
-    public boolean getShowUnconserved(
-    ) {
-        return this._showUnconserved;
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Returns the value of field 'textCol1'.
-     * 
-     * @return the value of field 'TextCol1'.
-     */
-    public int getTextCol1(
-    ) {
-        return this._textCol1;
-    }
-
-    /**
-     * Returns the value of field 'textCol2'.
-     * 
-     * @return the value of field 'TextCol2'.
-     */
-    public int getTextCol2(
-    ) {
-        return this._textCol2;
-    }
-
-    /**
-     * Returns the value of field 'textColThreshold'.
-     * 
-     * @return the value of field 'TextColThreshold'.
-     */
-    public int getTextColThreshold(
-    ) {
-        return this._textColThreshold;
-    }
-
-    /**
-     * Method hasColourText.
-     * 
-     * @return true if at least one ColourText has been added
-     */
-    public boolean hasColourText(
-    ) {
-        return this._has_colourText;
-    }
-
-    /**
-     * Method hasConsThreshold.
-     * 
-     * @return true if at least one ConsThreshold has been added
-     */
-    public boolean hasConsThreshold(
-    ) {
-        return this._has_consThreshold;
-    }
-
-    /**
-     * Method hasDisplayBoxes.
-     * 
-     * @return true if at least one DisplayBoxes has been added
-     */
-    public boolean hasDisplayBoxes(
-    ) {
-        return this._has_displayBoxes;
-    }
-
-    /**
-     * Method hasDisplayText.
-     * 
-     * @return true if at least one DisplayText has been added
-     */
-    public boolean hasDisplayText(
-    ) {
-        return this._has_displayText;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasIgnoreGapsinConsensus.
-     * 
-     * @return true if at least one IgnoreGapsinConsensus has been
-     * added
-     */
-    public boolean hasIgnoreGapsinConsensus(
-    ) {
-        return this._has_ignoreGapsinConsensus;
-    }
-
-    /**
-     * Method hasNormaliseSequenceLogo.
-     * 
-     * @return true if at least one NormaliseSequenceLogo has been
-     * added
-     */
-    public boolean hasNormaliseSequenceLogo(
-    ) {
-        return this._has_normaliseSequenceLogo;
-    }
-
-    /**
-     * Method hasOutlineColour.
-     * 
-     * @return true if at least one OutlineColour has been added
-     */
-    public boolean hasOutlineColour(
-    ) {
-        return this._has_outlineColour;
-    }
-
-    /**
-     * Method hasPidThreshold.
-     * 
-     * @return true if at least one PidThreshold has been added
-     */
-    public boolean hasPidThreshold(
-    ) {
-        return this._has_pidThreshold;
-    }
-
-    /**
-     * Method hasShowConsensusHistogram.
-     * 
-     * @return true if at least one ShowConsensusHistogram has been
-     * added
-     */
-    public boolean hasShowConsensusHistogram(
-    ) {
-        return this._has_showConsensusHistogram;
-    }
-
-    /**
-     * Method hasShowSequenceLogo.
-     * 
-     * @return true if at least one ShowSequenceLogo has been added
-     */
-    public boolean hasShowSequenceLogo(
-    ) {
-        return this._has_showSequenceLogo;
-    }
-
-    /**
-     * Method hasShowUnconserved.
-     * 
-     * @return true if at least one ShowUnconserved has been added
-     */
-    public boolean hasShowUnconserved(
-    ) {
-        return this._has_showUnconserved;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method hasTextCol1.
-     * 
-     * @return true if at least one TextCol1 has been added
-     */
-    public boolean hasTextCol1(
-    ) {
-        return this._has_textCol1;
-    }
-
-    /**
-     * Method hasTextCol2.
-     * 
-     * @return true if at least one TextCol2 has been added
-     */
-    public boolean hasTextCol2(
-    ) {
-        return this._has_textCol2;
-    }
-
-    /**
-     * Method hasTextColThreshold.
-     * 
-     * @return true if at least one TextColThreshold has been added
-     */
-    public boolean hasTextColThreshold(
-    ) {
-        return this._has_textColThreshold;
-    }
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return the value of field 'ColourText'.
-     */
-    public boolean isColourText(
-    ) {
-        return this._colourText;
-    }
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return the value of field 'DisplayBoxes'.
-     */
-    public boolean isDisplayBoxes(
-    ) {
-        return this._displayBoxes;
-    }
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return the value of field 'DisplayText'.
-     */
-    public boolean isDisplayText(
-    ) {
-        return this._displayText;
-    }
-
-    /**
-     * Returns the value of field 'ignoreGapsinConsensus'.
-     * 
-     * @return the value of field 'IgnoreGapsinConsensus'.
-     */
-    public boolean isIgnoreGapsinConsensus(
-    ) {
-        return this._ignoreGapsinConsensus;
-    }
-
-    /**
-     * Returns the value of field 'normaliseSequenceLogo'.
-     * 
-     * @return the value of field 'NormaliseSequenceLogo'.
-     */
-    public boolean isNormaliseSequenceLogo(
-    ) {
-        return this._normaliseSequenceLogo;
-    }
-
-    /**
-     * Returns the value of field 'showConsensusHistogram'.
-     * 
-     * @return the value of field 'ShowConsensusHistogram'.
-     */
-    public boolean isShowConsensusHistogram(
-    ) {
-        return this._showConsensusHistogram;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceLogo'.
-     * 
-     * @return the value of field 'ShowSequenceLogo'.
-     */
-    public boolean isShowSequenceLogo(
-    ) {
-        return this._showSequenceLogo;
-    }
-
-    /**
-     * Returns the value of field 'showUnconserved'.
-     * 
-     * @return the value of field 'ShowUnconserved'.
-     */
-    public boolean isShowUnconserved(
-    ) {
-        return this._showUnconserved;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllSeq(
-    ) {
-        this._seqList.clear();
-    }
-
-    /**
-     * Method removeSeq.
-     * 
-     * @param vSeq
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSeq(
-            final java.lang.String vSeq) {
-        boolean removed = _seqList.remove(vSeq);
-        return removed;
-    }
-
-    /**
-     * Method removeSeqAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public java.lang.String removeSeqAt(
-            final int index) {
-        java.lang.Object obj = this._seqList.remove(index);
-        return (java.lang.String) obj;
-    }
-
-    /**
-     * Sets the value of field 'annotationColours'.
-     * 
-     * @param annotationColours the value of field
-     * 'annotationColours'.
-     */
-    public void setAnnotationColours(
-            final jalview.schemabinding.version2.AnnotationColours annotationColours) {
-        this._annotationColours = annotationColours;
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final java.lang.String colour) {
-        this._colour = colour;
-    }
-
-    /**
-     * Sets the value of field 'colourText'.
-     * 
-     * @param colourText the value of field 'colourText'.
-     */
-    public void setColourText(
-            final boolean colourText) {
-        this._colourText = colourText;
-        this._has_colourText = true;
-    }
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(
-            final int consThreshold) {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'displayBoxes'.
-     * 
-     * @param displayBoxes the value of field 'displayBoxes'.
-     */
-    public void setDisplayBoxes(
-            final boolean displayBoxes) {
-        this._displayBoxes = displayBoxes;
-        this._has_displayBoxes = true;
-    }
-
-    /**
-     * Sets the value of field 'displayText'.
-     * 
-     * @param displayText the value of field 'displayText'.
-     */
-    public void setDisplayText(
-            final boolean displayText) {
-        this._displayText = displayText;
-        this._has_displayText = true;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'id'. The field 'id' has the
-     * following description: Optional sequence group ID (only
-     *  needs to be
-     *  unique for this
-     *  alignment)
-     *  
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'ignoreGapsinConsensus'.
-     * 
-     * @param ignoreGapsinConsensus the value of field
-     * 'ignoreGapsinConsensus'.
-     */
-    public void setIgnoreGapsinConsensus(
-            final boolean ignoreGapsinConsensus) {
-        this._ignoreGapsinConsensus = ignoreGapsinConsensus;
-        this._has_ignoreGapsinConsensus = true;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'normaliseSequenceLogo'.
-     * 
-     * @param normaliseSequenceLogo the value of field
-     * 'normaliseSequenceLogo'.
-     */
-    public void setNormaliseSequenceLogo(
-            final boolean normaliseSequenceLogo) {
-        this._normaliseSequenceLogo = normaliseSequenceLogo;
-        this._has_normaliseSequenceLogo = true;
-    }
-
-    /**
-     * Sets the value of field 'outlineColour'.
-     * 
-     * @param outlineColour the value of field 'outlineColour'.
-     */
-    public void setOutlineColour(
-            final int outlineColour) {
-        this._outlineColour = outlineColour;
-        this._has_outlineColour = true;
-    }
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(
-            final int pidThreshold) {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSeq(
-            final int index,
-            final java.lang.String vSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._seqList.size()) {
-            throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
-        }
-        
-        this._seqList.set(index, vSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSeqArray
-     */
-    public void setSeq(
-            final java.lang.String[] vSeqArray) {
-        //-- copy array
-        _seqList.clear();
-        
-        for (int i = 0; i < vSeqArray.length; i++) {
-                this._seqList.add(vSeqArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'showConsensusHistogram'.
-     * 
-     * @param showConsensusHistogram the value of field
-     * 'showConsensusHistogram'.
-     */
-    public void setShowConsensusHistogram(
-            final boolean showConsensusHistogram) {
-        this._showConsensusHistogram = showConsensusHistogram;
-        this._has_showConsensusHistogram = true;
-    }
-
-    /**
-     * Sets the value of field 'showSequenceLogo'.
-     * 
-     * @param showSequenceLogo the value of field 'showSequenceLogo'
-     */
-    public void setShowSequenceLogo(
-            final boolean showSequenceLogo) {
-        this._showSequenceLogo = showSequenceLogo;
-        this._has_showSequenceLogo = true;
-    }
-
-    /**
-     * Sets the value of field 'showUnconserved'.
-     * 
-     * @param showUnconserved the value of field 'showUnconserved'.
-     */
-    public void setShowUnconserved(
-            final boolean showUnconserved) {
-        this._showUnconserved = showUnconserved;
-        this._has_showUnconserved = true;
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Sets the value of field 'textCol1'.
-     * 
-     * @param textCol1 the value of field 'textCol1'.
-     */
-    public void setTextCol1(
-            final int textCol1) {
-        this._textCol1 = textCol1;
-        this._has_textCol1 = true;
-    }
-
-    /**
-     * Sets the value of field 'textCol2'.
-     * 
-     * @param textCol2 the value of field 'textCol2'.
-     */
-    public void setTextCol2(
-            final int textCol2) {
-        this._textCol2 = textCol2;
-        this._has_textCol2 = true;
-    }
-
-    /**
-     * Sets the value of field 'textColThreshold'.
-     * 
-     * @param textColThreshold the value of field 'textColThreshold'
-     */
-    public void setTextColThreshold(
-            final int textColThreshold) {
-        this._textColThreshold = textColThreshold;
-        this._has_textColThreshold = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.JGroup
-     */
-    public static jalview.schemabinding.version2.JGroup unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JGroup implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _colour.
+   */
+  private java.lang.String _colour;
+
+  /**
+   * Field _consThreshold.
+   */
+  private int _consThreshold;
+
+  /**
+   * keeps track of state for field: _consThreshold
+   */
+  private boolean _has_consThreshold;
+
+  /**
+   * Field _pidThreshold.
+   */
+  private int _pidThreshold;
+
+  /**
+   * keeps track of state for field: _pidThreshold
+   */
+  private boolean _has_pidThreshold;
+
+  /**
+   * Field _outlineColour.
+   */
+  private int _outlineColour;
+
+  /**
+   * keeps track of state for field: _outlineColour
+   */
+  private boolean _has_outlineColour;
+
+  /**
+   * Field _displayBoxes.
+   */
+  private boolean _displayBoxes;
+
+  /**
+   * keeps track of state for field: _displayBoxes
+   */
+  private boolean _has_displayBoxes;
+
+  /**
+   * Field _displayText.
+   */
+  private boolean _displayText;
+
+  /**
+   * keeps track of state for field: _displayText
+   */
+  private boolean _has_displayText;
+
+  /**
+   * Field _colourText.
+   */
+  private boolean _colourText;
+
+  /**
+   * keeps track of state for field: _colourText
+   */
+  private boolean _has_colourText;
+
+  /**
+   * Field _textCol1.
+   */
+  private int _textCol1;
+
+  /**
+   * keeps track of state for field: _textCol1
+   */
+  private boolean _has_textCol1;
+
+  /**
+   * Field _textCol2.
+   */
+  private int _textCol2;
+
+  /**
+   * keeps track of state for field: _textCol2
+   */
+  private boolean _has_textCol2;
+
+  /**
+   * Field _textColThreshold.
+   */
+  private int _textColThreshold;
+
+  /**
+   * keeps track of state for field: _textColThreshold
+   */
+  private boolean _has_textColThreshold;
+
+  /**
+   * Field _showUnconserved.
+   */
+  private boolean _showUnconserved;
+
+  /**
+   * keeps track of state for field: _showUnconserved
+   */
+  private boolean _has_showUnconserved;
+
+  /**
+   * Field _ignoreGapsinConsensus.
+   */
+  private boolean _ignoreGapsinConsensus = true;
+
+  /**
+   * keeps track of state for field: _ignoreGapsinConsensus
+   */
+  private boolean _has_ignoreGapsinConsensus;
+
+  /**
+   * Field _showConsensusHistogram.
+   */
+  private boolean _showConsensusHistogram = true;
+
+  /**
+   * keeps track of state for field: _showConsensusHistogram
+   */
+  private boolean _has_showConsensusHistogram;
+
+  /**
+   * Field _showSequenceLogo.
+   */
+  private boolean _showSequenceLogo = false;
+
+  /**
+   * keeps track of state for field: _showSequenceLogo
+   */
+  private boolean _has_showSequenceLogo;
+
+  /**
+   * Field _normaliseSequenceLogo.
+   */
+  private boolean _normaliseSequenceLogo = false;
+
+  /**
+   * keeps track of state for field: _normaliseSequenceLogo
+   */
+  private boolean _has_normaliseSequenceLogo;
+
+  /**
+   * Optional sequence group ID (only needs to be unique for this alignment)
+   * 
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _seqList.
+   */
+  private java.util.Vector _seqList;
+
+  /**
+   * Field _annotationColours.
+   */
+  private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JGroup()
+  {
+    super();
+    this._seqList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSeq(final java.lang.String vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._seqList.addElement(vSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSeq(final int index, final java.lang.String vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._seqList.add(index, vSeq);
+  }
+
+  /**
+     */
+  public void deleteColourText()
+  {
+    this._has_colourText = false;
+  }
+
+  /**
+     */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  }
+
+  /**
+     */
+  public void deleteDisplayBoxes()
+  {
+    this._has_displayBoxes = false;
+  }
+
+  /**
+     */
+  public void deleteDisplayText()
+  {
+    this._has_displayText = false;
+  }
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+     */
+  public void deleteIgnoreGapsinConsensus()
+  {
+    this._has_ignoreGapsinConsensus = false;
+  }
+
+  /**
+     */
+  public void deleteNormaliseSequenceLogo()
+  {
+    this._has_normaliseSequenceLogo = false;
+  }
+
+  /**
+     */
+  public void deleteOutlineColour()
+  {
+    this._has_outlineColour = false;
+  }
+
+  /**
+     */
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  }
+
+  /**
+     */
+  public void deleteShowConsensusHistogram()
+  {
+    this._has_showConsensusHistogram = false;
+  }
+
+  /**
+     */
+  public void deleteShowSequenceLogo()
+  {
+    this._has_showSequenceLogo = false;
+  }
+
+  /**
+     */
+  public void deleteShowUnconserved()
+  {
+    this._has_showUnconserved = false;
+  }
+
+  /**
+     */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+     */
+  public void deleteTextCol1()
+  {
+    this._has_textCol1 = false;
+  }
+
+  /**
+     */
+  public void deleteTextCol2()
+  {
+    this._has_textCol2 = false;
+  }
+
+  /**
+     */
+  public void deleteTextColThreshold()
+  {
+    this._has_textColThreshold = false;
+  }
+
+  /**
+   * Method enumerateSeq.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateSeq()
+  {
+    return this._seqList.elements();
+  }
+
+  /**
+   * Returns the value of field 'annotationColours'.
+   * 
+   * @return the value of field 'AnnotationColours'.
+   */
+  public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+  {
+    return this._annotationColours;
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public java.lang.String getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'colourText'.
+   * 
+   * @return the value of field 'ColourText'.
+   */
+  public boolean getColourText()
+  {
+    return this._colourText;
+  }
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   * 
+   * @return the value of field 'ConsThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  }
+
+  /**
+   * Returns the value of field 'displayBoxes'.
+   * 
+   * @return the value of field 'DisplayBoxes'.
+   */
+  public boolean getDisplayBoxes()
+  {
+    return this._displayBoxes;
+  }
+
+  /**
+   * Returns the value of field 'displayText'.
+   * 
+   * @return the value of field 'DisplayText'.
+   */
+  public boolean getDisplayText()
+  {
+    return this._displayText;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'id'. The field 'id' has the following
+   * description: Optional sequence group ID (only needs to be unique for this
+   * alignment)
+   * 
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'ignoreGapsinConsensus'.
+   * 
+   * @return the value of field 'IgnoreGapsinConsensus'.
+   */
+  public boolean getIgnoreGapsinConsensus()
+  {
+    return this._ignoreGapsinConsensus;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'normaliseSequenceLogo'.
+   * 
+   * @return the value of field 'NormaliseSequenceLogo'.
+   */
+  public boolean getNormaliseSequenceLogo()
+  {
+    return this._normaliseSequenceLogo;
+  }
+
+  /**
+   * Returns the value of field 'outlineColour'.
+   * 
+   * @return the value of field 'OutlineColour'.
+   */
+  public int getOutlineColour()
+  {
+    return this._outlineColour;
+  }
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   * 
+   * @return the value of field 'PidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  }
+
+  /**
+   * Method getSeq.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
+    {
+      throw new IndexOutOfBoundsException("getSeq: Index value '" + index
+              + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _seqList.get(index);
+  }
+
+  /**
+   * Method getSeq.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getSeq()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._seqList.toArray(array);
+  }
+
+  /**
+   * Method getSeqCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSeqCount()
+  {
+    return this._seqList.size();
+  }
+
+  /**
+   * Returns the value of field 'showConsensusHistogram'.
+   * 
+   * @return the value of field 'ShowConsensusHistogram'.
+   */
+  public boolean getShowConsensusHistogram()
+  {
+    return this._showConsensusHistogram;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceLogo'.
+   * 
+   * @return the value of field 'ShowSequenceLogo'.
+   */
+  public boolean getShowSequenceLogo()
+  {
+    return this._showSequenceLogo;
+  }
+
+  /**
+   * Returns the value of field 'showUnconserved'.
+   * 
+   * @return the value of field 'ShowUnconserved'.
+   */
+  public boolean getShowUnconserved()
+  {
+    return this._showUnconserved;
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Returns the value of field 'textCol1'.
+   * 
+   * @return the value of field 'TextCol1'.
+   */
+  public int getTextCol1()
+  {
+    return this._textCol1;
+  }
+
+  /**
+   * Returns the value of field 'textCol2'.
+   * 
+   * @return the value of field 'TextCol2'.
+   */
+  public int getTextCol2()
+  {
+    return this._textCol2;
+  }
+
+  /**
+   * Returns the value of field 'textColThreshold'.
+   * 
+   * @return the value of field 'TextColThreshold'.
+   */
+  public int getTextColThreshold()
+  {
+    return this._textColThreshold;
+  }
+
+  /**
+   * Method hasColourText.
+   * 
+   * @return true if at least one ColourText has been added
+   */
+  public boolean hasColourText()
+  {
+    return this._has_colourText;
+  }
+
+  /**
+   * Method hasConsThreshold.
+   * 
+   * @return true if at least one ConsThreshold has been added
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  }
+
+  /**
+   * Method hasDisplayBoxes.
+   * 
+   * @return true if at least one DisplayBoxes has been added
+   */
+  public boolean hasDisplayBoxes()
+  {
+    return this._has_displayBoxes;
+  }
+
+  /**
+   * Method hasDisplayText.
+   * 
+   * @return true if at least one DisplayText has been added
+   */
+  public boolean hasDisplayText()
+  {
+    return this._has_displayText;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasIgnoreGapsinConsensus.
+   * 
+   * @return true if at least one IgnoreGapsinConsensus has been added
+   */
+  public boolean hasIgnoreGapsinConsensus()
+  {
+    return this._has_ignoreGapsinConsensus;
+  }
+
+  /**
+   * Method hasNormaliseSequenceLogo.
+   * 
+   * @return true if at least one NormaliseSequenceLogo has been added
+   */
+  public boolean hasNormaliseSequenceLogo()
+  {
+    return this._has_normaliseSequenceLogo;
+  }
+
+  /**
+   * Method hasOutlineColour.
+   * 
+   * @return true if at least one OutlineColour has been added
+   */
+  public boolean hasOutlineColour()
+  {
+    return this._has_outlineColour;
+  }
+
+  /**
+   * Method hasPidThreshold.
+   * 
+   * @return true if at least one PidThreshold has been added
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  }
+
+  /**
+   * Method hasShowConsensusHistogram.
+   * 
+   * @return true if at least one ShowConsensusHistogram has been added
+   */
+  public boolean hasShowConsensusHistogram()
+  {
+    return this._has_showConsensusHistogram;
+  }
+
+  /**
+   * Method hasShowSequenceLogo.
+   * 
+   * @return true if at least one ShowSequenceLogo has been added
+   */
+  public boolean hasShowSequenceLogo()
+  {
+    return this._has_showSequenceLogo;
+  }
+
+  /**
+   * Method hasShowUnconserved.
+   * 
+   * @return true if at least one ShowUnconserved has been added
+   */
+  public boolean hasShowUnconserved()
+  {
+    return this._has_showUnconserved;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method hasTextCol1.
+   * 
+   * @return true if at least one TextCol1 has been added
+   */
+  public boolean hasTextCol1()
+  {
+    return this._has_textCol1;
+  }
+
+  /**
+   * Method hasTextCol2.
+   * 
+   * @return true if at least one TextCol2 has been added
+   */
+  public boolean hasTextCol2()
+  {
+    return this._has_textCol2;
+  }
+
+  /**
+   * Method hasTextColThreshold.
+   * 
+   * @return true if at least one TextColThreshold has been added
+   */
+  public boolean hasTextColThreshold()
+  {
+    return this._has_textColThreshold;
+  }
+
+  /**
+   * Returns the value of field 'colourText'.
+   * 
+   * @return the value of field 'ColourText'.
+   */
+  public boolean isColourText()
+  {
+    return this._colourText;
+  }
+
+  /**
+   * Returns the value of field 'displayBoxes'.
+   * 
+   * @return the value of field 'DisplayBoxes'.
+   */
+  public boolean isDisplayBoxes()
+  {
+    return this._displayBoxes;
+  }
+
+  /**
+   * Returns the value of field 'displayText'.
+   * 
+   * @return the value of field 'DisplayText'.
+   */
+  public boolean isDisplayText()
+  {
+    return this._displayText;
+  }
+
+  /**
+   * Returns the value of field 'ignoreGapsinConsensus'.
+   * 
+   * @return the value of field 'IgnoreGapsinConsensus'.
+   */
+  public boolean isIgnoreGapsinConsensus()
+  {
+    return this._ignoreGapsinConsensus;
+  }
+
+  /**
+   * Returns the value of field 'normaliseSequenceLogo'.
+   * 
+   * @return the value of field 'NormaliseSequenceLogo'.
+   */
+  public boolean isNormaliseSequenceLogo()
+  {
+    return this._normaliseSequenceLogo;
+  }
+
+  /**
+   * Returns the value of field 'showConsensusHistogram'.
+   * 
+   * @return the value of field 'ShowConsensusHistogram'.
+   */
+  public boolean isShowConsensusHistogram()
+  {
+    return this._showConsensusHistogram;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceLogo'.
+   * 
+   * @return the value of field 'ShowSequenceLogo'.
+   */
+  public boolean isShowSequenceLogo()
+  {
+    return this._showSequenceLogo;
+  }
+
+  /**
+   * Returns the value of field 'showUnconserved'.
+   * 
+   * @return the value of field 'ShowUnconserved'.
+   */
+  public boolean isShowUnconserved()
+  {
+    return this._showUnconserved;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllSeq()
+  {
+    this._seqList.clear();
+  }
+
+  /**
+   * Method removeSeq.
+   * 
+   * @param vSeq
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSeq(final java.lang.String vSeq)
+  {
+    boolean removed = _seqList.remove(vSeq);
+    return removed;
+  }
+
+  /**
+   * Method removeSeqAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeSeqAt(final int index)
+  {
+    java.lang.Object obj = this._seqList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * Sets the value of field 'annotationColours'.
+   * 
+   * @param annotationColours
+   *          the value of field 'annotationColours'.
+   */
+  public void setAnnotationColours(
+          final jalview.schemabinding.version2.AnnotationColours annotationColours)
+  {
+    this._annotationColours = annotationColours;
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *          the value of field 'colour'.
+   */
+  public void setColour(final java.lang.String colour)
+  {
+    this._colour = colour;
+  }
+
+  /**
+   * Sets the value of field 'colourText'.
+   * 
+   * @param colourText
+   *          the value of field 'colourText'.
+   */
+  public void setColourText(final boolean colourText)
+  {
+    this._colourText = colourText;
+    this._has_colourText = true;
+  }
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   * 
+   * @param consThreshold
+   *          the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(final int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'displayBoxes'.
+   * 
+   * @param displayBoxes
+   *          the value of field 'displayBoxes'.
+   */
+  public void setDisplayBoxes(final boolean displayBoxes)
+  {
+    this._displayBoxes = displayBoxes;
+    this._has_displayBoxes = true;
+  }
+
+  /**
+   * Sets the value of field 'displayText'.
+   * 
+   * @param displayText
+   *          the value of field 'displayText'.
+   */
+  public void setDisplayText(final boolean displayText)
+  {
+    this._displayText = displayText;
+    this._has_displayText = true;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'id'. The field 'id' has the following description:
+   * Optional sequence group ID (only needs to be unique for this alignment)
+   * 
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'ignoreGapsinConsensus'.
+   * 
+   * @param ignoreGapsinConsensus
+   *          the value of field 'ignoreGapsinConsensus'.
+   */
+  public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
+  {
+    this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+    this._has_ignoreGapsinConsensus = true;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'normaliseSequenceLogo'.
+   * 
+   * @param normaliseSequenceLogo
+   *          the value of field 'normaliseSequenceLogo'.
+   */
+  public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
+  {
+    this._normaliseSequenceLogo = normaliseSequenceLogo;
+    this._has_normaliseSequenceLogo = true;
+  }
+
+  /**
+   * Sets the value of field 'outlineColour'.
+   * 
+   * @param outlineColour
+   *          the value of field 'outlineColour'.
+   */
+  public void setOutlineColour(final int outlineColour)
+  {
+    this._outlineColour = outlineColour;
+    this._has_outlineColour = true;
+  }
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   * 
+   * @param pidThreshold
+   *          the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(final int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSeq(final int index, final java.lang.String vSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._seqList.size())
+    {
+      throw new IndexOutOfBoundsException("setSeq: Index value '" + index
+              + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+    }
+
+    this._seqList.set(index, vSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSeqArray
+   */
+  public void setSeq(final java.lang.String[] vSeqArray)
+  {
+    // -- copy array
+    _seqList.clear();
+
+    for (int i = 0; i < vSeqArray.length; i++)
+    {
+      this._seqList.add(vSeqArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'showConsensusHistogram'.
+   * 
+   * @param showConsensusHistogram
+   *          the value of field 'showConsensusHistogram'.
+   */
+  public void setShowConsensusHistogram(final boolean showConsensusHistogram)
+  {
+    this._showConsensusHistogram = showConsensusHistogram;
+    this._has_showConsensusHistogram = true;
+  }
+
+  /**
+   * Sets the value of field 'showSequenceLogo'.
+   * 
+   * @param showSequenceLogo
+   *          the value of field 'showSequenceLogo'
+   */
+  public void setShowSequenceLogo(final boolean showSequenceLogo)
+  {
+    this._showSequenceLogo = showSequenceLogo;
+    this._has_showSequenceLogo = true;
+  }
+
+  /**
+   * Sets the value of field 'showUnconserved'.
+   * 
+   * @param showUnconserved
+   *          the value of field 'showUnconserved'.
+   */
+  public void setShowUnconserved(final boolean showUnconserved)
+  {
+    this._showUnconserved = showUnconserved;
+    this._has_showUnconserved = true;
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *          the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Sets the value of field 'textCol1'.
+   * 
+   * @param textCol1
+   *          the value of field 'textCol1'.
+   */
+  public void setTextCol1(final int textCol1)
+  {
+    this._textCol1 = textCol1;
+    this._has_textCol1 = true;
+  }
+
+  /**
+   * Sets the value of field 'textCol2'.
+   * 
+   * @param textCol2
+   *          the value of field 'textCol2'.
+   */
+  public void setTextCol2(final int textCol2)
+  {
+    this._textCol2 = textCol2;
+    this._has_textCol2 = true;
+  }
+
+  /**
+   * Sets the value of field 'textColThreshold'.
+   * 
+   * @param textColThreshold
+   *          the value of field 'textColThreshold'
+   */
+  public void setTextColThreshold(final int textColThreshold)
+  {
+    this._textColThreshold = textColThreshold;
+    this._has_textColThreshold = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.JGroup
+   */
+  public static jalview.schemabinding.version2.JGroup unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.JGroup.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 193b005..9ca6708 100644
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,958 +19,1020 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JSeq implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _hidden.
-     */
-    private boolean _hidden;
-
-    /**
-     * keeps track of state for field: _hidden
-     */
-    private boolean _has_hidden;
-
-    /**
-     * Field _featuresList.
-     */
-    private java.util.Vector _featuresList;
-
-    /**
-     * Field _pdbidsList.
-     */
-    private java.util.Vector _pdbidsList;
-
-    /**
-     * Field _hiddenSequencesList.
-     */
-    private java.util.Vector _hiddenSequencesList;
-
-    /**
-     * Reference to a viewer showing RNA structure
-     *  for this sequence. Schema supports one viewer showing
-     * multiple
-     *  annotations for multiple sequences, though currently only
-     * one
-     *  annotation for one sequence (gapped or trimmed) is used
-     *  
-     */
-    private java.util.Vector _rnaViewerList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JSeq() {
-        super();
-        this._featuresList = new java.util.Vector();
-        this._pdbidsList = new java.util.Vector();
-        this._hiddenSequencesList = new java.util.Vector();
-        this._rnaViewerList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addFeatures(
-            final jalview.schemabinding.version2.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        this._featuresList.addElement(vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addFeatures(
-            final int index,
-            final jalview.schemabinding.version2.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        this._featuresList.add(index, vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param vHiddenSequences
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addHiddenSequences(
-            final int vHiddenSequences)
-    throws java.lang.IndexOutOfBoundsException {
-        this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vHiddenSequences
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addHiddenSequences(
-            final int index,
-            final int vHiddenSequences)
-    throws java.lang.IndexOutOfBoundsException {
-        this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences));
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbids(
-            final jalview.schemabinding.version2.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        this._pdbidsList.addElement(vPdbids);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbids(
-            final int index,
-            final jalview.schemabinding.version2.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        this._pdbidsList.add(index, vPdbids);
-    }
-
-    /**
-     * 
-     * 
-     * @param vRnaViewer
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addRnaViewer(
-            final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-    throws java.lang.IndexOutOfBoundsException {
-        this._rnaViewerList.addElement(vRnaViewer);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vRnaViewer
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addRnaViewer(
-            final int index,
-            final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-    throws java.lang.IndexOutOfBoundsException {
-        this._rnaViewerList.add(index, vRnaViewer);
-    }
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteHidden(
-    ) {
-        this._has_hidden= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Method enumerateFeatures.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Features elements
-     */
-    public java.util.Enumeration enumerateFeatures(
-    ) {
-        return this._featuresList.elements();
-    }
-
-    /**
-     * Method enumerateHiddenSequences.
-     * 
-     * @return an Enumeration over all int elements
-     */
-    public java.util.Enumeration enumerateHiddenSequences(
-    ) {
-        return this._hiddenSequencesList.elements();
-    }
-
-    /**
-     * Method enumeratePdbids.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Pdbids elements
-     */
-    public java.util.Enumeration enumeratePdbids(
-    ) {
-        return this._pdbidsList.elements();
-    }
-
-    /**
-     * Method enumerateRnaViewer.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.RnaViewer elements
-     */
-    public java.util.Enumeration enumerateRnaViewer(
-    ) {
-        return this._rnaViewerList.elements();
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Method getFeatures.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Features at the given index
-     */
-    public jalview.schemabinding.version2.Features getFeatures(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._featuresList.size()) {
-            throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Features) _featuresList.get(index);
-    }
-
-    /**
-     * Method getFeatures.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Features[] getFeatures(
-    ) {
-        jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
-        return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array);
-    }
-
-    /**
-     * Method getFeaturesCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getFeaturesCount(
-    ) {
-        return this._featuresList.size();
-    }
-
-    /**
-     * Returns the value of field 'hidden'.
-     * 
-     * @return the value of field 'Hidden'.
-     */
-    public boolean getHidden(
-    ) {
-        return this._hidden;
-    }
-
-    /**
-     * Method getHiddenSequences.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the int at the given index
-     */
-    public int getHiddenSequences(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._hiddenSequencesList.size()) {
-            throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
-        }
-        
-        return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
-    }
-
-    /**
-     * Method getHiddenSequences.Returns the contents of the
-     * collection in an Array.  
-     * 
-     * @return this collection as an Array
-     */
-    public int[] getHiddenSequences(
-    ) {
-        int size = this._hiddenSequencesList.size();
-        int[] array = new int[size];
-        java.util.Iterator iter = _hiddenSequencesList.iterator();
-        for (int index = 0; index < size; index++) {
-            array[index] = ((java.lang.Integer) iter.next()).intValue();
-        }
-        return array;
-    }
-
-    /**
-     * Method getHiddenSequencesCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getHiddenSequencesCount(
-    ) {
-        return this._hiddenSequencesList.size();
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Method getPdbids.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Pdbids at the given index
-     */
-    public jalview.schemabinding.version2.Pdbids getPdbids(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._pdbidsList.size()) {
-            throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
-    }
-
-    /**
-     * Method getPdbids.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Pdbids[] getPdbids(
-    ) {
-        jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
-        return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array);
-    }
-
-    /**
-     * Method getPdbidsCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPdbidsCount(
-    ) {
-        return this._pdbidsList.size();
-    }
-
-    /**
-     * Method getRnaViewer.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.RnaViewer at the given index
-     */
-    public jalview.schemabinding.version2.RnaViewer getRnaViewer(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._rnaViewerList.size()) {
-            throw new IndexOutOfBoundsException("getRnaViewer: Index value '" + index + "' not in range [0.." + (this._rnaViewerList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList.get(index);
-    }
-
-    /**
-     * Method getRnaViewer.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.RnaViewer[] getRnaViewer(
-    ) {
-        jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
-        return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList.toArray(array);
-    }
-
-    /**
-     * Method getRnaViewerCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getRnaViewerCount(
-    ) {
-        return this._rnaViewerList.size();
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasHidden.
-     * 
-     * @return true if at least one Hidden has been added
-     */
-    public boolean hasHidden(
-    ) {
-        return this._has_hidden;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Returns the value of field 'hidden'.
-     * 
-     * @return the value of field 'Hidden'.
-     */
-    public boolean isHidden(
-    ) {
-        return this._hidden;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllFeatures(
-    ) {
-        this._featuresList.clear();
-    }
-
-    /**
-     */
-    public void removeAllHiddenSequences(
-    ) {
-        this._hiddenSequencesList.clear();
-    }
-
-    /**
-     */
-    public void removeAllPdbids(
-    ) {
-        this._pdbidsList.clear();
-    }
-
-    /**
-     */
-    public void removeAllRnaViewer(
-    ) {
-        this._rnaViewerList.clear();
-    }
-
-    /**
-     * Method removeFeatures.
-     * 
-     * @param vFeatures
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeFeatures(
-            final jalview.schemabinding.version2.Features vFeatures) {
-        boolean removed = _featuresList.remove(vFeatures);
-        return removed;
-    }
-
-    /**
-     * Method removeFeaturesAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Features removeFeaturesAt(
-            final int index) {
-        java.lang.Object obj = this._featuresList.remove(index);
-        return (jalview.schemabinding.version2.Features) obj;
-    }
-
-    /**
-     * Method removeHiddenSequences.
-     * 
-     * @param vHiddenSequences
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeHiddenSequences(
-            final int vHiddenSequences) {
-        boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences));
-        return removed;
-    }
-
-    /**
-     * Method removeHiddenSequencesAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public int removeHiddenSequencesAt(
-            final int index) {
-        java.lang.Object obj = this._hiddenSequencesList.remove(index);
-        return ((java.lang.Integer) obj).intValue();
-    }
-
-    /**
-     * Method removePdbids.
-     * 
-     * @param vPdbids
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePdbids(
-            final jalview.schemabinding.version2.Pdbids vPdbids) {
-        boolean removed = _pdbidsList.remove(vPdbids);
-        return removed;
-    }
-
-    /**
-     * Method removePdbidsAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Pdbids removePdbidsAt(
-            final int index) {
-        java.lang.Object obj = this._pdbidsList.remove(index);
-        return (jalview.schemabinding.version2.Pdbids) obj;
-    }
-
-    /**
-     * Method removeRnaViewer.
-     * 
-     * @param vRnaViewer
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeRnaViewer(
-            final jalview.schemabinding.version2.RnaViewer vRnaViewer) {
-        boolean removed = _rnaViewerList.remove(vRnaViewer);
-        return removed;
-    }
-
-    /**
-     * Method removeRnaViewerAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
-            final int index) {
-        java.lang.Object obj = this._rnaViewerList.remove(index);
-        return (jalview.schemabinding.version2.RnaViewer) obj;
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setFeatures(
-            final int index,
-            final jalview.schemabinding.version2.Features vFeatures)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._featuresList.size()) {
-            throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
-        }
-        
-        this._featuresList.set(index, vFeatures);
-    }
-
-    /**
-     * 
-     * 
-     * @param vFeaturesArray
-     */
-    public void setFeatures(
-            final jalview.schemabinding.version2.Features[] vFeaturesArray) {
-        //-- copy array
-        _featuresList.clear();
-        
-        for (int i = 0; i < vFeaturesArray.length; i++) {
-                this._featuresList.add(vFeaturesArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'hidden'.
-     * 
-     * @param hidden the value of field 'hidden'.
-     */
-    public void setHidden(
-            final boolean hidden) {
-        this._hidden = hidden;
-        this._has_hidden = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vHiddenSequences
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setHiddenSequences(
-            final int index,
-            final int vHiddenSequences)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._hiddenSequencesList.size()) {
-            throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
-        }
-        
-        this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences));
-    }
-
-    /**
-     * 
-     * 
-     * @param vHiddenSequencesArray
-     */
-    public void setHiddenSequences(
-            final int[] vHiddenSequencesArray) {
-        //-- copy array
-        _hiddenSequencesList.clear();
-        
-        for (int i = 0; i < vHiddenSequencesArray.length; i++) {
-                this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i]));
-        }
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setPdbids(
-            final int index,
-            final jalview.schemabinding.version2.Pdbids vPdbids)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._pdbidsList.size()) {
-            throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
-        }
-        
-        this._pdbidsList.set(index, vPdbids);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPdbidsArray
-     */
-    public void setPdbids(
-            final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) {
-        //-- copy array
-        _pdbidsList.clear();
-        
-        for (int i = 0; i < vPdbidsArray.length; i++) {
-                this._pdbidsList.add(vPdbidsArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vRnaViewer
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setRnaViewer(
-            final int index,
-            final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._rnaViewerList.size()) {
-            throw new IndexOutOfBoundsException("setRnaViewer: Index value '" + index + "' not in range [0.." + (this._rnaViewerList.size() - 1) + "]");
-        }
-        
-        this._rnaViewerList.set(index, vRnaViewer);
-    }
-
-    /**
-     * 
-     * 
-     * @param vRnaViewerArray
-     */
-    public void setRnaViewer(
-            final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray) {
-        //-- copy array
-        _rnaViewerList.clear();
-        
-        for (int i = 0; i < vRnaViewerArray.length; i++) {
-                this._rnaViewerList.add(vRnaViewerArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.JSeq
-     */
-    public static jalview.schemabinding.version2.JSeq unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JSeq implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _hidden.
+   */
+  private boolean _hidden;
+
+  /**
+   * keeps track of state for field: _hidden
+   */
+  private boolean _has_hidden;
+
+  /**
+   * Field _featuresList.
+   */
+  private java.util.Vector _featuresList;
+
+  /**
+   * Field _pdbidsList.
+   */
+  private java.util.Vector _pdbidsList;
+
+  /**
+   * Field _hiddenSequencesList.
+   */
+  private java.util.Vector _hiddenSequencesList;
+
+  /**
+   * Reference to a viewer showing RNA structure for this sequence. Schema
+   * supports one viewer showing multiple annotations for multiple sequences,
+   * though currently only one annotation for one sequence (gapped or trimmed)
+   * is used
+   * 
+   */
+  private java.util.Vector _rnaViewerList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JSeq()
+  {
+    super();
+    this._featuresList = new java.util.Vector();
+    this._pdbidsList = new java.util.Vector();
+    this._hiddenSequencesList = new java.util.Vector();
+    this._rnaViewerList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(
+          final jalview.schemabinding.version2.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.addElement(vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFeatures(final int index,
+          final jalview.schemabinding.version2.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._featuresList.add(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vHiddenSequences
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addHiddenSequences(final int vHiddenSequences)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenSequencesList.addElement(new java.lang.Integer(
+            vHiddenSequences));
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenSequences
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addHiddenSequences(final int index, final int vHiddenSequences)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenSequencesList.add(index, new java.lang.Integer(
+            vHiddenSequences));
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.addElement(vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbids(final int index,
+          final jalview.schemabinding.version2.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._pdbidsList.add(index, vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param vRnaViewer
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addRnaViewer(
+          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._rnaViewerList.addElement(vRnaViewer);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vRnaViewer
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addRnaViewer(final int index,
+          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._rnaViewerList.add(index, vRnaViewer);
+  }
+
+  /**
+     */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+     */
+  public void deleteHidden()
+  {
+    this._has_hidden = false;
+  }
+
+  /**
+     */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Method enumerateFeatures.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Features
+   *         elements
+   */
+  public java.util.Enumeration enumerateFeatures()
+  {
+    return this._featuresList.elements();
+  }
+
+  /**
+   * Method enumerateHiddenSequences.
+   * 
+   * @return an Enumeration over all int elements
+   */
+  public java.util.Enumeration enumerateHiddenSequences()
+  {
+    return this._hiddenSequencesList.elements();
+  }
+
+  /**
+   * Method enumeratePdbids.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Pdbids
+   *         elements
+   */
+  public java.util.Enumeration enumeratePdbids()
+  {
+    return this._pdbidsList.elements();
+  }
+
+  /**
+   * Method enumerateRnaViewer.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.RnaViewer
+   *         elements
+   */
+  public java.util.Enumeration enumerateRnaViewer()
+  {
+    return this._rnaViewerList.elements();
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Method getFeatures.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Features at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Features getFeatures(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("getFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Features) _featuresList
+            .get(index);
+  }
+
+  /**
+   * Method getFeatures.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Features[] getFeatures()
+  {
+    jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
+    return (jalview.schemabinding.version2.Features[]) this._featuresList
+            .toArray(array);
+  }
+
+  /**
+   * Method getFeaturesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getFeaturesCount()
+  {
+    return this._featuresList.size();
+  }
+
+  /**
+   * Returns the value of field 'hidden'.
+   * 
+   * @return the value of field 'Hidden'.
+   */
+  public boolean getHidden()
+  {
+    return this._hidden;
+  }
+
+  /**
+   * Method getHiddenSequences.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the int at the given index
+   */
+  public int getHiddenSequences(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenSequencesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getHiddenSequences: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._hiddenSequencesList.size() - 1) + "]");
+    }
+
+    return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
+  }
+
+  /**
+   * Method getHiddenSequences.Returns the contents of the collection in an
+   * Array.
+   * 
+   * @return this collection as an Array
+   */
+  public int[] getHiddenSequences()
+  {
+    int size = this._hiddenSequencesList.size();
+    int[] array = new int[size];
+    java.util.Iterator iter = _hiddenSequencesList.iterator();
+    for (int index = 0; index < size; index++)
+    {
+      array[index] = ((java.lang.Integer) iter.next()).intValue();
+    }
+    return array;
+  }
+
+  /**
+   * Method getHiddenSequencesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getHiddenSequencesCount()
+  {
+    return this._hiddenSequencesList.size();
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbids.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Pdbids at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.Pdbids getPdbids(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
+  }
+
+  /**
+   * Method getPdbids.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Pdbids[] getPdbids()
+  {
+    jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
+    return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList
+            .toArray(array);
+  }
+
+  /**
+   * Method getPdbidsCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbidsCount()
+  {
+    return this._pdbidsList.size();
+  }
+
+  /**
+   * Method getRnaViewer.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.RnaViewer at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.RnaViewer getRnaViewer(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._rnaViewerList.size())
+    {
+      throw new IndexOutOfBoundsException("getRnaViewer: Index value '"
+              + index + "' not in range [0.."
+              + (this._rnaViewerList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList
+            .get(index);
+  }
+
+  /**
+   * Method getRnaViewer.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.RnaViewer[] getRnaViewer()
+  {
+    jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
+    return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList
+            .toArray(array);
+  }
+
+  /**
+   * Method getRnaViewerCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getRnaViewerCount()
+  {
+    return this._rnaViewerList.size();
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasHidden.
+   * 
+   * @return true if at least one Hidden has been added
+   */
+  public boolean hasHidden()
+  {
+    return this._has_hidden;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Returns the value of field 'hidden'.
+   * 
+   * @return the value of field 'Hidden'.
+   */
+  public boolean isHidden()
+  {
+    return this._hidden;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllFeatures()
+  {
+    this._featuresList.clear();
+  }
+
+  /**
+     */
+  public void removeAllHiddenSequences()
+  {
+    this._hiddenSequencesList.clear();
+  }
+
+  /**
+     */
+  public void removeAllPdbids()
+  {
+    this._pdbidsList.clear();
+  }
+
+  /**
+     */
+  public void removeAllRnaViewer()
+  {
+    this._rnaViewerList.clear();
+  }
+
+  /**
+   * Method removeFeatures.
+   * 
+   * @param vFeatures
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeFeatures(
+          final jalview.schemabinding.version2.Features vFeatures)
+  {
+    boolean removed = _featuresList.remove(vFeatures);
+    return removed;
+  }
+
+  /**
+   * Method removeFeaturesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Features removeFeaturesAt(
+          final int index)
+  {
+    java.lang.Object obj = this._featuresList.remove(index);
+    return (jalview.schemabinding.version2.Features) obj;
+  }
+
+  /**
+   * Method removeHiddenSequences.
+   * 
+   * @param vHiddenSequences
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeHiddenSequences(final int vHiddenSequences)
+  {
+    boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(
+            vHiddenSequences));
+    return removed;
+  }
+
+  /**
+   * Method removeHiddenSequencesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public int removeHiddenSequencesAt(final int index)
+  {
+    java.lang.Object obj = this._hiddenSequencesList.remove(index);
+    return ((java.lang.Integer) obj).intValue();
+  }
+
+  /**
+   * Method removePdbids.
+   * 
+   * @param vPdbids
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbids(
+          final jalview.schemabinding.version2.Pdbids vPdbids)
+  {
+    boolean removed = _pdbidsList.remove(vPdbids);
+    return removed;
+  }
+
+  /**
+   * Method removePdbidsAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Pdbids removePdbidsAt(
+          final int index)
+  {
+    java.lang.Object obj = this._pdbidsList.remove(index);
+    return (jalview.schemabinding.version2.Pdbids) obj;
+  }
+
+  /**
+   * Method removeRnaViewer.
+   * 
+   * @param vRnaViewer
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeRnaViewer(
+          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+  {
+    boolean removed = _rnaViewerList.remove(vRnaViewer);
+    return removed;
+  }
+
+  /**
+   * Method removeRnaViewerAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
+          final int index)
+  {
+    java.lang.Object obj = this._rnaViewerList.remove(index);
+    return (jalview.schemabinding.version2.RnaViewer) obj;
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *          the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFeatures
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setFeatures(final int index,
+          final jalview.schemabinding.version2.Features vFeatures)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._featuresList.size())
+    {
+      throw new IndexOutOfBoundsException("setFeatures: Index value '"
+              + index + "' not in range [0.."
+              + (this._featuresList.size() - 1) + "]");
+    }
+
+    this._featuresList.set(index, vFeatures);
+  }
+
+  /**
+   * 
+   * 
+   * @param vFeaturesArray
+   */
+  public void setFeatures(
+          final jalview.schemabinding.version2.Features[] vFeaturesArray)
+  {
+    // -- copy array
+    _featuresList.clear();
+
+    for (int i = 0; i < vFeaturesArray.length; i++)
+    {
+      this._featuresList.add(vFeaturesArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'hidden'.
+   * 
+   * @param hidden
+   *          the value of field 'hidden'.
+   */
+  public void setHidden(final boolean hidden)
+  {
+    this._hidden = hidden;
+    this._has_hidden = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenSequences
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setHiddenSequences(final int index, final int vHiddenSequences)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenSequencesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setHiddenSequences: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._hiddenSequencesList.size() - 1) + "]");
+    }
+
+    this._hiddenSequencesList.set(index, new java.lang.Integer(
+            vHiddenSequences));
+  }
+
+  /**
+   * 
+   * 
+   * @param vHiddenSequencesArray
+   */
+  public void setHiddenSequences(final int[] vHiddenSequencesArray)
+  {
+    // -- copy array
+    _hiddenSequencesList.clear();
+
+    for (int i = 0; i < vHiddenSequencesArray.length; i++)
+    {
+      this._hiddenSequencesList.add(new java.lang.Integer(
+              vHiddenSequencesArray[i]));
+    }
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbids
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setPdbids(final int index,
+          final jalview.schemabinding.version2.Pdbids vPdbids)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._pdbidsList.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbids: Index value '"
+              + index + "' not in range [0.."
+              + (this._pdbidsList.size() - 1) + "]");
+    }
+
+    this._pdbidsList.set(index, vPdbids);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbidsArray
+   */
+  public void setPdbids(
+          final jalview.schemabinding.version2.Pdbids[] vPdbidsArray)
+  {
+    // -- copy array
+    _pdbidsList.clear();
+
+    for (int i = 0; i < vPdbidsArray.length; i++)
+    {
+      this._pdbidsList.add(vPdbidsArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vRnaViewer
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setRnaViewer(final int index,
+          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._rnaViewerList.size())
+    {
+      throw new IndexOutOfBoundsException("setRnaViewer: Index value '"
+              + index + "' not in range [0.."
+              + (this._rnaViewerList.size() - 1) + "]");
+    }
+
+    this._rnaViewerList.set(index, vRnaViewer);
+  }
+
+  /**
+   * 
+   * 
+   * @param vRnaViewerArray
+   */
+  public void setRnaViewer(
+          final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray)
+  {
+    // -- copy array
+    _rnaViewerList.clear();
+
+    for (int i = 0; i < vRnaViewerArray.length; i++)
+    {
+      this._rnaViewerList.add(vRnaViewerArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *          the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.JSeq
+   */
+  public static jalview.schemabinding.version2.JSeq unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.JSeq.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java
index eec356c..c13ef64 100644
--- a/src/jalview/schemabinding/version2/JalviewModel.java
+++ b/src/jalview/schemabinding/version2/JalviewModel.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,203 +19,217 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModel implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _creationDate.
-     */
-    private java.util.Date _creationDate;
-
-    /**
-     * Field _version.
-     */
-    private java.lang.String _version;
-
-    /**
-     * Field _vamsasModel.
-     */
-    private jalview.schemabinding.version2.VamsasModel _vamsasModel;
-
-    /**
-     * Field _jalviewModelSequence.
-     */
-    private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModel() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'creationDate'.
-     * 
-     * @return the value of field 'CreationDate'.
-     */
-    public java.util.Date getCreationDate(
-    ) {
-        return this._creationDate;
-    }
-
-    /**
-     * Returns the value of field 'jalviewModelSequence'.
-     * 
-     * @return the value of field 'JalviewModelSequence'.
-     */
-    public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence(
-    ) {
-        return this._jalviewModelSequence;
-    }
-
-    /**
-     * Returns the value of field 'vamsasModel'.
-     * 
-     * @return the value of field 'VamsasModel'.
-     */
-    public jalview.schemabinding.version2.VamsasModel getVamsasModel(
-    ) {
-        return this._vamsasModel;
-    }
-
-    /**
-     * Returns the value of field 'version'.
-     * 
-     * @return the value of field 'Version'.
-     */
-    public java.lang.String getVersion(
-    ) {
-        return this._version;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'creationDate'.
-     * 
-     * @param creationDate the value of field 'creationDate'.
-     */
-    public void setCreationDate(
-            final java.util.Date creationDate) {
-        this._creationDate = creationDate;
-    }
-
-    /**
-     * Sets the value of field 'jalviewModelSequence'.
-     * 
-     * @param jalviewModelSequence the value of field
-     * 'jalviewModelSequence'.
-     */
-    public void setJalviewModelSequence(
-            final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence) {
-        this._jalviewModelSequence = jalviewModelSequence;
-    }
-
-    /**
-     * Sets the value of field 'vamsasModel'.
-     * 
-     * @param vamsasModel the value of field 'vamsasModel'.
-     */
-    public void setVamsasModel(
-            final jalview.schemabinding.version2.VamsasModel vamsasModel) {
-        this._vamsasModel = vamsasModel;
-    }
-
-    /**
-     * Sets the value of field 'version'.
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(
-            final java.lang.String version) {
-        this._version = version;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.JalviewModel
-     */
-    public static jalview.schemabinding.version2.JalviewModel unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class JalviewModel implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _creationDate.
+   */
+  private java.util.Date _creationDate;
+
+  /**
+   * Field _version.
+   */
+  private java.lang.String _version;
+
+  /**
+   * Field _vamsasModel.
+   */
+  private jalview.schemabinding.version2.VamsasModel _vamsasModel;
+
+  /**
+   * Field _jalviewModelSequence.
+   */
+  private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModel()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'creationDate'.
+   * 
+   * @return the value of field 'CreationDate'.
+   */
+  public java.util.Date getCreationDate()
+  {
+    return this._creationDate;
+  }
+
+  /**
+   * Returns the value of field 'jalviewModelSequence'.
+   * 
+   * @return the value of field 'JalviewModelSequence'.
+   */
+  public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()
+  {
+    return this._jalviewModelSequence;
+  }
+
+  /**
+   * Returns the value of field 'vamsasModel'.
+   * 
+   * @return the value of field 'VamsasModel'.
+   */
+  public jalview.schemabinding.version2.VamsasModel getVamsasModel()
+  {
+    return this._vamsasModel;
+  }
+
+  /**
+   * Returns the value of field 'version'.
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'creationDate'.
+   * 
+   * @param creationDate
+   *          the value of field 'creationDate'.
+   */
+  public void setCreationDate(final java.util.Date creationDate)
+  {
+    this._creationDate = creationDate;
+  }
+
+  /**
+   * Sets the value of field 'jalviewModelSequence'.
+   * 
+   * @param jalviewModelSequence
+   *          the value of field 'jalviewModelSequence'.
+   */
+  public void setJalviewModelSequence(
+          final jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence)
+  {
+    this._jalviewModelSequence = jalviewModelSequence;
+  }
+
+  /**
+   * Sets the value of field 'vamsasModel'.
+   * 
+   * @param vamsasModel
+   *          the value of field 'vamsasModel'.
+   */
+  public void setVamsasModel(
+          final jalview.schemabinding.version2.VamsasModel vamsasModel)
+  {
+    this._vamsasModel = vamsasModel;
+  }
+
+  /**
+   * Sets the value of field 'version'.
+   * 
+   * @param version
+   *          the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.JalviewModel
+   */
+  public static jalview.schemabinding.version2.JalviewModel unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JalviewModel) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.JalviewModel.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index cf69934..c7c02c5 100644
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,907 +19,968 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequence implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _JSeqList.
-     */
-    private java.util.Vector _JSeqList;
-
-    /**
-     * Field _JGroupList.
-     */
-    private java.util.Vector _JGroupList;
-
-    /**
-     * Field _viewportList.
-     */
-    private java.util.Vector _viewportList;
-
-    /**
-     * Field _userColoursList.
-     */
-    private java.util.Vector _userColoursList;
-
-    /**
-     * Field _treeList.
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _featureSettings.
-     */
-    private jalview.schemabinding.version2.FeatureSettings _featureSettings;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelSequence() {
-        super();
-        this._JSeqList = new java.util.Vector();
-        this._JGroupList = new java.util.Vector();
-        this._viewportList = new java.util.Vector();
-        this._userColoursList = new java.util.Vector();
-        this._treeList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJGroup(
-            final jalview.schemabinding.version2.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JGroupList.addElement(vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJGroup(
-            final int index,
-            final jalview.schemabinding.version2.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JGroupList.add(index, vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJSeq(
-            final jalview.schemabinding.version2.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JSeqList.addElement(vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addJSeq(
-            final int index,
-            final jalview.schemabinding.version2.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        this._JSeqList.add(index, vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final jalview.schemabinding.version2.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.addElement(vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final int index,
-            final jalview.schemabinding.version2.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.add(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addUserColours(
-            final jalview.schemabinding.version2.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        this._userColoursList.addElement(vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addUserColours(
-            final int index,
-            final jalview.schemabinding.version2.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        this._userColoursList.add(index, vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addViewport(
-            final jalview.schemabinding.version2.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        this._viewportList.addElement(vViewport);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addViewport(
-            final int index,
-            final jalview.schemabinding.version2.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        this._viewportList.add(index, vViewport);
-    }
-
-    /**
-     * Method enumerateJGroup.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.JGroup elements
-     */
-    public java.util.Enumeration enumerateJGroup(
-    ) {
-        return this._JGroupList.elements();
-    }
-
-    /**
-     * Method enumerateJSeq.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.JSeq elements
-     */
-    public java.util.Enumeration enumerateJSeq(
-    ) {
-        return this._JSeqList.elements();
-    }
-
-    /**
-     * Method enumerateTree.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Tree elements
-     */
-    public java.util.Enumeration enumerateTree(
-    ) {
-        return this._treeList.elements();
-    }
-
-    /**
-     * Method enumerateUserColours.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.UserColours elements
-     */
-    public java.util.Enumeration enumerateUserColours(
-    ) {
-        return this._userColoursList.elements();
-    }
-
-    /**
-     * Method enumerateViewport.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Viewport elements
-     */
-    public java.util.Enumeration enumerateViewport(
-    ) {
-        return this._viewportList.elements();
-    }
-
-    /**
-     * Returns the value of field 'featureSettings'.
-     * 
-     * @return the value of field 'FeatureSettings'.
-     */
-    public jalview.schemabinding.version2.FeatureSettings getFeatureSettings(
-    ) {
-        return this._featureSettings;
-    }
-
-    /**
-     * Method getJGroup.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.JGroup at the given index
-     */
-    public jalview.schemabinding.version2.JGroup getJGroup(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JGroupList.size()) {
-            throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
-    }
-
-    /**
-     * Method getJGroup.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.JGroup[] getJGroup(
-    ) {
-        jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
-        return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array);
-    }
-
-    /**
-     * Method getJGroupCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getJGroupCount(
-    ) {
-        return this._JGroupList.size();
-    }
-
-    /**
-     * Method getJSeq.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.schemabinding.version2.JSeq
-     * at the given index
-     */
-    public jalview.schemabinding.version2.JSeq getJSeq(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JSeqList.size()) {
-            throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
-    }
-
-    /**
-     * Method getJSeq.Returns the contents of the collection in an
-     * Array.  
Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.JSeq[] getJSeq(
-    ) {
-        jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
-        return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array);
-    }
-
-    /**
-     * Method getJSeqCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getJSeqCount(
-    ) {
-        return this._JSeqList.size();
-    }
-
-    /**
-     * Method getTree.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.schemabinding.version2.Tree
-     * at the given index
-     */
-    public jalview.schemabinding.version2.Tree getTree(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Tree) _treeList.get(index);
-    }
-
-    /**
-     * Method getTree.Returns the contents of the collection in an
-     * Array.  
Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Tree[] getTree(
-    ) {
-        jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
-        return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array);
-    }
-
-    /**
-     * Method getTreeCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getTreeCount(
-    ) {
-        return this._treeList.size();
-    }
-
-    /**
-     * Method getUserColours.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.UserColours at the given index
-     */
-    public jalview.schemabinding.version2.UserColours getUserColours(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._userColoursList.size()) {
-            throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index);
-    }
-
-    /**
-     * Method getUserColours.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.UserColours[] getUserColours(
-    ) {
-        jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
-        return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array);
-    }
-
-    /**
-     * Method getUserColoursCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getUserColoursCount(
-    ) {
-        return this._userColoursList.size();
-    }
-
-    /**
-     * Method getViewport.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Viewport at the given index
-     */
-    public jalview.schemabinding.version2.Viewport getViewport(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._viewportList.size()) {
-            throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Viewport) _viewportList.get(index);
-    }
-
-    /**
-     * Method getViewport.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Viewport[] getViewport(
-    ) {
-        jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
-        return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array);
-    }
-
-    /**
-     * Method getViewportCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getViewportCount(
-    ) {
-        return this._viewportList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllJGroup(
-    ) {
-        this._JGroupList.clear();
-    }
-
-    /**
-     */
-    public void removeAllJSeq(
-    ) {
-        this._JSeqList.clear();
-    }
-
-    /**
-     */
-    public void removeAllTree(
-    ) {
-        this._treeList.clear();
-    }
-
-    /**
-     */
-    public void removeAllUserColours(
-    ) {
-        this._userColoursList.clear();
-    }
-
-    /**
-     */
-    public void removeAllViewport(
-    ) {
-        this._viewportList.clear();
-    }
-
-    /**
-     * Method removeJGroup.
-     * 
-     * @param vJGroup
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeJGroup(
-            final jalview.schemabinding.version2.JGroup vJGroup) {
-        boolean removed = _JGroupList.remove(vJGroup);
-        return removed;
-    }
-
-    /**
-     * Method removeJGroupAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.JGroup removeJGroupAt(
-            final int index) {
-        java.lang.Object obj = this._JGroupList.remove(index);
-        return (jalview.schemabinding.version2.JGroup) obj;
-    }
-
-    /**
-     * Method removeJSeq.
-     * 
-     * @param vJSeq
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeJSeq(
-            final jalview.schemabinding.version2.JSeq vJSeq) {
-        boolean removed = _JSeqList.remove(vJSeq);
-        return removed;
-    }
-
-    /**
-     * Method removeJSeqAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.JSeq removeJSeqAt(
-            final int index) {
-        java.lang.Object obj = this._JSeqList.remove(index);
-        return (jalview.schemabinding.version2.JSeq) obj;
-    }
-
-    /**
-     * Method removeTree.
-     * 
-     * @param vTree
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeTree(
-            final jalview.schemabinding.version2.Tree vTree) {
-        boolean removed = _treeList.remove(vTree);
-        return removed;
-    }
-
-    /**
-     * Method removeTreeAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Tree removeTreeAt(
-            final int index) {
-        java.lang.Object obj = this._treeList.remove(index);
-        return (jalview.schemabinding.version2.Tree) obj;
-    }
-
-    /**
-     * Method removeUserColours.
-     * 
-     * @param vUserColours
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeUserColours(
-            final jalview.schemabinding.version2.UserColours vUserColours) {
-        boolean removed = _userColoursList.remove(vUserColours);
-        return removed;
-    }
-
-    /**
-     * Method removeUserColoursAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.UserColours removeUserColoursAt(
-            final int index) {
-        java.lang.Object obj = this._userColoursList.remove(index);
-        return (jalview.schemabinding.version2.UserColours) obj;
-    }
-
-    /**
-     * Method removeViewport.
-     * 
-     * @param vViewport
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeViewport(
-            final jalview.schemabinding.version2.Viewport vViewport) {
-        boolean removed = _viewportList.remove(vViewport);
-        return removed;
-    }
-
-    /**
-     * Method removeViewportAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Viewport removeViewportAt(
-            final int index) {
-        java.lang.Object obj = this._viewportList.remove(index);
-        return (jalview.schemabinding.version2.Viewport) obj;
-    }
-
-    /**
-     * Sets the value of field 'featureSettings'.
-     * 
-     * @param featureSettings the value of field 'featureSettings'.
-     */
-    public void setFeatureSettings(
-            final jalview.schemabinding.version2.FeatureSettings featureSettings) {
-        this._featureSettings = featureSettings;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setJGroup(
-            final int index,
-            final jalview.schemabinding.version2.JGroup vJGroup)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JGroupList.size()) {
-            throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
-        }
-        
-        this._JGroupList.set(index, vJGroup);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJGroupArray
-     */
-    public void setJGroup(
-            final jalview.schemabinding.version2.JGroup[] vJGroupArray) {
-        //-- copy array
-        _JGroupList.clear();
-        
-        for (int i = 0; i < vJGroupArray.length; i++) {
-                this._JGroupList.add(vJGroupArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setJSeq(
-            final int index,
-            final jalview.schemabinding.version2.JSeq vJSeq)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._JSeqList.size()) {
-            throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
-        }
-        
-        this._JSeqList.set(index, vJSeq);
-    }
-
-    /**
-     * 
-     * 
-     * @param vJSeqArray
-     */
-    public void setJSeq(
-            final jalview.schemabinding.version2.JSeq[] vJSeqArray) {
-        //-- copy array
-        _JSeqList.clear();
-        
-        for (int i = 0; i < vJSeqArray.length; i++) {
-                this._JSeqList.add(vJSeqArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setTree(
-            final int index,
-            final jalview.schemabinding.version2.Tree vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        this._treeList.set(index, vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTreeArray
-     */
-    public void setTree(
-            final jalview.schemabinding.version2.Tree[] vTreeArray) {
-        //-- copy array
-        _treeList.clear();
-        
-        for (int i = 0; i < vTreeArray.length; i++) {
-                this._treeList.add(vTreeArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setUserColours(
-            final int index,
-            final jalview.schemabinding.version2.UserColours vUserColours)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._userColoursList.size()) {
-            throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
-        }
-        
-        this._userColoursList.set(index, vUserColours);
-    }
-
-    /**
-     * 
-     * 
-     * @param vUserColoursArray
-     */
-    public void setUserColours(
-            final jalview.schemabinding.version2.UserColours[] vUserColoursArray) {
-        //-- copy array
-        _userColoursList.clear();
-        
-        for (int i = 0; i < vUserColoursArray.length; i++) {
-                this._userColoursList.add(vUserColoursArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setViewport(
-            final int index,
-            final jalview.schemabinding.version2.Viewport vViewport)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._viewportList.size()) {
-            throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
-        }
-        
-        this._viewportList.set(index, vViewport);
-    }
-
-    /**
-     * 
-     * 
-     * @param vViewportArray
-     */
-    public void setViewport(
-            final jalview.schemabinding.version2.Viewport[] vViewportArray) {
-        //-- copy array
-        _viewportList.clear();
-        
-        for (int i = 0; i < vViewportArray.length; i++) {
-                this._viewportList.add(vViewportArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.JalviewModelSequence
-     */
-    public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class JalviewModelSequence implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _JSeqList.
+   */
+  private java.util.Vector _JSeqList;
+
+  /**
+   * Field _JGroupList.
+   */
+  private java.util.Vector _JGroupList;
+
+  /**
+   * Field _viewportList.
+   */
+  private java.util.Vector _viewportList;
+
+  /**
+   * Field _userColoursList.
+   */
+  private java.util.Vector _userColoursList;
+
+  /**
+   * Field _treeList.
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _featureSettings.
+   */
+  private jalview.schemabinding.version2.FeatureSettings _featureSettings;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModelSequence()
+  {
+    super();
+    this._JSeqList = new java.util.Vector();
+    this._JGroupList = new java.util.Vector();
+    this._viewportList = new java.util.Vector();
+    this._userColoursList = new java.util.Vector();
+    this._treeList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JGroupList.addElement(vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addJGroup(final int index,
+          final jalview.schemabinding.version2.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JGroupList.add(index, vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JSeqList.addElement(vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addJSeq(final int index,
+          final jalview.schemabinding.version2.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._JSeqList.add(index, vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final jalview.schemabinding.version2.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.addElement(vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final int index,
+          final jalview.schemabinding.version2.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.add(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addUserColours(
+          final jalview.schemabinding.version2.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._userColoursList.addElement(vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addUserColours(final int index,
+          final jalview.schemabinding.version2.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._userColoursList.add(index, vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addViewport(
+          final jalview.schemabinding.version2.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._viewportList.addElement(vViewport);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addViewport(final int index,
+          final jalview.schemabinding.version2.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._viewportList.add(index, vViewport);
+  }
+
+  /**
+   * Method enumerateJGroup.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.JGroup
+   *         elements
+   */
+  public java.util.Enumeration enumerateJGroup()
+  {
+    return this._JGroupList.elements();
+  }
+
+  /**
+   * Method enumerateJSeq.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.JSeq
+   *         elements
+   */
+  public java.util.Enumeration enumerateJSeq()
+  {
+    return this._JSeqList.elements();
+  }
+
+  /**
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Tree
+   *         elements
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return this._treeList.elements();
+  }
+
+  /**
+   * Method enumerateUserColours.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.UserColours
+   *         elements
+   */
+  public java.util.Enumeration enumerateUserColours()
+  {
+    return this._userColoursList.elements();
+  }
+
+  /**
+   * Method enumerateViewport.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Viewport
+   *         elements
+   */
+  public java.util.Enumeration enumerateViewport()
+  {
+    return this._viewportList.elements();
+  }
+
+  /**
+   * Returns the value of field 'featureSettings'.
+   * 
+   * @return the value of field 'FeatureSettings'.
+   */
+  public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
+  {
+    return this._featureSettings;
+  }
+
+  /**
+   * Method getJGroup.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.JGroup at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.JGroup getJGroup(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
+    {
+      throw new IndexOutOfBoundsException("getJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
+  }
+
+  /**
+   * Method getJGroup.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.JGroup[] getJGroup()
+  {
+    jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
+    return (jalview.schemabinding.version2.JGroup[]) this._JGroupList
+            .toArray(array);
+  }
+
+  /**
+   * Method getJGroupCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getJGroupCount()
+  {
+    return this._JGroupList.size();
+  }
+
+  /**
+   * Method getJSeq.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.JSeq at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.JSeq getJSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
+    {
+      throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
+  }
+
+  /**
+   * Method getJSeq.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.JSeq[] getJSeq()
+  {
+    jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
+    return (jalview.schemabinding.version2.JSeq[]) this._JSeqList
+            .toArray(array);
+  }
+
+  /**
+   * Method getJSeqCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getJSeqCount()
+  {
+    return this._JSeqList.size();
+  }
+
+  /**
+   * Method getTree.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Tree at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.Tree getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Tree) _treeList.get(index);
+  }
+
+  /**
+   * Method getTree.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Tree[] getTree()
+  {
+    jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
+    return (jalview.schemabinding.version2.Tree[]) this._treeList
+            .toArray(array);
+  }
+
+  /**
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getTreeCount()
+  {
+    return this._treeList.size();
+  }
+
+  /**
+   * Method getUserColours.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.UserColours at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.UserColours getUserColours(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
+    {
+      throw new IndexOutOfBoundsException("getUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.UserColours) _userColoursList
+            .get(index);
+  }
+
+  /**
+   * Method getUserColours.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.UserColours[] getUserColours()
+  {
+    jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
+    return (jalview.schemabinding.version2.UserColours[]) this._userColoursList
+            .toArray(array);
+  }
+
+  /**
+   * Method getUserColoursCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getUserColoursCount()
+  {
+    return this._userColoursList.size();
+  }
+
+  /**
+   * Method getViewport.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Viewport at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Viewport getViewport(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
+    {
+      throw new IndexOutOfBoundsException("getViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Viewport) _viewportList
+            .get(index);
+  }
+
+  /**
+   * Method getViewport.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Viewport[] getViewport()
+  {
+    jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
+    return (jalview.schemabinding.version2.Viewport[]) this._viewportList
+            .toArray(array);
+  }
+
+  /**
+   * Method getViewportCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getViewportCount()
+  {
+    return this._viewportList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllJGroup()
+  {
+    this._JGroupList.clear();
+  }
+
+  /**
+     */
+  public void removeAllJSeq()
+  {
+    this._JSeqList.clear();
+  }
+
+  /**
+     */
+  public void removeAllTree()
+  {
+    this._treeList.clear();
+  }
+
+  /**
+     */
+  public void removeAllUserColours()
+  {
+    this._userColoursList.clear();
+  }
+
+  /**
+     */
+  public void removeAllViewport()
+  {
+    this._viewportList.clear();
+  }
+
+  /**
+   * Method removeJGroup.
+   * 
+   * @param vJGroup
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJGroup(
+          final jalview.schemabinding.version2.JGroup vJGroup)
+  {
+    boolean removed = _JGroupList.remove(vJGroup);
+    return removed;
+  }
+
+  /**
+   * Method removeJGroupAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.JGroup removeJGroupAt(
+          final int index)
+  {
+    java.lang.Object obj = this._JGroupList.remove(index);
+    return (jalview.schemabinding.version2.JGroup) obj;
+  }
+
+  /**
+   * Method removeJSeq.
+   * 
+   * @param vJSeq
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+  {
+    boolean removed = _JSeqList.remove(vJSeq);
+    return removed;
+  }
+
+  /**
+   * Method removeJSeqAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)
+  {
+    java.lang.Object obj = this._JSeqList.remove(index);
+    return (jalview.schemabinding.version2.JSeq) obj;
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)
+  {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
+
+  /**
+   * Method removeTreeAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Tree removeTreeAt(final int index)
+  {
+    java.lang.Object obj = this._treeList.remove(index);
+    return (jalview.schemabinding.version2.Tree) obj;
+  }
+
+  /**
+   * Method removeUserColours.
+   * 
+   * @param vUserColours
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeUserColours(
+          final jalview.schemabinding.version2.UserColours vUserColours)
+  {
+    boolean removed = _userColoursList.remove(vUserColours);
+    return removed;
+  }
+
+  /**
+   * Method removeUserColoursAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.UserColours removeUserColoursAt(
+          final int index)
+  {
+    java.lang.Object obj = this._userColoursList.remove(index);
+    return (jalview.schemabinding.version2.UserColours) obj;
+  }
+
+  /**
+   * Method removeViewport.
+   * 
+   * @param vViewport
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeViewport(
+          final jalview.schemabinding.version2.Viewport vViewport)
+  {
+    boolean removed = _viewportList.remove(vViewport);
+    return removed;
+  }
+
+  /**
+   * Method removeViewportAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Viewport removeViewportAt(
+          final int index)
+  {
+    java.lang.Object obj = this._viewportList.remove(index);
+    return (jalview.schemabinding.version2.Viewport) obj;
+  }
+
+  /**
+   * Sets the value of field 'featureSettings'.
+   * 
+   * @param featureSettings
+   *          the value of field 'featureSettings'.
+   */
+  public void setFeatureSettings(
+          final jalview.schemabinding.version2.FeatureSettings featureSettings)
+  {
+    this._featureSettings = featureSettings;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setJGroup(final int index,
+          final jalview.schemabinding.version2.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
+    {
+      throw new IndexOutOfBoundsException("setJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
+    }
+
+    this._JGroupList.set(index, vJGroup);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJGroupArray
+   */
+  public void setJGroup(
+          final jalview.schemabinding.version2.JGroup[] vJGroupArray)
+  {
+    // -- copy array
+    _JGroupList.clear();
+
+    for (int i = 0; i < vJGroupArray.length; i++)
+    {
+      this._JGroupList.add(vJGroupArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setJSeq(final int index,
+          final jalview.schemabinding.version2.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
+    {
+      throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+    }
+
+    this._JSeqList.set(index, vJSeq);
+  }
+
+  /**
+   * 
+   * 
+   * @param vJSeqArray
+   */
+  public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
+  {
+    // -- copy array
+    _JSeqList.clear();
+
+    for (int i = 0; i < vJSeqArray.length; i++)
+    {
+      this._JSeqList.add(vJSeqArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setTree(final int index,
+          final jalview.schemabinding.version2.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+    }
+
+    this._treeList.set(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTreeArray
+   */
+  public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
+  {
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
+    {
+      this._treeList.add(vTreeArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setUserColours(final int index,
+          final jalview.schemabinding.version2.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
+    {
+      throw new IndexOutOfBoundsException("setUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
+    }
+
+    this._userColoursList.set(index, vUserColours);
+  }
+
+  /**
+   * 
+   * 
+   * @param vUserColoursArray
+   */
+  public void setUserColours(
+          final jalview.schemabinding.version2.UserColours[] vUserColoursArray)
+  {
+    // -- copy array
+    _userColoursList.clear();
+
+    for (int i = 0; i < vUserColoursArray.length; i++)
+    {
+      this._userColoursList.add(vUserColoursArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setViewport(final int index,
+          final jalview.schemabinding.version2.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
+    {
+      throw new IndexOutOfBoundsException("setViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
+    }
+
+    this._viewportList.set(index, vViewport);
+  }
+
+  /**
+   * 
+   * 
+   * @param vViewportArray
+   */
+  public void setViewport(
+          final jalview.schemabinding.version2.Viewport[] vViewportArray)
+  {
+    // -- copy array
+    _viewportList.clear();
+
+    for (int i = 0; i < vViewportArray.length; i++)
+    {
+      this._viewportList.add(vViewportArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence
+   */
+  public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.JalviewModelSequence.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java
index e1f1a19..042f092 100644
--- a/src/jalview/schemabinding/version2/JalviewUserColours.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColours.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,313 +19,328 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewUserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _schemeName.
-     */
-    private java.lang.String _schemeName;
-
-    /**
-     * Jalview colour scheme document version.
-     *  
-     */
-    private java.lang.String _version;
-
-    /**
-     * Field _colourList.
-     */
-    private java.util.Vector _colourList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewUserColours() {
-        super();
-        this._colourList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addColour(
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        this._colourList.addElement(vColour);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addColour(
-            final int index,
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        this._colourList.add(index, vColour);
-    }
-
-    /**
-     * Method enumerateColour.
-     * 
-     * @return an Enumeration over all Colour elements
-     */
-    public java.util.Enumeration enumerateColour(
-    ) {
-        return this._colourList.elements();
-    }
-
-    /**
-     * Method getColour.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the Colour at the given index
-     */
-    public Colour getColour(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._colourList.size()) {
-            throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
-        }
-        
-        return (Colour) _colourList.get(index);
-    }
-
-    /**
-     * Method getColour.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public Colour[] getColour(
-    ) {
-        Colour[] array = new Colour[0];
-        return (Colour[]) this._colourList.toArray(array);
-    }
-
-    /**
-     * Method getColourCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getColourCount(
-    ) {
-        return this._colourList.size();
-    }
-
-    /**
-     * Returns the value of field 'schemeName'.
-     * 
-     * @return the value of field 'SchemeName'.
-     */
-    public java.lang.String getSchemeName(
-    ) {
-        return this._schemeName;
-    }
-
-    /**
-     * Returns the value of field 'version'. The field 'version'
-     * has the following description: Jalview colour scheme
-     * document version.
-     *  
-     * 
-     * @return the value of field 'Version'.
-     */
-    public java.lang.String getVersion(
-    ) {
-        return this._version;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllColour(
-    ) {
-        this._colourList.clear();
-    }
-
-    /**
-     * Method removeColour.
-     * 
-     * @param vColour
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeColour(
-            final Colour vColour) {
-        boolean removed = _colourList.remove(vColour);
-        return removed;
+public class JalviewUserColours implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _schemeName.
+   */
+  private java.lang.String _schemeName;
+
+  /**
+   * Jalview colour scheme document version.
+   * 
+   */
+  private java.lang.String _version;
+
+  /**
+   * Field _colourList.
+   */
+  private java.util.Vector _colourList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewUserColours()
+  {
+    super();
+    this._colourList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addColour(final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._colourList.addElement(vColour);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._colourList.add(index, vColour);
+  }
+
+  /**
+   * Method enumerateColour.
+   * 
+   * @return an Enumeration over all Colour elements
+   */
+  public java.util.Enumeration enumerateColour()
+  {
+    return this._colourList.elements();
+  }
+
+  /**
+   * Method getColour.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the Colour at the given index
+   */
+  public Colour getColour(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
+    {
+      throw new IndexOutOfBoundsException("getColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeColourAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public Colour removeColourAt(
-            final int index) {
-        java.lang.Object obj = this._colourList.remove(index);
-        return (Colour) obj;
+    return (Colour) _colourList.get(index);
+  }
+
+  /**
+   * Method getColour.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public Colour[] getColour()
+  {
+    Colour[] array = new Colour[0];
+    return (Colour[]) this._colourList.toArray(array);
+  }
+
+  /**
+   * Method getColourCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getColourCount()
+  {
+    return this._colourList.size();
+  }
+
+  /**
+   * Returns the value of field 'schemeName'.
+   * 
+   * @return the value of field 'SchemeName'.
+   */
+  public java.lang.String getSchemeName()
+  {
+    return this._schemeName;
+  }
+
+  /**
+   * Returns the value of field 'version'. The field 'version' has the following
+   * description: Jalview colour scheme document version.
+   * 
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vColour
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
      */
-    public void setColour(
-            final int index,
-            final Colour vColour)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._colourList.size()) {
-            throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
-        }
-        
-        this._colourList.set(index, vColour);
+  public void removeAllColour()
+  {
+    this._colourList.clear();
+  }
+
+  /**
+   * Method removeColour.
+   * 
+   * @param vColour
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeColour(final Colour vColour)
+  {
+    boolean removed = _colourList.remove(vColour);
+    return removed;
+  }
+
+  /**
+   * Method removeColourAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public Colour removeColourAt(final int index)
+  {
+    java.lang.Object obj = this._colourList.remove(index);
+    return (Colour) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
+    {
+      throw new IndexOutOfBoundsException("setColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param vColourArray
-     */
-    public void setColour(
-            final Colour[] vColourArray) {
-        //-- copy array
-        _colourList.clear();
-        
-        for (int i = 0; i < vColourArray.length; i++) {
-                this._colourList.add(vColourArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'schemeName'.
-     * 
-     * @param schemeName the value of field 'schemeName'.
-     */
-    public void setSchemeName(
-            final java.lang.String schemeName) {
-        this._schemeName = schemeName;
-    }
-
-    /**
-     * Sets the value of field 'version'. The field 'version' has
-     * the following description: Jalview colour scheme document
-     * version.
-     *  
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(
-            final java.lang.String version) {
-        this._version = version;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.JalviewUserColours
-     */
-    public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._colourList.set(index, vColour);
+  }
+
+  /**
+   * 
+   * 
+   * @param vColourArray
+   */
+  public void setColour(final Colour[] vColourArray)
+  {
+    // -- copy array
+    _colourList.clear();
+
+    for (int i = 0; i < vColourArray.length; i++)
+    {
+      this._colourList.add(vColourArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'schemeName'.
+   * 
+   * @param schemeName
+   *          the value of field 'schemeName'.
+   */
+  public void setSchemeName(final java.lang.String schemeName)
+  {
+    this._schemeName = schemeName;
+  }
+
+  /**
+   * Sets the value of field 'version'. The field 'version' has the following
+   * description: Jalview colour scheme document version.
+   * 
+   * 
+   * @param version
+   *          the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours
+   */
+  public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.JalviewUserColours.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/MapListFrom.java b/src/jalview/schemabinding/version2/MapListFrom.java
index eaa86c2..67bf1dc 100644
--- a/src/jalview/schemabinding/version2/MapListFrom.java
+++ b/src/jalview/schemabinding/version2/MapListFrom.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,198 +19,209 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListFrom implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListFrom() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MapListFrom
-     */
-    public static jalview.schemabinding.version2.MapListFrom unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MapListFrom) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListFrom.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class MapListFrom implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListFrom()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+     */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *          the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.MapListFrom
+   */
+  public static jalview.schemabinding.version2.MapListFrom unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MapListFrom) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MapListFrom.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/MapListTo.java b/src/jalview/schemabinding/version2/MapListTo.java
index c60750a..e59baf8 100644
--- a/src/jalview/schemabinding/version2/MapListTo.java
+++ b/src/jalview/schemabinding/version2/MapListTo.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,198 +19,209 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListTo implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _start.
-     */
-    private int _start;
-
-    /**
-     * keeps track of state for field: _start
-     */
-    private boolean _has_start;
-
-    /**
-     * Field _end.
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListTo() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteEnd(
-    ) {
-        this._has_end= false;
-    }
-
-    /**
-     */
-    public void deleteStart(
-    ) {
-        this._has_start= false;
-    }
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return the value of field 'End'.
-     */
-    public int getEnd(
-    ) {
-        return this._end;
-    }
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return the value of field 'Start'.
-     */
-    public int getStart(
-    ) {
-        return this._start;
-    }
-
-    /**
-     * Method hasEnd.
-     * 
-     * @return true if at least one End has been added
-     */
-    public boolean hasEnd(
-    ) {
-        return this._has_end;
-    }
-
-    /**
-     * Method hasStart.
-     * 
-     * @return true if at least one Start has been added
-     */
-    public boolean hasStart(
-    ) {
-        return this._has_start;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(
-            final int end) {
-        this._end = end;
-        this._has_end = true;
-    }
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(
-            final int start) {
-        this._start = start;
-        this._has_start = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MapListTo
-     */
-    public static jalview.schemabinding.version2.MapListTo unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MapListTo) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListTo.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class MapListTo implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _start.
+   */
+  private int _start;
+
+  /**
+   * keeps track of state for field: _start
+   */
+  private boolean _has_start;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListTo()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+     */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'start'.
+   * 
+   * @return the value of field 'Start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * Method hasStart.
+   * 
+   * @return true if at least one Start has been added
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'start'.
+   * 
+   * @param start
+   *          the value of field 'start'.
+   */
+  public void setStart(final int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.MapListTo
+   */
+  public static jalview.schemabinding.version2.MapListTo unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MapListTo) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MapListTo.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java
index 3efc950..cfb0752 100644
--- a/src/jalview/schemabinding/version2/MapListType.java
+++ b/src/jalview/schemabinding/version2/MapListType.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -17,566 +17,581 @@ import org.exolab.castor.xml.Unmarshaller;
 /**
  * developed after mapRangeType from
  * http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
- *  
- *  This effectively represents a java.util.MapList object
- *  
+ * 
+ * This effectively represents a java.util.MapList object
+ * 
  * 
  * @version $Revision$ $Date$
  */
-public class MapListType implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * number of dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     */
-    private long _mapFromUnit;
-
-    /**
-     * keeps track of state for field: _mapFromUnit
-     */
-    private boolean _has_mapFromUnit;
-
-    /**
-     * number of dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     */
-    private long _mapToUnit;
-
-    /**
-     * keeps track of state for field: _mapToUnit
-     */
-    private boolean _has_mapToUnit;
-
-    /**
-     * a region from start to end inclusive
-     */
-    private java.util.Vector _mapListFromList;
-
-    /**
-     * a region from start to end inclusive
-     */
-    private java.util.Vector _mapListToList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListType() {
-        super();
-        this._mapListFromList = new java.util.Vector();
-        this._mapListToList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vMapListFrom
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addMapListFrom(
-            final jalview.schemabinding.version2.MapListFrom vMapListFrom)
-    throws java.lang.IndexOutOfBoundsException {
-        this._mapListFromList.addElement(vMapListFrom);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vMapListFrom
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addMapListFrom(
-            final int index,
-            final jalview.schemabinding.version2.MapListFrom vMapListFrom)
-    throws java.lang.IndexOutOfBoundsException {
-        this._mapListFromList.add(index, vMapListFrom);
-    }
-
-    /**
-     * 
-     * 
-     * @param vMapListTo
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addMapListTo(
-            final jalview.schemabinding.version2.MapListTo vMapListTo)
-    throws java.lang.IndexOutOfBoundsException {
-        this._mapListToList.addElement(vMapListTo);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vMapListTo
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addMapListTo(
-            final int index,
-            final jalview.schemabinding.version2.MapListTo vMapListTo)
-    throws java.lang.IndexOutOfBoundsException {
-        this._mapListToList.add(index, vMapListTo);
-    }
-
-    /**
-     */
-    public void deleteMapFromUnit(
-    ) {
-        this._has_mapFromUnit= false;
-    }
-
-    /**
-     */
-    public void deleteMapToUnit(
-    ) {
-        this._has_mapToUnit= false;
-    }
-
-    /**
-     * Method enumerateMapListFrom.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.MapListFrom elements
-     */
-    public java.util.Enumeration enumerateMapListFrom(
-    ) {
-        return this._mapListFromList.elements();
-    }
-
-    /**
-     * Method enumerateMapListTo.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.MapListTo elements
-     */
-    public java.util.Enumeration enumerateMapListTo(
-    ) {
-        return this._mapListToList.elements();
-    }
-
-    /**
-     * Returns the value of field 'mapFromUnit'. The field
-     * 'mapFromUnit' has the following description: number of
-     * dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     * 
-     * @return the value of field 'MapFromUnit'.
-     */
-    public long getMapFromUnit(
-    ) {
-        return this._mapFromUnit;
-    }
-
-    /**
-     * Method getMapListFrom.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.MapListFrom at the given index
-     */
-    public jalview.schemabinding.version2.MapListFrom getMapListFrom(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._mapListFromList.size()) {
-            throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.MapListFrom) _mapListFromList.get(index);
-    }
-
-    /**
-     * Method getMapListFrom.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.MapListFrom[] getMapListFrom(
-    ) {
-        jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];
-        return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array);
-    }
-
-    /**
-     * Method getMapListFromCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getMapListFromCount(
-    ) {
-        return this._mapListFromList.size();
-    }
-
-    /**
-     * Method getMapListTo.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.MapListTo at the given index
-     */
-    public jalview.schemabinding.version2.MapListTo getMapListTo(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._mapListToList.size()) {
-            throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index);
-    }
-
-    /**
-     * Method getMapListTo.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.MapListTo[] getMapListTo(
-    ) {
-        jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];
-        return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array);
-    }
-
-    /**
-     * Method getMapListToCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getMapListToCount(
-    ) {
-        return this._mapListToList.size();
-    }
-
-    /**
-     * Returns the value of field 'mapToUnit'. The field
-     * 'mapToUnit' has the following description: number of
-     * dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     * 
-     * @return the value of field 'MapToUnit'.
-     */
-    public long getMapToUnit(
-    ) {
-        return this._mapToUnit;
-    }
-
-    /**
-     * Method hasMapFromUnit.
-     * 
-     * @return true if at least one MapFromUnit has been added
-     */
-    public boolean hasMapFromUnit(
-    ) {
-        return this._has_mapFromUnit;
-    }
-
-    /**
-     * Method hasMapToUnit.
-     * 
-     * @return true if at least one MapToUnit has been added
-     */
-    public boolean hasMapToUnit(
-    ) {
-        return this._has_mapToUnit;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllMapListFrom(
-    ) {
-        this._mapListFromList.clear();
-    }
-
-    /**
-     */
-    public void removeAllMapListTo(
-    ) {
-        this._mapListToList.clear();
-    }
-
-    /**
-     * Method removeMapListFrom.
-     * 
-     * @param vMapListFrom
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeMapListFrom(
-            final jalview.schemabinding.version2.MapListFrom vMapListFrom) {
-        boolean removed = _mapListFromList.remove(vMapListFrom);
-        return removed;
-    }
-
-    /**
-     * Method removeMapListFromAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(
-            final int index) {
-        java.lang.Object obj = this._mapListFromList.remove(index);
-        return (jalview.schemabinding.version2.MapListFrom) obj;
-    }
-
-    /**
-     * Method removeMapListTo.
-     * 
-     * @param vMapListTo
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeMapListTo(
-            final jalview.schemabinding.version2.MapListTo vMapListTo) {
-        boolean removed = _mapListToList.remove(vMapListTo);
-        return removed;
-    }
-
-    /**
-     * Method removeMapListToAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.MapListTo removeMapListToAt(
-            final int index) {
-        java.lang.Object obj = this._mapListToList.remove(index);
-        return (jalview.schemabinding.version2.MapListTo) obj;
-    }
-
-    /**
-     * Sets the value of field 'mapFromUnit'. The field
-     * 'mapFromUnit' has the following description: number of
-     * dictionary symbol widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     * 
-     * @param mapFromUnit the value of field 'mapFromUnit'.
-     */
-    public void setMapFromUnit(
-            final long mapFromUnit) {
-        this._mapFromUnit = mapFromUnit;
-        this._has_mapFromUnit = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vMapListFrom
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setMapListFrom(
-            final int index,
-            final jalview.schemabinding.version2.MapListFrom vMapListFrom)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._mapListFromList.size()) {
-            throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");
-        }
-        
-        this._mapListFromList.set(index, vMapListFrom);
-    }
-
-    /**
-     * 
-     * 
-     * @param vMapListFromArray
-     */
-    public void setMapListFrom(
-            final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) {
-        //-- copy array
-        _mapListFromList.clear();
-        
-        for (int i = 0; i < vMapListFromArray.length; i++) {
-                this._mapListFromList.add(vMapListFromArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vMapListTo
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setMapListTo(
-            final int index,
-            final jalview.schemabinding.version2.MapListTo vMapListTo)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._mapListToList.size()) {
-            throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");
-        }
-        
-        this._mapListToList.set(index, vMapListTo);
-    }
-
-    /**
-     * 
-     * 
-     * @param vMapListToArray
-     */
-    public void setMapListTo(
-            final jalview.schemabinding.version2.MapListTo[] vMapListToArray) {
-        //-- copy array
-        _mapListToList.clear();
-        
-        for (int i = 0; i < vMapListToArray.length; i++) {
-                this._mapListToList.add(vMapListToArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'mapToUnit'. The field 'mapToUnit'
-     * has the following description: number of dictionary symbol
-     * widths involved in each
-     *  mapped position on this sequence (for example, 3 for a dna
-     * sequence exon
-     *  region that is being mapped to a protein sequence). This is
-     * optional,
-     *  since the unit can be usually be inferred from the
-     * dictionary type of
-     *  each sequence involved in the mapping. 
-     * 
-     * @param mapToUnit the value of field 'mapToUnit'.
-     */
-    public void setMapToUnit(
-            final long mapToUnit) {
-        this._mapToUnit = mapToUnit;
-        this._has_mapToUnit = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MapListType
-     */
-    public static jalview.schemabinding.version2.MapListType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class MapListType implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * number of dictionary symbol widths involved in each mapped position on this
+   * sequence (for example, 3 for a dna sequence exon region that is being
+   * mapped to a protein sequence). This is optional, since the unit can be
+   * usually be inferred from the dictionary type of each sequence involved in
+   * the mapping.
+   */
+  private long _mapFromUnit;
+
+  /**
+   * keeps track of state for field: _mapFromUnit
+   */
+  private boolean _has_mapFromUnit;
+
+  /**
+   * number of dictionary symbol widths involved in each mapped position on this
+   * sequence (for example, 3 for a dna sequence exon region that is being
+   * mapped to a protein sequence). This is optional, since the unit can be
+   * usually be inferred from the dictionary type of each sequence involved in
+   * the mapping.
+   */
+  private long _mapToUnit;
+
+  /**
+   * keeps track of state for field: _mapToUnit
+   */
+  private boolean _has_mapToUnit;
+
+  /**
+   * a region from start to end inclusive
+   */
+  private java.util.Vector _mapListFromList;
+
+  /**
+   * a region from start to end inclusive
+   */
+  private java.util.Vector _mapListToList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListType()
+  {
+    super();
+    this._mapListFromList = new java.util.Vector();
+    this._mapListToList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vMapListFrom
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addMapListFrom(
+          final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._mapListFromList.addElement(vMapListFrom);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMapListFrom
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addMapListFrom(final int index,
+          final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._mapListFromList.add(index, vMapListFrom);
+  }
+
+  /**
+   * 
+   * 
+   * @param vMapListTo
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addMapListTo(
+          final jalview.schemabinding.version2.MapListTo vMapListTo)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._mapListToList.addElement(vMapListTo);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMapListTo
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addMapListTo(final int index,
+          final jalview.schemabinding.version2.MapListTo vMapListTo)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._mapListToList.add(index, vMapListTo);
+  }
+
+  /**
+     */
+  public void deleteMapFromUnit()
+  {
+    this._has_mapFromUnit = false;
+  }
+
+  /**
+     */
+  public void deleteMapToUnit()
+  {
+    this._has_mapToUnit = false;
+  }
+
+  /**
+   * Method enumerateMapListFrom.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.MapListFrom
+   *         elements
+   */
+  public java.util.Enumeration enumerateMapListFrom()
+  {
+    return this._mapListFromList.elements();
+  }
+
+  /**
+   * Method enumerateMapListTo.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.MapListTo
+   *         elements
+   */
+  public java.util.Enumeration enumerateMapListTo()
+  {
+    return this._mapListToList.elements();
+  }
+
+  /**
+   * Returns the value of field 'mapFromUnit'. The field 'mapFromUnit' has the
+   * following description: number of dictionary symbol widths involved in each
+   * mapped position on this sequence (for example, 3 for a dna sequence exon
+   * region that is being mapped to a protein sequence). This is optional, since
+   * the unit can be usually be inferred from the dictionary type of each
+   * sequence involved in the mapping.
+   * 
+   * @return the value of field 'MapFromUnit'.
+   */
+  public long getMapFromUnit()
+  {
+    return this._mapFromUnit;
+  }
+
+  /**
+   * Method getMapListFrom.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.MapListFrom at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.MapListFrom getMapListFrom(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._mapListFromList.size())
+    {
+      throw new IndexOutOfBoundsException("getMapListFrom: Index value '"
+              + index + "' not in range [0.."
+              + (this._mapListFromList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.MapListFrom) _mapListFromList
+            .get(index);
+  }
+
+  /**
+   * Method getMapListFrom.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.MapListFrom[] getMapListFrom()
+  {
+    jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];
+    return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList
+            .toArray(array);
+  }
+
+  /**
+   * Method getMapListFromCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getMapListFromCount()
+  {
+    return this._mapListFromList.size();
+  }
+
+  /**
+   * Method getMapListTo.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.MapListTo at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.MapListTo getMapListTo(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._mapListToList.size())
+    {
+      throw new IndexOutOfBoundsException("getMapListTo: Index value '"
+              + index + "' not in range [0.."
+              + (this._mapListToList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.MapListTo) _mapListToList
+            .get(index);
+  }
+
+  /**
+   * Method getMapListTo.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.MapListTo[] getMapListTo()
+  {
+    jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];
+    return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList
+            .toArray(array);
+  }
+
+  /**
+   * Method getMapListToCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getMapListToCount()
+  {
+    return this._mapListToList.size();
+  }
+
+  /**
+   * Returns the value of field 'mapToUnit'. The field 'mapToUnit' has the
+   * following description: number of dictionary symbol widths involved in each
+   * mapped position on this sequence (for example, 3 for a dna sequence exon
+   * region that is being mapped to a protein sequence). This is optional, since
+   * the unit can be usually be inferred from the dictionary type of each
+   * sequence involved in the mapping.
+   * 
+   * @return the value of field 'MapToUnit'.
+   */
+  public long getMapToUnit()
+  {
+    return this._mapToUnit;
+  }
+
+  /**
+   * Method hasMapFromUnit.
+   * 
+   * @return true if at least one MapFromUnit has been added
+   */
+  public boolean hasMapFromUnit()
+  {
+    return this._has_mapFromUnit;
+  }
+
+  /**
+   * Method hasMapToUnit.
+   * 
+   * @return true if at least one MapToUnit has been added
+   */
+  public boolean hasMapToUnit()
+  {
+    return this._has_mapToUnit;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllMapListFrom()
+  {
+    this._mapListFromList.clear();
+  }
+
+  /**
+     */
+  public void removeAllMapListTo()
+  {
+    this._mapListToList.clear();
+  }
+
+  /**
+   * Method removeMapListFrom.
+   * 
+   * @param vMapListFrom
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeMapListFrom(
+          final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+  {
+    boolean removed = _mapListFromList.remove(vMapListFrom);
+    return removed;
+  }
+
+  /**
+   * Method removeMapListFromAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(
+          final int index)
+  {
+    java.lang.Object obj = this._mapListFromList.remove(index);
+    return (jalview.schemabinding.version2.MapListFrom) obj;
+  }
+
+  /**
+   * Method removeMapListTo.
+   * 
+   * @param vMapListTo
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeMapListTo(
+          final jalview.schemabinding.version2.MapListTo vMapListTo)
+  {
+    boolean removed = _mapListToList.remove(vMapListTo);
+    return removed;
+  }
+
+  /**
+   * Method removeMapListToAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.MapListTo removeMapListToAt(
+          final int index)
+  {
+    java.lang.Object obj = this._mapListToList.remove(index);
+    return (jalview.schemabinding.version2.MapListTo) obj;
+  }
+
+  /**
+   * Sets the value of field 'mapFromUnit'. The field 'mapFromUnit' has the
+   * following description: number of dictionary symbol widths involved in each
+   * mapped position on this sequence (for example, 3 for a dna sequence exon
+   * region that is being mapped to a protein sequence). This is optional, since
+   * the unit can be usually be inferred from the dictionary type of each
+   * sequence involved in the mapping.
+   * 
+   * @param mapFromUnit
+   *          the value of field 'mapFromUnit'.
+   */
+  public void setMapFromUnit(final long mapFromUnit)
+  {
+    this._mapFromUnit = mapFromUnit;
+    this._has_mapFromUnit = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMapListFrom
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setMapListFrom(final int index,
+          final jalview.schemabinding.version2.MapListFrom vMapListFrom)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._mapListFromList.size())
+    {
+      throw new IndexOutOfBoundsException("setMapListFrom: Index value '"
+              + index + "' not in range [0.."
+              + (this._mapListFromList.size() - 1) + "]");
+    }
+
+    this._mapListFromList.set(index, vMapListFrom);
+  }
+
+  /**
+   * 
+   * 
+   * @param vMapListFromArray
+   */
+  public void setMapListFrom(
+          final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray)
+  {
+    // -- copy array
+    _mapListFromList.clear();
+
+    for (int i = 0; i < vMapListFromArray.length; i++)
+    {
+      this._mapListFromList.add(vMapListFromArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMapListTo
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setMapListTo(final int index,
+          final jalview.schemabinding.version2.MapListTo vMapListTo)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._mapListToList.size())
+    {
+      throw new IndexOutOfBoundsException("setMapListTo: Index value '"
+              + index + "' not in range [0.."
+              + (this._mapListToList.size() - 1) + "]");
+    }
+
+    this._mapListToList.set(index, vMapListTo);
+  }
+
+  /**
+   * 
+   * 
+   * @param vMapListToArray
+   */
+  public void setMapListTo(
+          final jalview.schemabinding.version2.MapListTo[] vMapListToArray)
+  {
+    // -- copy array
+    _mapListToList.clear();
+
+    for (int i = 0; i < vMapListToArray.length; i++)
+    {
+      this._mapListToList.add(vMapListToArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'mapToUnit'. The field 'mapToUnit' has the
+   * following description: number of dictionary symbol widths involved in each
+   * mapped position on this sequence (for example, 3 for a dna sequence exon
+   * region that is being mapped to a protein sequence). This is optional, since
+   * the unit can be usually be inferred from the dictionary type of each
+   * sequence involved in the mapping.
+   * 
+   * @param mapToUnit
+   *          the value of field 'mapToUnit'.
+   */
+  public void setMapToUnit(final long mapToUnit)
+  {
+    this._mapToUnit = mapToUnit;
+    this._has_mapToUnit = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.MapListType
+   */
+  public static jalview.schemabinding.version2.MapListType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MapListType) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MapListType.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Mapping.java b/src/jalview/schemabinding/version2/Mapping.java
index 068fd9f..9d71e1d 100644
--- a/src/jalview/schemabinding/version2/Mapping.java
+++ b/src/jalview/schemabinding/version2/Mapping.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,147 +19,155 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Mapping extends jalview.schemabinding.version2.MapListType 
-implements java.io.Serializable
+public class Mapping extends jalview.schemabinding.version2.MapListType
+        implements java.io.Serializable
 {
 
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Internal choice value storage
-     */
-    private java.lang.Object _choiceValue;
-
-    /**
-     * Field _mappingChoice.
-     */
-    private jalview.schemabinding.version2.MappingChoice _mappingChoice;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Mapping() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'choiceValue'. The field
-     * 'choiceValue' has the following description: Internal choice
-     * value storage
-     * 
-     * @return the value of field 'ChoiceValue'.
-     */
-    public java.lang.Object getChoiceValue(
-    ) {
-        return this._choiceValue;
-    }
-
-    /**
-     * Returns the value of field 'mappingChoice'.
-     * 
-     * @return the value of field 'MappingChoice'.
-     */
-    public jalview.schemabinding.version2.MappingChoice getMappingChoice(
-    ) {
-        return this._mappingChoice;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'mappingChoice'.
-     * 
-     * @param mappingChoice the value of field 'mappingChoice'.
-     */
-    public void setMappingChoice(
-            final jalview.schemabinding.version2.MappingChoice mappingChoice) {
-        this._mappingChoice = mappingChoice;
-        this._choiceValue = mappingChoice;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MapListType
-     */
-    public static jalview.schemabinding.version2.MapListType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Mapping.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Internal choice value storage
+   */
+  private java.lang.Object _choiceValue;
+
+  /**
+   * Field _mappingChoice.
+   */
+  private jalview.schemabinding.version2.MappingChoice _mappingChoice;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Mapping()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'choiceValue'. The field 'choiceValue' has the
+   * following description: Internal choice value storage
+   * 
+   * @return the value of field 'ChoiceValue'.
+   */
+  public java.lang.Object getChoiceValue()
+  {
+    return this._choiceValue;
+  }
+
+  /**
+   * Returns the value of field 'mappingChoice'.
+   * 
+   * @return the value of field 'MappingChoice'.
+   */
+  public jalview.schemabinding.version2.MappingChoice getMappingChoice()
+  {
+    return this._mappingChoice;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'mappingChoice'.
+   * 
+   * @param mappingChoice
+   *          the value of field 'mappingChoice'.
+   */
+  public void setMappingChoice(
+          final jalview.schemabinding.version2.MappingChoice mappingChoice)
+  {
+    this._mappingChoice = mappingChoice;
+    this._choiceValue = mappingChoice;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.MapListType
+   */
+  public static jalview.schemabinding.version2.MapListType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MapListType) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Mapping.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/MappingChoice.java b/src/jalview/schemabinding/version2/MappingChoice.java
index 297ed89..e50efa7 100644
--- a/src/jalview/schemabinding/version2/MappingChoice.java
+++ b/src/jalview/schemabinding/version2/MappingChoice.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,152 +19,164 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class MappingChoice implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _sequence.
-     */
-    private jalview.schemabinding.version2.Sequence _sequence;
-
-    /**
-     * Field _dseqFor.
-     */
-    private java.lang.String _dseqFor;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MappingChoice() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'dseqFor'.
-     * 
-     * @return the value of field 'DseqFor'.
-     */
-    public java.lang.String getDseqFor(
-    ) {
-        return this._dseqFor;
-    }
-
-    /**
-     * Returns the value of field 'sequence'.
-     * 
-     * @return the value of field 'Sequence'.
-     */
-    public jalview.schemabinding.version2.Sequence getSequence(
-    ) {
-        return this._sequence;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'dseqFor'.
-     * 
-     * @param dseqFor the value of field 'dseqFor'.
-     */
-    public void setDseqFor(
-            final java.lang.String dseqFor) {
-        this._dseqFor = dseqFor;
-    }
-
-    /**
-     * Sets the value of field 'sequence'.
-     * 
-     * @param sequence the value of field 'sequence'.
-     */
-    public void setSequence(
-            final jalview.schemabinding.version2.Sequence sequence) {
-        this._sequence = sequence;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.MappingChoice
-     */
-    public static jalview.schemabinding.version2.MappingChoice unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.MappingChoice) Unmarshaller.unmarshal(jalview.schemabinding.version2.MappingChoice.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class MappingChoice implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _sequence.
+   */
+  private jalview.schemabinding.version2.Sequence _sequence;
+
+  /**
+   * Field _dseqFor.
+   */
+  private java.lang.String _dseqFor;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MappingChoice()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'dseqFor'.
+   * 
+   * @return the value of field 'DseqFor'.
+   */
+  public java.lang.String getDseqFor()
+  {
+    return this._dseqFor;
+  }
+
+  /**
+   * Returns the value of field 'sequence'.
+   * 
+   * @return the value of field 'Sequence'.
+   */
+  public jalview.schemabinding.version2.Sequence getSequence()
+  {
+    return this._sequence;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'dseqFor'.
+   * 
+   * @param dseqFor
+   *          the value of field 'dseqFor'.
+   */
+  public void setDseqFor(final java.lang.String dseqFor)
+  {
+    this._dseqFor = dseqFor;
+  }
+
+  /**
+   * Sets the value of field 'sequence'.
+   * 
+   * @param sequence
+   *          the value of field 'sequence'.
+   */
+  public void setSequence(
+          final jalview.schemabinding.version2.Sequence sequence)
+  {
+    this._sequence = sequence;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.MappingChoice
+   */
+  public static jalview.schemabinding.version2.MappingChoice unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.MappingChoice) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MappingChoice.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java
index 3cdd86e..fb6b276 100644
--- a/src/jalview/schemabinding/version2/OtherData.java
+++ b/src/jalview/schemabinding/version2/OtherData.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,152 +19,163 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class OtherData implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _key.
-     */
-    private java.lang.String _key;
-
-    /**
-     * Field _value.
-     */
-    private java.lang.String _value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public OtherData() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'key'.
-     * 
-     * @return the value of field 'Key'.
-     */
-    public java.lang.String getKey(
-    ) {
-        return this._key;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public java.lang.String getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'key'.
-     * 
-     * @param key the value of field 'key'.
-     */
-    public void setKey(
-            final java.lang.String key) {
-        this._key = key;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final java.lang.String value) {
-        this._value = value;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.OtherData
-     */
-    public static jalview.schemabinding.version2.OtherData unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class OtherData implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _key.
+   */
+  private java.lang.String _key;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public OtherData()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'key'.
+   * 
+   * @return the value of field 'Key'.
+   */
+  public java.lang.String getKey()
+  {
+    return this._key;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'key'.
+   * 
+   * @param key
+   *          the value of field 'key'.
+   */
+  public void setKey(final java.lang.String key)
+  {
+    this._key = key;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *          the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.OtherData
+   */
+  public static jalview.schemabinding.version2.OtherData unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.OtherData) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.OtherData.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java
index b5acfbd..65de364 100644
--- a/src/jalview/schemabinding/version2/Pdbentry.java
+++ b/src/jalview/schemabinding/version2/Pdbentry.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,334 +19,357 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbentry implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _file.
-     */
-    private java.lang.String _file;
-
-    /**
-     * Field _items.
-     */
-    private java.util.Vector _items;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Pdbentry() {
-        super();
-        this._items = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.addElement(vPdbentryItem);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final int index,
-            final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.add(index, vPdbentryItem);
-    }
-
-    /**
-     * Method enumeratePdbentryItem.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.PdbentryItem elements
-     */
-    public java.util.Enumeration enumeratePdbentryItem(
-    ) {
-        return this._items.elements();
-    }
-
-    /**
-     * Returns the value of field 'file'.
-     * 
-     * @return the value of field 'File'.
-     */
-    public java.lang.String getFile(
-    ) {
-        return this._file;
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Method getPdbentryItem.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.PdbentryItem at the given inde
-     */
-    public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);
-    }
-
-    /**
-     * Method getPdbentryItem.Returns the contents of the
-     * collection in an Array.  
Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we know that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem(
-    ) {
-        jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];
-        return (jalview.schemabinding.version2.PdbentryItem[]) this._items.toArray(array);
-    }
-
-    /**
-     * Method getPdbentryItemCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPdbentryItemCount(
-    ) {
-        return this._items.size();
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllPdbentryItem(
-    ) {
-        this._items.clear();
-    }
-
-    /**
-     * Method removePdbentryItem.
-     * 
-     * @param vPdbentryItem
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePdbentryItem(
-            final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) {
-        boolean removed = _items.remove(vPdbentryItem);
-        return removed;
-    }
-
-    /**
-     * Method removePdbentryItemAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(
-            final int index) {
-        java.lang.Object obj = this._items.remove(index);
-        return (jalview.schemabinding.version2.PdbentryItem) obj;
-    }
-
-    /**
-     * Sets the value of field 'file'.
-     * 
-     * @param file the value of field 'file'.
-     */
-    public void setFile(
-            final java.lang.String file) {
-        this._file = file;
+public class Pdbentry implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _file.
+   */
+  private java.lang.String _file;
+
+  /**
+   * Field _items.
+   */
+  private java.util.Vector _items;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Pdbentry()
+  {
+    super();
+    this._items = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.addElement(vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(final int index,
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.add(index, vPdbentryItem);
+  }
+
+  /**
+   * Method enumeratePdbentryItem.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem
+   *         elements
+   */
+  public java.util.Enumeration enumeratePdbentryItem()
+  {
+    return this._items.elements();
+  }
+
+  /**
+   * Returns the value of field 'file'.
+   * 
+   * @return the value of field 'File'.
+   */
+  public java.lang.String getFile()
+  {
+    return this._file;
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbentryItem.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.PdbentryItem at the
+   *         given inde
+   */
+  public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
+    return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);
+  }
+
+  /**
+   * Method getPdbentryItem.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()
+  {
+    jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];
+    return (jalview.schemabinding.version2.PdbentryItem[]) this._items
+            .toArray(array);
+  }
+
+  /**
+   * Method getPdbentryItemCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbentryItemCount()
+  {
+    return this._items.size();
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
      */
-    public void setPdbentryItem(
-            final int index,
-            final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        this._items.set(index, vPdbentryItem);
+  public void removeAllPdbentryItem()
+  {
+    this._items.clear();
+  }
+
+  /**
+   * Method removePdbentryItem.
+   * 
+   * @param vPdbentryItem
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbentryItem(
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+  {
+    boolean removed = _items.remove(vPdbentryItem);
+    return removed;
+  }
+
+  /**
+   * Method removePdbentryItemAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(
+          final int index)
+  {
+    java.lang.Object obj = this._items.remove(index);
+    return (jalview.schemabinding.version2.PdbentryItem) obj;
+  }
+
+  /**
+   * Sets the value of field 'file'.
+   * 
+   * @param file
+   *          the value of field 'file'.
+   */
+  public void setFile(final java.lang.String file)
+  {
+    this._file = file;
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setPdbentryItem(final int index,
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param vPdbentryItemArray
-     */
-    public void setPdbentryItem(
-            final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) {
-        //-- copy array
-        _items.clear();
-        
-        for (int i = 0; i < vPdbentryItemArray.length; i++) {
-                this._items.add(vPdbentryItemArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Pdbentry
-     */
-    public static jalview.schemabinding.version2.Pdbentry unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._items.set(index, vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItemArray
+   */
+  public void setPdbentryItem(
+          final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray)
+  {
+    // -- copy array
+    _items.clear();
+
+    for (int i = 0; i < vPdbentryItemArray.length; i++)
+    {
+      this._items.add(vPdbentryItemArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *          the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Pdbentry
+   */
+  public static jalview.schemabinding.version2.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Pdbentry) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Pdbentry.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java
index 129bcc7..5554b49 100644
--- a/src/jalview/schemabinding/version2/PdbentryItem.java
+++ b/src/jalview/schemabinding/version2/PdbentryItem.java
@@ -12,181 +12,193 @@ package jalview.schemabinding.version2;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbentryItem implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _propertyList.
-     */
-    private java.util.Vector _propertyList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryItem() {
-        super();
-        this._propertyList = new java.util.Vector();
+public class PdbentryItem implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _propertyList.
+   */
+  private java.util.Vector _propertyList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PdbentryItem()
+  {
+    super();
+    this._propertyList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addProperty(
+          final jalview.schemabinding.version2.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.addElement(vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addProperty(final int index,
+          final jalview.schemabinding.version2.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._propertyList.add(index, vProperty);
+  }
+
+  /**
+   * Method enumerateProperty.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Property
+   *         elements
+   */
+  public java.util.Enumeration enumerateProperty()
+  {
+    return this._propertyList.elements();
+  }
+
+  /**
+   * Method getProperty.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Property at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Property getProperty(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("getProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
     }
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
+    return (jalview.schemabinding.version2.Property) _propertyList
+            .get(index);
+  }
+
+  /**
+   * Method getProperty.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Property[] getProperty()
+  {
+    jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
+    return (jalview.schemabinding.version2.Property[]) this._propertyList
+            .toArray(array);
+  }
+
+  /**
+   * Method getPropertyCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPropertyCount()
+  {
+    return this._propertyList.size();
+  }
+
+  /**
      */
-    public void addProperty(
-            final jalview.schemabinding.version2.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.addElement(vProperty);
+  public void removeAllProperty()
+  {
+    this._propertyList.clear();
+  }
+
+  /**
+   * Method removeProperty.
+   * 
+   * @param vProperty
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeProperty(
+          final jalview.schemabinding.version2.Property vProperty)
+  {
+    boolean removed = _propertyList.remove(vProperty);
+    return removed;
+  }
+
+  /**
+   * Method removePropertyAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Property removePropertyAt(
+          final int index)
+  {
+    java.lang.Object obj = this._propertyList.remove(index);
+    return (jalview.schemabinding.version2.Property) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setProperty(final int index,
+          final jalview.schemabinding.version2.Property vProperty)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size())
+    {
+      throw new IndexOutOfBoundsException("setProperty: Index value '"
+              + index + "' not in range [0.."
+              + (this._propertyList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addProperty(
-            final int index,
-            final jalview.schemabinding.version2.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        this._propertyList.add(index, vProperty);
-    }
-
-    /**
-     * Method enumerateProperty.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Property elements
-     */
-    public java.util.Enumeration enumerateProperty(
-    ) {
-        return this._propertyList.elements();
-    }
-
-    /**
-     * Method getProperty.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Property at the given index
-     */
-    public jalview.schemabinding.version2.Property getProperty(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Property) _propertyList.get(index);
-    }
-
-    /**
-     * Method getProperty.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Property[] getProperty(
-    ) {
-        jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
-        return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array);
-    }
-
-    /**
-     * Method getPropertyCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPropertyCount(
-    ) {
-        return this._propertyList.size();
-    }
-
-    /**
-     */
-    public void removeAllProperty(
-    ) {
-        this._propertyList.clear();
-    }
-
-    /**
-     * Method removeProperty.
-     * 
-     * @param vProperty
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeProperty(
-            final jalview.schemabinding.version2.Property vProperty) {
-        boolean removed = _propertyList.remove(vProperty);
-        return removed;
-    }
-
-    /**
-     * Method removePropertyAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Property removePropertyAt(
-            final int index) {
-        java.lang.Object obj = this._propertyList.remove(index);
-        return (jalview.schemabinding.version2.Property) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setProperty(
-            final int index,
-            final jalview.schemabinding.version2.Property vProperty)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._propertyList.size()) {
-            throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
-        }
-        
-        this._propertyList.set(index, vProperty);
-    }
-
-    /**
-     * 
-     * 
-     * @param vPropertyArray
-     */
-    public void setProperty(
-            final jalview.schemabinding.version2.Property[] vPropertyArray) {
-        //-- copy array
-        _propertyList.clear();
-        
-        for (int i = 0; i < vPropertyArray.length; i++) {
-                this._propertyList.add(vPropertyArray[i]);
-        }
+    this._propertyList.set(index, vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPropertyArray
+   */
+  public void setProperty(
+          final jalview.schemabinding.version2.Property[] vPropertyArray)
+  {
+    // -- copy array
+    _propertyList.clear();
+
+    for (int i = 0; i < vPropertyArray.length; i++)
+    {
+      this._propertyList.add(vPropertyArray[i]);
     }
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
index 5266b99..978df5b 100644
--- a/src/jalview/schemabinding/version2/Pdbids.java
+++ b/src/jalview/schemabinding/version2/Pdbids.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,262 +19,285 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbids extends jalview.schemabinding.version2.Pdbentry 
-implements java.io.Serializable
+public class Pdbids extends jalview.schemabinding.version2.Pdbentry
+        implements java.io.Serializable
 {
 
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _structureStateList.
+   */
+  private java.util.Vector _structureStateList;
 
-    /**
-     * Field _structureStateList.
-     */
-    private java.util.Vector _structureStateList;
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
+  public Pdbids()
+  {
+    super();
+    this._structureStateList = new java.util.Vector();
+  }
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    public Pdbids() {
-        super();
-        this._structureStateList = new java.util.Vector();
-    }
+  /**
+   * 
+   * 
+   * @param vStructureState
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addStructureState(
+          final jalview.schemabinding.version2.StructureState vStructureState)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._structureStateList.addElement(vStructureState);
+  }
 
+  /**
+   * 
+   * 
+   * @param index
+   * @param vStructureState
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addStructureState(
+          final int index,
+          final jalview.schemabinding.version2.StructureState vStructureState)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._structureStateList.add(index, vStructureState);
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method enumerateStructureState.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.StructureState elements
+   */
+  public java.util.Enumeration enumerateStructureState()
+  {
+    return this._structureStateList.elements();
+  }
 
-    /**
-     * 
-     * 
-     * @param vStructureState
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addStructureState(
-            final jalview.schemabinding.version2.StructureState vStructureState)
-    throws java.lang.IndexOutOfBoundsException {
-        this._structureStateList.addElement(vStructureState);
+  /**
+   * Method getStructureState.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.StructureState at
+   *         the given index
+   */
+  public jalview.schemabinding.version2.StructureState getStructureState(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._structureStateList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getStructureState: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._structureStateList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vStructureState
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addStructureState(
-            final int index,
-            final jalview.schemabinding.version2.StructureState vStructureState)
-    throws java.lang.IndexOutOfBoundsException {
-        this._structureStateList.add(index, vStructureState);
-    }
+    return (jalview.schemabinding.version2.StructureState) _structureStateList
+            .get(index);
+  }
 
-    /**
-     * Method enumerateStructureState.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.StructureState elements
-     */
-    public java.util.Enumeration enumerateStructureState(
-    ) {
-        return this._structureStateList.elements();
-    }
+  /**
+   * Method getStructureState.Returns the contents of the collection in an
+   * Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.StructureState[] getStructureState()
+  {
+    jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];
+    return (jalview.schemabinding.version2.StructureState[]) this._structureStateList
+            .toArray(array);
+  }
 
-    /**
-     * Method getStructureState.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.StructureState at the given
-     * index
-     */
-    public jalview.schemabinding.version2.StructureState getStructureState(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._structureStateList.size()) {
-            throw new IndexOutOfBoundsException("getStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.StructureState) _structureStateList.get(index);
-    }
+  /**
+   * Method getStructureStateCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getStructureStateCount()
+  {
+    return this._structureStateList.size();
+  }
 
-    /**
-     * Method getStructureState.Returns the contents of the
-     * collection in an Array.  
Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we know that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.StructureState[] getStructureState(
-    ) {
-        jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];
-        return (jalview.schemabinding.version2.StructureState[]) this._structureStateList.toArray(array);
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * Method getStructureStateCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getStructureStateCount(
-    ) {
-        return this._structureStateList.size();
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+  /**
      */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  public void removeAllStructureState()
+  {
+    this._structureStateList.clear();
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * Method removeStructureState.
+   * 
+   * @param vStructureState
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeStructureState(
+          final jalview.schemabinding.version2.StructureState vStructureState)
+  {
+    boolean removed = _structureStateList.remove(vStructureState);
+    return removed;
+  }
 
-    /**
-     */
-    public void removeAllStructureState(
-    ) {
-        this._structureStateList.clear();
-    }
+  /**
+   * Method removeStructureStateAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.StructureState removeStructureStateAt(
+          final int index)
+  {
+    java.lang.Object obj = this._structureStateList.remove(index);
+    return (jalview.schemabinding.version2.StructureState) obj;
+  }
 
-    /**
-     * Method removeStructureState.
-     * 
-     * @param vStructureState
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeStructureState(
-            final jalview.schemabinding.version2.StructureState vStructureState) {
-        boolean removed = _structureStateList.remove(vStructureState);
-        return removed;
+  /**
+   * 
+   * 
+   * @param index
+   * @param vStructureState
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setStructureState(
+          final int index,
+          final jalview.schemabinding.version2.StructureState vStructureState)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._structureStateList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setStructureState: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._structureStateList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeStructureStateAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.StructureState removeStructureStateAt(
-            final int index) {
-        java.lang.Object obj = this._structureStateList.remove(index);
-        return (jalview.schemabinding.version2.StructureState) obj;
-    }
+    this._structureStateList.set(index, vStructureState);
+  }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vStructureState
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setStructureState(
-            final int index,
-            final jalview.schemabinding.version2.StructureState vStructureState)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._structureStateList.size()) {
-            throw new IndexOutOfBoundsException("setStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");
-        }
-        
-        this._structureStateList.set(index, vStructureState);
-    }
+  /**
+   * 
+   * 
+   * @param vStructureStateArray
+   */
+  public void setStructureState(
+          final jalview.schemabinding.version2.StructureState[] vStructureStateArray)
+  {
+    // -- copy array
+    _structureStateList.clear();
 
-    /**
-     * 
-     * 
-     * @param vStructureStateArray
-     */
-    public void setStructureState(
-            final jalview.schemabinding.version2.StructureState[] vStructureStateArray) {
-        //-- copy array
-        _structureStateList.clear();
-        
-        for (int i = 0; i < vStructureStateArray.length; i++) {
-                this._structureStateList.add(vStructureStateArray[i]);
-        }
+    for (int i = 0; i < vStructureStateArray.length; i++)
+    {
+      this._structureStateList.add(vStructureStateArray[i]);
     }
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Pdbentry
-     */
-    public static jalview.schemabinding.version2.Pdbentry unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Pdbentry
+   */
+  public static jalview.schemabinding.version2.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Pdbentry) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java
index 714544d..dbf96bf 100644
--- a/src/jalview/schemabinding/version2/Property.java
+++ b/src/jalview/schemabinding/version2/Property.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,152 +19,163 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Property implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-    /**
-     * Field _value.
-     */
-    private java.lang.String _value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Property() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public java.lang.String getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final java.lang.String value) {
-        this._value = value;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Property
-     */
-    public static jalview.schemabinding.version2.Property unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class Property implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Property()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *          the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Property
+   */
+  public static jalview.schemabinding.version2.Property unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Property) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Property.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/RnaViewer.java b/src/jalview/schemabinding/version2/RnaViewer.java
index 96c4195..543d053 100644
--- a/src/jalview/schemabinding/version2/RnaViewer.java
+++ b/src/jalview/schemabinding/version2/RnaViewer.java
@@ -7,637 +7,662 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 
 /**
- * Reference to a viewer showing RNA structure
- *  for this sequence. Schema supports one viewer showing multiple
- *  annotations for multiple sequences, though currently only one
- *  annotation for one sequence (gapped or trimmed) is used
- *  
+ * Reference to a viewer showing RNA structure for this sequence. Schema
+ * supports one viewer showing multiple annotations for multiple sequences,
+ * though currently only one annotation for one sequence (gapped or trimmed) is
+ * used
+ * 
  * 
  * @version $Revision$ $Date$
  */
-public class RnaViewer implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * An id unique to the RNA viewer panel
-     *  
-     */
-    private java.lang.String _viewId;
-
-    /**
-     * horizontal position of split pane divider
-     *  
-     */
-    private int _dividerLocation;
-
-    /**
-     * keeps track of state for field: _dividerLocation
-     */
-    private boolean _has_dividerLocation;
-
-    /**
-     * Index of the selected structure in the
-     *  viewer panel
-     *  
-     */
-    private int _selectedRna;
-
-    /**
-     * keeps track of state for field: _selectedRna
-     */
-    private boolean _has_selectedRna;
-
-    /**
-     * 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 _secondaryStructureList.
-     */
-    private java.util.Vector _secondaryStructureList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public RnaViewer() {
-        super();
-        this._secondaryStructureList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vSecondaryStructure
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSecondaryStructure(
-            final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
-    throws java.lang.IndexOutOfBoundsException {
-        this._secondaryStructureList.addElement(vSecondaryStructure);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSecondaryStructure
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSecondaryStructure(
-            final int index,
-            final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
-    throws java.lang.IndexOutOfBoundsException {
-        this._secondaryStructureList.add(index, vSecondaryStructure);
-    }
-
-    /**
-     */
-    public void deleteDividerLocation(
-    ) {
-        this._has_dividerLocation= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deleteSelectedRna(
-    ) {
-        this._has_selectedRna= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Method enumerateSecondaryStructure.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.SecondaryStructure elements
-     */
-    public java.util.Enumeration enumerateSecondaryStructure(
-    ) {
-        return this._secondaryStructureList.elements();
-    }
-
-    /**
-     * Returns the value of field 'dividerLocation'. The field
-     * 'dividerLocation' has the following description: horizontal
-     * position of split pane divider
-     *  
-     * 
-     * @return the value of field 'DividerLocation'.
-     */
-    public int getDividerLocation(
-    ) {
-        return this._dividerLocation;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Method getSecondaryStructure.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.SecondaryStructure at the
-     * given index
-     */
-    public jalview.schemabinding.version2.SecondaryStructure getSecondaryStructure(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._secondaryStructureList.size()) {
-            throw new IndexOutOfBoundsException("getSecondaryStructure: Index value '" + index + "' not in range [0.." + (this._secondaryStructureList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.SecondaryStructure) _secondaryStructureList.get(index);
-    }
-
-    /**
-     * Method getSecondaryStructure.Returns the contents of the
-     * collection in an Array.  
Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we know that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.SecondaryStructure[] getSecondaryStructure(
-    ) {
-        jalview.schemabinding.version2.SecondaryStructure[] array = new jalview.schemabinding.version2.SecondaryStructure[0];
-        return (jalview.schemabinding.version2.SecondaryStructure[]) this._secondaryStructureList.toArray(array);
-    }
-
-    /**
-     * Method getSecondaryStructureCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSecondaryStructureCount(
-    ) {
-        return this._secondaryStructureList.size();
-    }
-
-    /**
-     * Returns the value of field 'selectedRna'. The field
-     * 'selectedRna' has the following description: Index of the
-     * selected structure in the
-     *  viewer panel
-     *  
-     * 
-     * @return the value of field 'SelectedRna'.
-     */
-    public int getSelectedRna(
-    ) {
-        return this._selectedRna;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'viewId'. The field 'viewId' has
-     * the following description: An id unique to the RNA viewer
-     * panel
-     *  
-     * 
-     * @return the value of field 'ViewId'.
-     */
-    public java.lang.String getViewId(
-    ) {
-        return this._viewId;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasDividerLocation.
-     * 
-     * @return true if at least one DividerLocation has been added
-     */
-    public boolean hasDividerLocation(
-    ) {
-        return this._has_dividerLocation;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasSelectedRna.
-     * 
-     * @return true if at least one SelectedRna has been added
-     */
-    public boolean hasSelectedRna(
-    ) {
-        return this._has_selectedRna;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllSecondaryStructure(
-    ) {
-        this._secondaryStructureList.clear();
-    }
-
-    /**
-     * Method removeSecondaryStructure.
-     * 
-     * @param vSecondaryStructure
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSecondaryStructure(
-            final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure) {
-        boolean removed = _secondaryStructureList.remove(vSecondaryStructure);
-        return removed;
-    }
-
-    /**
-     * Method removeSecondaryStructureAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.SecondaryStructure removeSecondaryStructureAt(
-            final int index) {
-        java.lang.Object obj = this._secondaryStructureList.remove(index);
-        return (jalview.schemabinding.version2.SecondaryStructure) obj;
-    }
-
-    /**
-     * Sets the value of field 'dividerLocation'. The field
-     * 'dividerLocation' has the following description: horizontal
-     * position of split pane divider
-     *  
-     * 
-     * @param dividerLocation the value of field 'dividerLocation'.
-     */
-    public void setDividerLocation(
-            final int dividerLocation) {
-        this._dividerLocation = dividerLocation;
-        this._has_dividerLocation = true;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSecondaryStructure
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSecondaryStructure(
-            final int index,
-            final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._secondaryStructureList.size()) {
-            throw new IndexOutOfBoundsException("setSecondaryStructure: Index value '" + index + "' not in range [0.." + (this._secondaryStructureList.size() - 1) + "]");
-        }
-        
-        this._secondaryStructureList.set(index, vSecondaryStructure);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSecondaryStructureArray
-     */
-    public void setSecondaryStructure(
-            final jalview.schemabinding.version2.SecondaryStructure[] vSecondaryStructureArray) {
-        //-- copy array
-        _secondaryStructureList.clear();
-        
-        for (int i = 0; i < vSecondaryStructureArray.length; i++) {
-                this._secondaryStructureList.add(vSecondaryStructureArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'selectedRna'. The field
-     * 'selectedRna' has the following description: Index of the
-     * selected structure in the
-     *  viewer panel
-     *  
-     * 
-     * @param selectedRna the value of field 'selectedRna'.
-     */
-    public void setSelectedRna(
-            final int selectedRna) {
-        this._selectedRna = selectedRna;
-        this._has_selectedRna = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'viewId'. The field 'viewId' has the
-     * following description: An id unique to the RNA viewer panel
-     *  
-     * 
-     * @param viewId the value of field 'viewId'.
-     */
-    public void setViewId(
-            final java.lang.String viewId) {
-        this._viewId = viewId;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.RnaViewer
-     */
-    public static jalview.schemabinding.version2.RnaViewer unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.RnaViewer) Unmarshaller.unmarshal(jalview.schemabinding.version2.RnaViewer.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class RnaViewer implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _title.
+   */
+  private java.lang.String _title;
+
+  /**
+   * An id unique to the RNA viewer panel
+   * 
+   */
+  private java.lang.String _viewId;
+
+  /**
+   * horizontal position of split pane divider
+   * 
+   */
+  private int _dividerLocation;
+
+  /**
+   * keeps track of state for field: _dividerLocation
+   */
+  private boolean _has_dividerLocation;
+
+  /**
+   * Index of the selected structure in the viewer panel
+   * 
+   */
+  private int _selectedRna;
+
+  /**
+   * keeps track of state for field: _selectedRna
+   */
+  private boolean _has_selectedRna;
+
+  /**
+   * 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 _secondaryStructureList.
+   */
+  private java.util.Vector _secondaryStructureList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public RnaViewer()
+  {
+    super();
+    this._secondaryStructureList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vSecondaryStructure
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSecondaryStructure(
+          final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._secondaryStructureList.addElement(vSecondaryStructure);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSecondaryStructure
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSecondaryStructure(
+          final int index,
+          final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._secondaryStructureList.add(index, vSecondaryStructure);
+  }
+
+  /**
+     */
+  public void deleteDividerLocation()
+  {
+    this._has_dividerLocation = false;
+  }
+
+  /**
+     */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+     */
+  public void deleteSelectedRna()
+  {
+    this._has_selectedRna = false;
+  }
+
+  /**
+     */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+     */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+     */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Method enumerateSecondaryStructure.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.SecondaryStructure elements
+   */
+  public java.util.Enumeration enumerateSecondaryStructure()
+  {
+    return this._secondaryStructureList.elements();
+  }
+
+  /**
+   * Returns the value of field 'dividerLocation'. The field 'dividerLocation'
+   * has the following description: horizontal position of split pane divider
+   * 
+   * 
+   * @return the value of field 'DividerLocation'.
+   */
+  public int getDividerLocation()
+  {
+    return this._dividerLocation;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Method getSecondaryStructure.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.SecondaryStructure
+   *         at the given index
+   */
+  public jalview.schemabinding.version2.SecondaryStructure getSecondaryStructure(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._secondaryStructureList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getSecondaryStructure: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._secondaryStructureList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.SecondaryStructure) _secondaryStructureList
+            .get(index);
+  }
+
+  /**
+   * Method getSecondaryStructure.Returns the contents of the collection in an
+   * Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.SecondaryStructure[] getSecondaryStructure()
+  {
+    jalview.schemabinding.version2.SecondaryStructure[] array = new jalview.schemabinding.version2.SecondaryStructure[0];
+    return (jalview.schemabinding.version2.SecondaryStructure[]) this._secondaryStructureList
+            .toArray(array);
+  }
+
+  /**
+   * Method getSecondaryStructureCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSecondaryStructureCount()
+  {
+    return this._secondaryStructureList.size();
+  }
+
+  /**
+   * Returns the value of field 'selectedRna'. The field 'selectedRna' has the
+   * following description: Index of the selected structure in the viewer panel
+   * 
+   * 
+   * @return the value of field 'SelectedRna'.
+   */
+  public int getSelectedRna()
+  {
+    return this._selectedRna;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'viewId'. The field 'viewId' has the following
+   * description: An id unique to the RNA viewer panel
+   * 
+   * 
+   * @return the value of field 'ViewId'.
+   */
+  public java.lang.String getViewId()
+  {
+    return this._viewId;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasDividerLocation.
+   * 
+   * @return true if at least one DividerLocation has been added
+   */
+  public boolean hasDividerLocation()
+  {
+    return this._has_dividerLocation;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasSelectedRna.
+   * 
+   * @return true if at least one SelectedRna has been added
+   */
+  public boolean hasSelectedRna()
+  {
+    return this._has_selectedRna;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllSecondaryStructure()
+  {
+    this._secondaryStructureList.clear();
+  }
+
+  /**
+   * Method removeSecondaryStructure.
+   * 
+   * @param vSecondaryStructure
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSecondaryStructure(
+          final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+  {
+    boolean removed = _secondaryStructureList.remove(vSecondaryStructure);
+    return removed;
+  }
+
+  /**
+   * Method removeSecondaryStructureAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.SecondaryStructure removeSecondaryStructureAt(
+          final int index)
+  {
+    java.lang.Object obj = this._secondaryStructureList.remove(index);
+    return (jalview.schemabinding.version2.SecondaryStructure) obj;
+  }
+
+  /**
+   * Sets the value of field 'dividerLocation'. The field 'dividerLocation' has
+   * the following description: horizontal position of split pane divider
+   * 
+   * 
+   * @param dividerLocation
+   *          the value of field 'dividerLocation'.
+   */
+  public void setDividerLocation(final int dividerLocation)
+  {
+    this._dividerLocation = dividerLocation;
+    this._has_dividerLocation = true;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *          the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSecondaryStructure
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSecondaryStructure(
+          final int index,
+          final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._secondaryStructureList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setSecondaryStructure: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._secondaryStructureList.size() - 1) + "]");
+    }
+
+    this._secondaryStructureList.set(index, vSecondaryStructure);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSecondaryStructureArray
+   */
+  public void setSecondaryStructure(
+          final jalview.schemabinding.version2.SecondaryStructure[] vSecondaryStructureArray)
+  {
+    // -- copy array
+    _secondaryStructureList.clear();
+
+    for (int i = 0; i < vSecondaryStructureArray.length; i++)
+    {
+      this._secondaryStructureList.add(vSecondaryStructureArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'selectedRna'. The field 'selectedRna' has the
+   * following description: Index of the selected structure in the viewer panel
+   * 
+   * 
+   * @param selectedRna
+   *          the value of field 'selectedRna'.
+   */
+  public void setSelectedRna(final int selectedRna)
+  {
+    this._selectedRna = selectedRna;
+    this._has_selectedRna = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *          the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'viewId'. The field 'viewId' has the following
+   * description: An id unique to the RNA viewer panel
+   * 
+   * 
+   * @param viewId
+   *          the value of field 'viewId'.
+   */
+  public void setViewId(final java.lang.String viewId)
+  {
+    this._viewId = viewId;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *          the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *          the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *          the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.RnaViewer
+   */
+  public static jalview.schemabinding.version2.RnaViewer unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.RnaViewer) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.RnaViewer.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/SecondaryStructure.java b/src/jalview/schemabinding/version2/SecondaryStructure.java
index d2f97fb..eb88fc4 100644
--- a/src/jalview/schemabinding/version2/SecondaryStructure.java
+++ b/src/jalview/schemabinding/version2/SecondaryStructure.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,272 +19,272 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SecondaryStructure implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * id attribute of Annotation in
-     *  vamsasModel for
-     *  the secondary structure annotation shown
-     *  in the viewer
-     *  
-     */
-    private java.lang.String _annotationId;
-
-    /**
-     * if true the RNA structure is shown with gaps, if false
-     * without
-     *  
-     */
-    private boolean _gapped;
-
-    /**
-     * keeps track of state for field: _gapped
-     */
-    private boolean _has_gapped;
-
-    /**
-     * name of the project jar entry that holds
-     *  the VARNA viewer state for the structure
-     *  
-     */
-    private java.lang.String _viewerState;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SecondaryStructure() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteGapped(
-    ) {
-        this._has_gapped= false;
-    }
-
-    /**
-     * Returns the value of field 'annotationId'. The field
-     * 'annotationId' has the following description: id attribute
-     * of Annotation in
-     *  vamsasModel for
-     *  the secondary structure annotation shown
-     *  in the viewer
-     *  
-     * 
-     * @return the value of field 'AnnotationId'.
-     */
-    public java.lang.String getAnnotationId(
-    ) {
-        return this._annotationId;
-    }
-
-    /**
-     * Returns the value of field 'gapped'. The field 'gapped' has
-     * the following description: if true the RNA structure is
-     * shown with gaps, if false without
-     *  
-     * 
-     * @return the value of field 'Gapped'.
-     */
-    public boolean getGapped(
-    ) {
-        return this._gapped;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'viewerState'. The field
-     * 'viewerState' has the following description: name of the
-     * project jar entry that holds
-     *  the VARNA viewer state for the structure
-     *  
-     * 
-     * @return the value of field 'ViewerState'.
-     */
-    public java.lang.String getViewerState(
-    ) {
-        return this._viewerState;
-    }
-
-    /**
-     * Method hasGapped.
-     * 
-     * @return true if at least one Gapped has been added
-     */
-    public boolean hasGapped(
-    ) {
-        return this._has_gapped;
-    }
-
-    /**
-     * Returns the value of field 'gapped'. The field 'gapped' has
-     * the following description: if true the RNA structure is
-     * shown with gaps, if false without
-     *  
-     * 
-     * @return the value of field 'Gapped'.
-     */
-    public boolean isGapped(
-    ) {
-        return this._gapped;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'annotationId'. The field
-     * 'annotationId' has the following description: id attribute
-     * of Annotation in
-     *  vamsasModel for
-     *  the secondary structure annotation shown
-     *  in the viewer
-     *  
-     * 
-     * @param annotationId the value of field 'annotationId'.
-     */
-    public void setAnnotationId(
-            final java.lang.String annotationId) {
-        this._annotationId = annotationId;
-    }
-
-    /**
-     * Sets the value of field 'gapped'. The field 'gapped' has the
-     * following description: if true the RNA structure is shown
-     * with gaps, if false without
-     *  
-     * 
-     * @param gapped the value of field 'gapped'.
-     */
-    public void setGapped(
-            final boolean gapped) {
-        this._gapped = gapped;
-        this._has_gapped = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'viewerState'. The field
-     * 'viewerState' has the following description: name of the
-     * project jar entry that holds
-     *  the VARNA viewer state for the structure
-     *  
-     * 
-     * @param viewerState the value of field 'viewerState'.
-     */
-    public void setViewerState(
-            final java.lang.String viewerState) {
-        this._viewerState = viewerState;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.SecondaryStructure
-     */
-    public static jalview.schemabinding.version2.SecondaryStructure unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller.unmarshal(jalview.schemabinding.version2.SecondaryStructure.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
+public class SecondaryStructure implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _title.
+   */
+  private java.lang.String _title;
+
+  /**
+   * id attribute of Annotation in vamsasModel for the secondary structure
+   * annotation shown in the viewer
+   * 
+   */
+  private java.lang.String _annotationId;
+
+  /**
+   * if true the RNA structure is shown with gaps, if false without
+   * 
+   */
+  private boolean _gapped;
+
+  /**
+   * keeps track of state for field: _gapped
+   */
+  private boolean _has_gapped;
+
+  /**
+   * name of the project jar entry that holds the VARNA viewer state for the
+   * structure
+   * 
+   */
+  private java.lang.String _viewerState;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SecondaryStructure()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
      */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+  public void deleteGapped()
+  {
+    this._has_gapped = false;
+  }
+
+  /**
+   * Returns the value of field 'annotationId'. The field 'annotationId' has the
+   * following description: id attribute of Annotation in vamsasModel for the
+   * secondary structure annotation shown in the viewer
+   * 
+   * 
+   * @return the value of field 'AnnotationId'.
+   */
+  public java.lang.String getAnnotationId()
+  {
+    return this._annotationId;
+  }
+
+  /**
+   * Returns the value of field 'gapped'. The field 'gapped' has the following
+   * description: if true the RNA structure is shown with gaps, if false without
+   * 
+   * 
+   * @return the value of field 'Gapped'.
+   */
+  public boolean getGapped()
+  {
+    return this._gapped;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'viewerState'. The field 'viewerState' has the
+   * following description: name of the project jar entry that holds the VARNA
+   * viewer state for the structure
+   * 
+   * 
+   * @return the value of field 'ViewerState'.
+   */
+  public java.lang.String getViewerState()
+  {
+    return this._viewerState;
+  }
+
+  /**
+   * Method hasGapped.
+   * 
+   * @return true if at least one Gapped has been added
+   */
+  public boolean hasGapped()
+  {
+    return this._has_gapped;
+  }
+
+  /**
+   * Returns the value of field 'gapped'. The field 'gapped' has the following
+   * description: if true the RNA structure is shown with gaps, if false without
+   * 
+   * 
+   * @return the value of field 'Gapped'.
+   */
+  public boolean isGapped()
+  {
+    return this._gapped;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'annotationId'. The field 'annotationId' has the
+   * following description: id attribute of Annotation in vamsasModel for the
+   * secondary structure annotation shown in the viewer
+   * 
+   * 
+   * @param annotationId
+   *          the value of field 'annotationId'.
+   */
+  public void setAnnotationId(final java.lang.String annotationId)
+  {
+    this._annotationId = annotationId;
+  }
+
+  /**
+   * Sets the value of field 'gapped'. The field 'gapped' has the following
+   * description: if true the RNA structure is shown with gaps, if false without
+   * 
+   * 
+   * @param gapped
+   *          the value of field 'gapped'.
+   */
+  public void setGapped(final boolean gapped)
+  {
+    this._gapped = gapped;
+    this._has_gapped = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *          the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'viewerState'. The field 'viewerState' has the
+   * following description: name of the project jar entry that holds the VARNA
+   * viewer state for the structure
+   * 
+   * 
+   * @param viewerState
+   *          the value of field 'viewerState'.
+   */
+  public void setViewerState(final java.lang.String viewerState)
+  {
+    this._viewerState = viewerState;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.SecondaryStructure
+   */
+  public static jalview.schemabinding.version2.SecondaryStructure unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.SecondaryStructure.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
index 14137d8..531ca66 100644
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,293 +19,310 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Sequence extends jalview.schemabinding.version2.SequenceType 
-implements java.io.Serializable
+public class Sequence extends jalview.schemabinding.version2.SequenceType
+        implements java.io.Serializable
 {
 
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * dataset sequence id for this sequence. Will be created as
-     * union of sequences.
-     *  
-     */
-    private java.lang.String _dsseqid;
-
-    /**
-     * Field _DBRefList.
-     */
-    private java.util.Vector _DBRefList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Sequence() {
-        super();
-        this._DBRefList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vDBRef
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addDBRef(
-            final jalview.schemabinding.version2.DBRef vDBRef)
-    throws java.lang.IndexOutOfBoundsException {
-        this._DBRefList.addElement(vDBRef);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vDBRef
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addDBRef(
-            final int index,
-            final jalview.schemabinding.version2.DBRef vDBRef)
-    throws java.lang.IndexOutOfBoundsException {
-        this._DBRefList.add(index, vDBRef);
-    }
-
-    /**
-     * Method enumerateDBRef.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.DBRef elements
-     */
-    public java.util.Enumeration enumerateDBRef(
-    ) {
-        return this._DBRefList.elements();
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * dataset sequence id for this sequence. Will be created as union of
+   * sequences.
+   * 
+   */
+  private java.lang.String _dsseqid;
+
+  /**
+   * Field _DBRefList.
+   */
+  private java.util.Vector _DBRefList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Sequence()
+  {
+    super();
+    this._DBRefList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vDBRef
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._DBRefList.addElement(vDBRef);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vDBRef
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addDBRef(final int index,
+          final jalview.schemabinding.version2.DBRef vDBRef)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._DBRefList.add(index, vDBRef);
+  }
+
+  /**
+   * Method enumerateDBRef.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.DBRef
+   *         elements
+   */
+  public java.util.Enumeration enumerateDBRef()
+  {
+    return this._DBRefList.elements();
+  }
+
+  /**
+   * Method getDBRef.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.DBRef at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.DBRef getDBRef(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._DBRefList.size())
+    {
+      throw new IndexOutOfBoundsException("getDBRef: Index value '" + index
+              + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
     }
 
-    /**
-     * Method getDBRef.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.DBRef at the given index
-     */
-    public jalview.schemabinding.version2.DBRef getDBRef(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._DBRefList.size()) {
-            throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
+    return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
+  }
+
+  /**
+   * Method getDBRef.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.DBRef[] getDBRef()
+  {
+    jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
+    return (jalview.schemabinding.version2.DBRef[]) this._DBRefList
+            .toArray(array);
+  }
+
+  /**
+   * Method getDBRefCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getDBRefCount()
+  {
+    return this._DBRefList.size();
+  }
+
+  /**
+   * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following
+   * description: dataset sequence id for this sequence. Will be created as
+   * union of sequences.
+   * 
+   * 
+   * @return the value of field 'Dsseqid'.
+   */
+  public java.lang.String getDsseqid()
+  {
+    return this._dsseqid;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Method getDBRef.Returns the contents of the collection in an
-     * Array.  
Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
      */
-    public jalview.schemabinding.version2.DBRef[] getDBRef(
-    ) {
-        jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
-        return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array);
+  public void removeAllDBRef()
+  {
+    this._DBRefList.clear();
+  }
+
+  /**
+   * Method removeDBRef.
+   * 
+   * @param vDBRef
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeDBRef(
+          final jalview.schemabinding.version2.DBRef vDBRef)
+  {
+    boolean removed = _DBRefList.remove(vDBRef);
+    return removed;
+  }
+
+  /**
+   * Method removeDBRefAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index)
+  {
+    java.lang.Object obj = this._DBRefList.remove(index);
+    return (jalview.schemabinding.version2.DBRef) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vDBRef
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setDBRef(final int index,
+          final jalview.schemabinding.version2.DBRef vDBRef)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._DBRefList.size())
+    {
+      throw new IndexOutOfBoundsException("setDBRef: Index value '" + index
+              + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
     }
 
-    /**
-     * Method getDBRefCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getDBRefCount(
-    ) {
-        return this._DBRefList.size();
-    }
-
-    /**
-     * Returns the value of field 'dsseqid'. The field 'dsseqid'
-     * has the following description: dataset sequence id for this
-     * sequence. Will be created as union of sequences.
-     *  
-     * 
-     * @return the value of field 'Dsseqid'.
-     */
-    public java.lang.String getDsseqid(
-    ) {
-        return this._dsseqid;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllDBRef(
-    ) {
-        this._DBRefList.clear();
-    }
-
-    /**
-     * Method removeDBRef.
-     * 
-     * @param vDBRef
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeDBRef(
-            final jalview.schemabinding.version2.DBRef vDBRef) {
-        boolean removed = _DBRefList.remove(vDBRef);
-        return removed;
-    }
-
-    /**
-     * Method removeDBRefAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.DBRef removeDBRefAt(
-            final int index) {
-        java.lang.Object obj = this._DBRefList.remove(index);
-        return (jalview.schemabinding.version2.DBRef) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vDBRef
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setDBRef(
-            final int index,
-            final jalview.schemabinding.version2.DBRef vDBRef)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._DBRefList.size()) {
-            throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
-        }
-        
-        this._DBRefList.set(index, vDBRef);
-    }
-
-    /**
-     * 
-     * 
-     * @param vDBRefArray
-     */
-    public void setDBRef(
-            final jalview.schemabinding.version2.DBRef[] vDBRefArray) {
-        //-- copy array
-        _DBRefList.clear();
-        
-        for (int i = 0; i < vDBRefArray.length; i++) {
-                this._DBRefList.add(vDBRefArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'dsseqid'. The field 'dsseqid' has
-     * the following description: dataset sequence id for this
-     * sequence. Will be created as union of sequences.
-     *  
-     * 
-     * @param dsseqid the value of field 'dsseqid'.
-     */
-    public void setDsseqid(
-            final java.lang.String dsseqid) {
-        this._dsseqid = dsseqid;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.SequenceType
-     */
-    public static jalview.schemabinding.version2.SequenceType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._DBRefList.set(index, vDBRef);
+  }
+
+  /**
+   * 
+   * 
+   * @param vDBRefArray
+   */
+  public void setDBRef(
+          final jalview.schemabinding.version2.DBRef[] vDBRefArray)
+  {
+    // -- copy array
+    _DBRefList.clear();
+
+    for (int i = 0; i < vDBRefArray.length; i++)
+    {
+      this._DBRefList.add(vDBRefArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following
+   * description: dataset sequence id for this sequence. Will be created as
+   * union of sequences.
+   * 
+   * 
+   * @param dsseqid
+   *          the value of field 'dsseqid'.
+   */
+  public void setDsseqid(final java.lang.String dsseqid)
+  {
+    this._dsseqid = dsseqid;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.SequenceType
+   */
+  public static jalview.schemabinding.version2.SequenceType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SequenceType) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Sequence.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 7b670a5..8be8022 100644
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,789 +19,854 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _gapChar.
-     */
-    private java.lang.String _gapChar;
-
-    /**
-     * reference to set where jalview will gather the dataset
-     * sequences for all sequences in the set. 
-     *  
-     */
-    private java.lang.String _datasetId;
-
-    /**
-     * Field _sequenceList.
-     */
-    private java.util.Vector _sequenceList;
-
-    /**
-     * Field _annotationList.
-     */
-    private java.util.Vector _annotationList;
-
-    /**
-     * Field _sequenceSetPropertiesList.
-     */
-    private java.util.Vector _sequenceSetPropertiesList;
-
-    /**
-     * Field _alcodonFrameList.
-     */
-    private java.util.Vector _alcodonFrameList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSet() {
-        super();
-        this._sequenceList = new java.util.Vector();
-        this._annotationList = new java.util.Vector();
-        this._sequenceSetPropertiesList = new java.util.Vector();
-        this._alcodonFrameList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vAlcodonFrame
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodonFrame(
-            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodonFrameList.addElement(vAlcodonFrame);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodonFrame
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAlcodonFrame(
-            final int index,
-            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
-    throws java.lang.IndexOutOfBoundsException {
-        this._alcodonFrameList.add(index, vAlcodonFrame);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotation(
-            final jalview.schemabinding.version2.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationList.addElement(vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addAnnotation(
-            final int index,
-            final jalview.schemabinding.version2.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        this._annotationList.add(index, vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequence(
-            final jalview.schemabinding.version2.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceList.addElement(vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequence(
-            final int index,
-            final jalview.schemabinding.version2.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceList.add(index, vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSetProperties
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSetProperties(
-            final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSetProperties
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSetProperties(
-            final int index,
-            final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);
-    }
-
-    /**
-     * Method enumerateAlcodonFrame.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.AlcodonFrame elements
-     */
-    public java.util.Enumeration enumerateAlcodonFrame(
-    ) {
-        return this._alcodonFrameList.elements();
-    }
-
-    /**
-     * Method enumerateAnnotation.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Annotation elements
-     */
-    public java.util.Enumeration enumerateAnnotation(
-    ) {
-        return this._annotationList.elements();
-    }
-
-    /**
-     * Method enumerateSequence.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.Sequence elements
-     */
-    public java.util.Enumeration enumerateSequence(
-    ) {
-        return this._sequenceList.elements();
-    }
-
-    /**
-     * Method enumerateSequenceSetProperties.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.SequenceSetProperties elements
-     */
-    public java.util.Enumeration enumerateSequenceSetProperties(
-    ) {
-        return this._sequenceSetPropertiesList.elements();
-    }
-
-    /**
-     * Method getAlcodonFrame.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.AlcodonFrame at the given inde
-     */
-    public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodonFrameList.size()) {
-            throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index);
-    }
-
-    /**
-     * Method getAlcodonFrame.Returns the contents of the
-     * collection in an Array.  
Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we know that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame(
-    ) {
-        jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
-        return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array);
-    }
-
-    /**
-     * Method getAlcodonFrameCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAlcodonFrameCount(
-    ) {
-        return this._alcodonFrameList.size();
-    }
-
-    /**
-     * Method getAnnotation.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Annotation at the given index
-     */
-    public jalview.schemabinding.version2.Annotation getAnnotation(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationList.size()) {
-            throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Annotation) _annotationList.get(index);
-    }
-
-    /**
-     * Method getAnnotation.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Annotation[] getAnnotation(
-    ) {
-        jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];
-        return (jalview.schemabinding.version2.Annotation[]) this._annotationList.toArray(array);
-    }
-
-    /**
-     * Method getAnnotationCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getAnnotationCount(
-    ) {
-        return this._annotationList.size();
-    }
-
-    /**
-     * Returns the value of field 'datasetId'. The field
-     * 'datasetId' has the following description: reference to set
-     * where jalview will gather the dataset sequences for all
-     * sequences in the set. 
-     *  
-     * 
-     * @return the value of field 'DatasetId'.
-     */
-    public java.lang.String getDatasetId(
-    ) {
-        return this._datasetId;
-    }
-
-    /**
-     * Returns the value of field 'gapChar'.
-     * 
-     * @return the value of field 'GapChar'.
-     */
-    public java.lang.String getGapChar(
-    ) {
-        return this._gapChar;
-    }
-
-    /**
-     * Method getSequence.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.Sequence at the given index
-     */
-    public jalview.schemabinding.version2.Sequence getSequence(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceList.size()) {
-            throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.Sequence) _sequenceList.get(index);
-    }
-
-    /**
-     * Method getSequence.Returns the contents of the collection in
-     * an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.Sequence[] getSequence(
-    ) {
-        jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];
-        return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array);
-    }
-
-    /**
-     * Method getSequenceCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceCount(
-    ) {
-        return this._sequenceList.size();
-    }
-
-    /**
-     * Method getSequenceSetProperties.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.SequenceSetProperties at the
-     * given index
-     */
-    public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {
-            throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index);
-    }
-
-    /**
-     * Method getSequenceSetProperties.Returns the contents of the
-     * collection in an Array.  
Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we know that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties(
-    ) {
-        jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
-        return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array);
-    }
-
-    /**
-     * Method getSequenceSetPropertiesCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceSetPropertiesCount(
-    ) {
-        return this._sequenceSetPropertiesList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Method removeAlcodonFrame.
-     * 
-     * @param vAlcodonFrame
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAlcodonFrame(
-            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) {
-        boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
-        return removed;
-    }
-
-    /**
-     * Method removeAlcodonFrameAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
-            final int index) {
-        java.lang.Object obj = this._alcodonFrameList.remove(index);
-        return (jalview.schemabinding.version2.AlcodonFrame) obj;
-    }
-
-    /**
-     */
-    public void removeAllAlcodonFrame(
-    ) {
-        this._alcodonFrameList.clear();
-    }
-
-    /**
-     */
-    public void removeAllAnnotation(
-    ) {
-        this._annotationList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSequence(
-    ) {
-        this._sequenceList.clear();
-    }
-
-    /**
-     */
-    public void removeAllSequenceSetProperties(
-    ) {
-        this._sequenceSetPropertiesList.clear();
-    }
-
-    /**
-     * Method removeAnnotation.
-     * 
-     * @param vAnnotation
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeAnnotation(
-            final jalview.schemabinding.version2.Annotation vAnnotation) {
-        boolean removed = _annotationList.remove(vAnnotation);
-        return removed;
-    }
-
-    /**
-     * Method removeAnnotationAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Annotation removeAnnotationAt(
-            final int index) {
-        java.lang.Object obj = this._annotationList.remove(index);
-        return (jalview.schemabinding.version2.Annotation) obj;
-    }
-
-    /**
-     * Method removeSequence.
-     * 
-     * @param vSequence
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequence(
-            final jalview.schemabinding.version2.Sequence vSequence) {
-        boolean removed = _sequenceList.remove(vSequence);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.Sequence removeSequenceAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceList.remove(index);
-        return (jalview.schemabinding.version2.Sequence) obj;
-    }
-
-    /**
-     * Method removeSequenceSetProperties.
-     * 
-     * @param vSequenceSetProperties
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequenceSetProperties(
-            final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) {
-        boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceSetPropertiesAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
-        return (jalview.schemabinding.version2.SequenceSetProperties) obj;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAlcodonFrame
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAlcodonFrame(
-            final int index,
-            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._alcodonFrameList.size()) {
-            throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
-        }
-        
-        this._alcodonFrameList.set(index, vAlcodonFrame);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAlcodonFrameArray
-     */
-    public void setAlcodonFrame(
-            final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) {
-        //-- copy array
-        _alcodonFrameList.clear();
-        
-        for (int i = 0; i < vAlcodonFrameArray.length; i++) {
-                this._alcodonFrameList.add(vAlcodonFrameArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setAnnotation(
-            final int index,
-            final jalview.schemabinding.version2.Annotation vAnnotation)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._annotationList.size()) {
-            throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
-        }
-        
-        this._annotationList.set(index, vAnnotation);
-    }
-
-    /**
-     * 
-     * 
-     * @param vAnnotationArray
-     */
-    public void setAnnotation(
-            final jalview.schemabinding.version2.Annotation[] vAnnotationArray) {
-        //-- copy array
-        _annotationList.clear();
-        
-        for (int i = 0; i < vAnnotationArray.length; i++) {
-                this._annotationList.add(vAnnotationArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'datasetId'. The field 'datasetId'
-     * has the following description: reference to set where
-     * jalview will gather the dataset sequences for all sequences
-     * in the set. 
-     *  
-     * 
-     * @param datasetId the value of field 'datasetId'.
-     */
-    public void setDatasetId(
-            final java.lang.String datasetId) {
-        this._datasetId = datasetId;
-    }
-
-    /**
-     * Sets the value of field 'gapChar'.
-     * 
-     * @param gapChar the value of field 'gapChar'.
-     */
-    public void setGapChar(
-            final java.lang.String gapChar) {
-        this._gapChar = gapChar;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequence(
-            final int index,
-            final jalview.schemabinding.version2.Sequence vSequence)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceList.size()) {
-            throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
-        }
-        
-        this._sequenceList.set(index, vSequence);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceArray
-     */
-    public void setSequence(
-            final jalview.schemabinding.version2.Sequence[] vSequenceArray) {
-        //-- copy array
-        _sequenceList.clear();
-        
-        for (int i = 0; i < vSequenceArray.length; i++) {
-                this._sequenceList.add(vSequenceArray[i]);
-        }
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSetProperties
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequenceSetProperties(
-            final int index,
-            final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {
-            throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");
-        }
-        
-        this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSetPropertiesArray
-     */
-    public void setSequenceSetProperties(
-            final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) {
-        //-- copy array
-        _sequenceSetPropertiesList.clear();
-        
-        for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) {
-                this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);
-        }
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.SequenceSet
-     */
-    public static jalview.schemabinding.version2.SequenceSet unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class SequenceSet implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _gapChar.
+   */
+  private java.lang.String _gapChar;
+
+  /**
+   * reference to set where jalview will gather the dataset sequences for all
+   * sequences in the set.
+   * 
+   */
+  private java.lang.String _datasetId;
+
+  /**
+   * Field _sequenceList.
+   */
+  private java.util.Vector _sequenceList;
+
+  /**
+   * Field _annotationList.
+   */
+  private java.util.Vector _annotationList;
+
+  /**
+   * Field _sequenceSetPropertiesList.
+   */
+  private java.util.Vector _sequenceSetPropertiesList;
+
+  /**
+   * Field _alcodonFrameList.
+   */
+  private java.util.Vector _alcodonFrameList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSet()
+  {
+    super();
+    this._sequenceList = new java.util.Vector();
+    this._annotationList = new java.util.Vector();
+    this._sequenceSetPropertiesList = new java.util.Vector();
+    this._alcodonFrameList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAlcodonFrame
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlcodonFrame(
+          final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodonFrameList.addElement(vAlcodonFrame);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodonFrame
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAlcodonFrame(final int index,
+          final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._alcodonFrameList.add(index, vAlcodonFrame);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAnnotation(
+          final jalview.schemabinding.version2.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationList.addElement(vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAnnotation(final int index,
+          final jalview.schemabinding.version2.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._annotationList.add(index, vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequence(
+          final jalview.schemabinding.version2.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceList.addElement(vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequence(final int index,
+          final jalview.schemabinding.version2.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceList.add(index, vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSetProperties
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSetProperties(
+          final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSetProperties
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSetProperties(
+          final int index,
+          final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);
+  }
+
+  /**
+   * Method enumerateAlcodonFrame.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame
+   *         elements
+   */
+  public java.util.Enumeration enumerateAlcodonFrame()
+  {
+    return this._alcodonFrameList.elements();
+  }
+
+  /**
+   * Method enumerateAnnotation.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Annotation
+   *         elements
+   */
+  public java.util.Enumeration enumerateAnnotation()
+  {
+    return this._annotationList.elements();
+  }
+
+  /**
+   * Method enumerateSequence.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Sequence
+   *         elements
+   */
+  public java.util.Enumeration enumerateSequence()
+  {
+    return this._sequenceList.elements();
+  }
+
+  /**
+   * Method enumerateSequenceSetProperties.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.SequenceSetProperties elements
+   */
+  public java.util.Enumeration enumerateSequenceSetProperties()
+  {
+    return this._sequenceSetPropertiesList.elements();
+  }
+
+  /**
+   * Method getAlcodonFrame.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.AlcodonFrame at the
+   *         given inde
+   */
+  public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodonFrameList.size())
+    {
+      throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonFrameList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList
+            .get(index);
+  }
+
+  /**
+   * Method getAlcodonFrame.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame()
+  {
+    jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
+    return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAlcodonFrameCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAlcodonFrameCount()
+  {
+    return this._alcodonFrameList.size();
+  }
+
+  /**
+   * Method getAnnotation.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Annotation at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Annotation getAnnotation(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationList.size())
+    {
+      throw new IndexOutOfBoundsException("getAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Annotation) _annotationList
+            .get(index);
+  }
+
+  /**
+   * Method getAnnotation.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Annotation[] getAnnotation()
+  {
+    jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];
+    return (jalview.schemabinding.version2.Annotation[]) this._annotationList
+            .toArray(array);
+  }
+
+  /**
+   * Method getAnnotationCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAnnotationCount()
+  {
+    return this._annotationList.size();
+  }
+
+  /**
+   * Returns the value of field 'datasetId'. The field 'datasetId' has the
+   * following description: reference to set where jalview will gather the
+   * dataset sequences for all sequences in the set.
+   * 
+   * 
+   * @return the value of field 'DatasetId'.
+   */
+  public java.lang.String getDatasetId()
+  {
+    return this._datasetId;
+  }
+
+  /**
+   * Returns the value of field 'gapChar'.
+   * 
+   * @return the value of field 'GapChar'.
+   */
+  public java.lang.String getGapChar()
+  {
+    return this._gapChar;
+  }
+
+  /**
+   * Method getSequence.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Sequence at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.Sequence getSequence(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceList.size())
+    {
+      throw new IndexOutOfBoundsException("getSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.Sequence) _sequenceList
+            .get(index);
+  }
+
+  /**
+   * Method getSequence.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.Sequence[] getSequence()
+  {
+    jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];
+    return (jalview.schemabinding.version2.Sequence[]) this._sequenceList
+            .toArray(array);
+  }
+
+  /**
+   * Method getSequenceCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceCount()
+  {
+    return this._sequenceList.size();
+  }
+
+  /**
+   * Method getSequenceSetProperties.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the
+   *         jalview.schemabinding.version2.SequenceSetProperties at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetPropertiesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getSequenceSetProperties: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._sequenceSetPropertiesList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList
+            .get(index);
+  }
+
+  /**
+   * Method getSequenceSetProperties.Returns the contents of the collection in
+   * an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()
+  {
+    jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
+    return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList
+            .toArray(array);
+  }
+
+  /**
+   * Method getSequenceSetPropertiesCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceSetPropertiesCount()
+  {
+    return this._sequenceSetPropertiesList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method removeAlcodonFrame.
+   * 
+   * @param vAlcodonFrame
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAlcodonFrame(
+          final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+  {
+    boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
+    return removed;
+  }
+
+  /**
+   * Method removeAlcodonFrameAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
+          final int index)
+  {
+    java.lang.Object obj = this._alcodonFrameList.remove(index);
+    return (jalview.schemabinding.version2.AlcodonFrame) obj;
+  }
+
+  /**
+     */
+  public void removeAllAlcodonFrame()
+  {
+    this._alcodonFrameList.clear();
+  }
+
+  /**
+     */
+  public void removeAllAnnotation()
+  {
+    this._annotationList.clear();
+  }
+
+  /**
+     */
+  public void removeAllSequence()
+  {
+    this._sequenceList.clear();
+  }
+
+  /**
+     */
+  public void removeAllSequenceSetProperties()
+  {
+    this._sequenceSetPropertiesList.clear();
+  }
+
+  /**
+   * Method removeAnnotation.
+   * 
+   * @param vAnnotation
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAnnotation(
+          final jalview.schemabinding.version2.Annotation vAnnotation)
+  {
+    boolean removed = _annotationList.remove(vAnnotation);
+    return removed;
+  }
+
+  /**
+   * Method removeAnnotationAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Annotation removeAnnotationAt(
+          final int index)
+  {
+    java.lang.Object obj = this._annotationList.remove(index);
+    return (jalview.schemabinding.version2.Annotation) obj;
+  }
+
+  /**
+   * Method removeSequence.
+   * 
+   * @param vSequence
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequence(
+          final jalview.schemabinding.version2.Sequence vSequence)
+  {
+    boolean removed = _sequenceList.remove(vSequence);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.Sequence removeSequenceAt(
+          final int index)
+  {
+    java.lang.Object obj = this._sequenceList.remove(index);
+    return (jalview.schemabinding.version2.Sequence) obj;
+  }
+
+  /**
+   * Method removeSequenceSetProperties.
+   * 
+   * @param vSequenceSetProperties
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequenceSetProperties(
+          final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+  {
+    boolean removed = _sequenceSetPropertiesList
+            .remove(vSequenceSetProperties);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceSetPropertiesAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
+          final int index)
+  {
+    java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
+    return (jalview.schemabinding.version2.SequenceSetProperties) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAlcodonFrame
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAlcodonFrame(final int index,
+          final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._alcodonFrameList.size())
+    {
+      throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonFrameList.size() - 1) + "]");
+    }
+
+    this._alcodonFrameList.set(index, vAlcodonFrame);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAlcodonFrameArray
+   */
+  public void setAlcodonFrame(
+          final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray)
+  {
+    // -- copy array
+    _alcodonFrameList.clear();
+
+    for (int i = 0; i < vAlcodonFrameArray.length; i++)
+    {
+      this._alcodonFrameList.add(vAlcodonFrameArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAnnotation
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAnnotation(final int index,
+          final jalview.schemabinding.version2.Annotation vAnnotation)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._annotationList.size())
+    {
+      throw new IndexOutOfBoundsException("setAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
+    }
+
+    this._annotationList.set(index, vAnnotation);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAnnotationArray
+   */
+  public void setAnnotation(
+          final jalview.schemabinding.version2.Annotation[] vAnnotationArray)
+  {
+    // -- copy array
+    _annotationList.clear();
+
+    for (int i = 0; i < vAnnotationArray.length; i++)
+    {
+      this._annotationList.add(vAnnotationArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'datasetId'. The field 'datasetId' has the
+   * following description: reference to set where jalview will gather the
+   * dataset sequences for all sequences in the set.
+   * 
+   * 
+   * @param datasetId
+   *          the value of field 'datasetId'.
+   */
+  public void setDatasetId(final java.lang.String datasetId)
+  {
+    this._datasetId = datasetId;
+  }
+
+  /**
+   * Sets the value of field 'gapChar'.
+   * 
+   * @param gapChar
+   *          the value of field 'gapChar'.
+   */
+  public void setGapChar(final java.lang.String gapChar)
+  {
+    this._gapChar = gapChar;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequence
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSequence(final int index,
+          final jalview.schemabinding.version2.Sequence vSequence)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceList.size())
+    {
+      throw new IndexOutOfBoundsException("setSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
+    }
+
+    this._sequenceList.set(index, vSequence);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceArray
+   */
+  public void setSequence(
+          final jalview.schemabinding.version2.Sequence[] vSequenceArray)
+  {
+    // -- copy array
+    _sequenceList.clear();
+
+    for (int i = 0; i < vSequenceArray.length; i++)
+    {
+      this._sequenceList.add(vSequenceArray[i]);
+    }
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSetProperties
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSequenceSetProperties(
+          final int index,
+          final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetPropertiesList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setSequenceSetProperties: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._sequenceSetPropertiesList.size() - 1) + "]");
+    }
+
+    this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSetPropertiesArray
+   */
+  public void setSequenceSetProperties(
+          final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray)
+  {
+    // -- copy array
+    _sequenceSetPropertiesList.clear();
+
+    for (int i = 0; i < vSequenceSetPropertiesArray.length; i++)
+    {
+      this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.SequenceSet
+   */
+  public static jalview.schemabinding.version2.SequenceSet unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SequenceSet) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.SequenceSet.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceSetProperties.java b/src/jalview/schemabinding/version2/SequenceSetProperties.java
index a078c78..3a7d172 100644
--- a/src/jalview/schemabinding/version2/SequenceSetProperties.java
+++ b/src/jalview/schemabinding/version2/SequenceSetProperties.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,152 +19,165 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSetProperties implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _key.
-     */
-    private java.lang.String _key;
-
-    /**
-     * Field _value.
-     */
-    private java.lang.String _value;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSetProperties() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'key'.
-     * 
-     * @return the value of field 'Key'.
-     */
-    public java.lang.String getKey(
-    ) {
-        return this._key;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public java.lang.String getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'key'.
-     * 
-     * @param key the value of field 'key'.
-     */
-    public void setKey(
-            final java.lang.String key) {
-        this._key = key;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final java.lang.String value) {
-        this._value = value;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.SequenceSetProperties
-     */
-    public static jalview.schemabinding.version2.SequenceSetProperties unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSetProperties.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class SequenceSetProperties implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _key.
+   */
+  private java.lang.String _key;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSetProperties()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'key'.
+   * 
+   * @return the value of field 'Key'.
+   */
+  public java.lang.String getKey()
+  {
+    return this._key;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'key'.
+   * 
+   * @param key
+   *          the value of field 'key'.
+   */
+  public void setKey(final java.lang.String key)
+  {
+    this._key = key;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *          the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled
+   *         jalview.schemabinding.version2.SequenceSetProperties
+   */
+  public static jalview.schemabinding.version2.SequenceSetProperties unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.SequenceSetProperties.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java
index 5886fbb..f213ebb 100644
--- a/src/jalview/schemabinding/version2/SequenceType.java
+++ b/src/jalview/schemabinding/version2/SequenceType.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,202 +19,215 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceType implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _description.
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _sequence.
-     */
-    private java.lang.String _sequence;
-
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceType() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'sequence'.
-     * 
-     * @return the value of field 'Sequence'.
-     */
-    public java.lang.String getSequence(
-    ) {
-        return this._sequence;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'sequence'.
-     * 
-     * @param sequence the value of field 'sequence'.
-     */
-    public void setSequence(
-            final java.lang.String sequence) {
-        this._sequence = sequence;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.SequenceType
-     */
-    public static jalview.schemabinding.version2.SequenceType unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class SequenceType implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _sequence.
+   */
+  private java.lang.String _sequence;
+
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceType()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'sequence'.
+   * 
+   * @return the value of field 'Sequence'.
+   */
+  public java.lang.String getSequence()
+  {
+    return this._sequence;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *          the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'sequence'.
+   * 
+   * @param sequence
+   *          the value of field 'sequence'.
+   */
+  public void setSequence(final java.lang.String sequence)
+  {
+    this._sequence = sequence;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.SequenceType
+   */
+  public static jalview.schemabinding.version2.SequenceType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SequenceType) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.SequenceType.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java
index 2c19f1f..c458971 100644
--- a/src/jalview/schemabinding/version2/Setting.java
+++ b/src/jalview/schemabinding/version2/Setting.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,670 +19,671 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Setting implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-    /**
-     * Field _display.
-     */
-    private boolean _display;
-
-    /**
-     * keeps track of state for field: _display
-     */
-    private boolean _has_display;
-
-    /**
-     * Field _order.
-     */
-    private float _order;
-
-    /**
-     * keeps track of state for field: _order
-     */
-    private boolean _has_order;
-
-    /**
-     * Optional minimum colour
-     *  for graduated
-     *  feature
-     *  colour
-     *  
-     */
-    private int _mincolour;
-
-    /**
-     * keeps track of state for field: _mincolour
-     */
-    private boolean _has_mincolour;
-
-    /**
-     * threshold value for
-     *  graduated feature colour
-     *  
-     */
-    private float _threshold;
-
-    /**
-     * keeps track of state for field: _threshold
-     */
-    private boolean _has_threshold;
-
-    /**
-     * threshold type for
-     *  graduated feature colour
-     *  
-     */
-    private int _threshstate;
-
-    /**
-     * keeps track of state for field: _threshstate
-     */
-    private boolean _has_threshstate;
-
-    /**
-     * Field _max.
-     */
-    private float _max;
-
-    /**
-     * keeps track of state for field: _max
-     */
-    private boolean _has_max;
-
-    /**
-     * Field _min.
-     */
-    private float _min;
-
-    /**
-     * keeps track of state for field: _min
-     */
-    private boolean _has_min;
-
-    /**
-     * Field _colourByLabel.
-     */
-    private boolean _colourByLabel;
-
-    /**
-     * keeps track of state for field: _colourByLabel
-     */
-    private boolean _has_colourByLabel;
-
-    /**
-     * Field _autoScale.
-     */
-    private boolean _autoScale;
-
-    /**
-     * keeps track of state for field: _autoScale
-     */
-    private boolean _has_autoScale;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Setting() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteAutoScale(
-    ) {
-        this._has_autoScale= false;
-    }
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteColourByLabel(
-    ) {
-        this._has_colourByLabel= false;
-    }
-
-    /**
-     */
-    public void deleteDisplay(
-    ) {
-        this._has_display= false;
-    }
-
-    /**
-     */
-    public void deleteMax(
-    ) {
-        this._has_max= false;
-    }
-
-    /**
-     */
-    public void deleteMin(
-    ) {
-        this._has_min= false;
-    }
-
-    /**
-     */
-    public void deleteMincolour(
-    ) {
-        this._has_mincolour= false;
-    }
-
-    /**
-     */
-    public void deleteOrder(
-    ) {
-        this._has_order= false;
-    }
-
-    /**
-     */
-    public void deleteThreshold(
-    ) {
-        this._has_threshold= false;
-    }
-
-    /**
-     */
-    public void deleteThreshstate(
-    ) {
-        this._has_threshstate= false;
-    }
-
-    /**
-     * Returns the value of field 'autoScale'.
-     * 
-     * @return the value of field 'AutoScale'.
-     */
-    public boolean getAutoScale(
-    ) {
-        return this._autoScale;
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'colourByLabel'.
-     * 
-     * @return the value of field 'ColourByLabel'.
-     */
-    public boolean getColourByLabel(
-    ) {
-        return this._colourByLabel;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean getDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Returns the value of field 'max'.
-     * 
-     * @return the value of field 'Max'.
-     */
-    public float getMax(
-    ) {
-        return this._max;
-    }
-
-    /**
-     * Returns the value of field 'min'.
-     * 
-     * @return the value of field 'Min'.
-     */
-    public float getMin(
-    ) {
-        return this._min;
-    }
-
-    /**
-     * Returns the value of field 'mincolour'. The field
-     * 'mincolour' has the following description: Optional minimum
-     * colour
-     *  for graduated
-     *  feature
-     *  colour
-     *  
-     * 
-     * @return the value of field 'Mincolour'.
-     */
-    public int getMincolour(
-    ) {
-        return this._mincolour;
-    }
-
-    /**
-     * Returns the value of field 'order'.
-     * 
-     * @return the value of field 'Order'.
-     */
-    public float getOrder(
-    ) {
-        return this._order;
-    }
-
-    /**
-     * Returns the value of field 'threshold'. The field
-     * 'threshold' has the following description: threshold value
-     * for
-     *  graduated feature colour
-     *  
-     * 
-     * @return the value of field 'Threshold'.
-     */
-    public float getThreshold(
-    ) {
-        return this._threshold;
-    }
-
-    /**
-     * Returns the value of field 'threshstate'. The field
-     * 'threshstate' has the following description: threshold type
-     * for
-     *  graduated feature colour
-     *  
-     * 
-     * @return the value of field 'Threshstate'.
-     */
-    public int getThreshstate(
-    ) {
-        return this._threshstate;
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method hasAutoScale.
-     * 
-     * @return true if at least one AutoScale has been added
-     */
-    public boolean hasAutoScale(
-    ) {
-        return this._has_autoScale;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasColourByLabel.
-     * 
-     * @return true if at least one ColourByLabel has been added
-     */
-    public boolean hasColourByLabel(
-    ) {
-        return this._has_colourByLabel;
-    }
-
-    /**
-     * Method hasDisplay.
-     * 
-     * @return true if at least one Display has been added
-     */
-    public boolean hasDisplay(
-    ) {
-        return this._has_display;
-    }
-
-    /**
-     * Method hasMax.
-     * 
-     * @return true if at least one Max has been added
-     */
-    public boolean hasMax(
-    ) {
-        return this._has_max;
-    }
-
-    /**
-     * Method hasMin.
-     * 
-     * @return true if at least one Min has been added
-     */
-    public boolean hasMin(
-    ) {
-        return this._has_min;
-    }
-
-    /**
-     * Method hasMincolour.
-     * 
-     * @return true if at least one Mincolour has been added
-     */
-    public boolean hasMincolour(
-    ) {
-        return this._has_mincolour;
-    }
-
-    /**
-     * Method hasOrder.
-     * 
-     * @return true if at least one Order has been added
-     */
-    public boolean hasOrder(
-    ) {
-        return this._has_order;
-    }
-
-    /**
-     * Method hasThreshold.
-     * 
-     * @return true if at least one Threshold has been added
-     */
-    public boolean hasThreshold(
-    ) {
-        return this._has_threshold;
-    }
-
-    /**
-     * Method hasThreshstate.
-     * 
-     * @return true if at least one Threshstate has been added
-     */
-    public boolean hasThreshstate(
-    ) {
-        return this._has_threshstate;
-    }
-
-    /**
-     * Returns the value of field 'autoScale'.
-     * 
-     * @return the value of field 'AutoScale'.
-     */
-    public boolean isAutoScale(
-    ) {
-        return this._autoScale;
-    }
-
-    /**
-     * Returns the value of field 'colourByLabel'.
-     * 
-     * @return the value of field 'ColourByLabel'.
-     */
-    public boolean isColourByLabel(
-    ) {
-        return this._colourByLabel;
-    }
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return the value of field 'Display'.
-     */
-    public boolean isDisplay(
-    ) {
-        return this._display;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'autoScale'.
-     * 
-     * @param autoScale the value of field 'autoScale'.
-     */
-    public void setAutoScale(
-            final boolean autoScale) {
-        this._autoScale = autoScale;
-        this._has_autoScale = true;
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'colourByLabel'.
-     * 
-     * @param colourByLabel the value of field 'colourByLabel'.
-     */
-    public void setColourByLabel(
-            final boolean colourByLabel) {
-        this._colourByLabel = colourByLabel;
-        this._has_colourByLabel = true;
-    }
-
-    /**
-     * Sets the value of field 'display'.
-     * 
-     * @param display the value of field 'display'.
-     */
-    public void setDisplay(
-            final boolean display) {
-        this._display = display;
-        this._has_display = true;
-    }
-
-    /**
-     * Sets the value of field 'max'.
-     * 
-     * @param max the value of field 'max'.
-     */
-    public void setMax(
-            final float max) {
-        this._max = max;
-        this._has_max = true;
-    }
-
-    /**
-     * Sets the value of field 'min'.
-     * 
-     * @param min the value of field 'min'.
-     */
-    public void setMin(
-            final float min) {
-        this._min = min;
-        this._has_min = true;
-    }
-
-    /**
-     * Sets the value of field 'mincolour'. The field 'mincolour'
-     * has the following description: Optional minimum colour
-     *  for graduated
-     *  feature
-     *  colour
-     *  
-     * 
-     * @param mincolour the value of field 'mincolour'.
-     */
-    public void setMincolour(
-            final int mincolour) {
-        this._mincolour = mincolour;
-        this._has_mincolour = true;
-    }
-
-    /**
-     * Sets the value of field 'order'.
-     * 
-     * @param order the value of field 'order'.
-     */
-    public void setOrder(
-            final float order) {
-        this._order = order;
-        this._has_order = true;
-    }
-
-    /**
-     * Sets the value of field 'threshold'. The field 'threshold'
-     * has the following description: threshold value for
-     *  graduated feature colour
-     *  
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(
-            final float threshold) {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    }
-
-    /**
-     * Sets the value of field 'threshstate'. The field
-     * 'threshstate' has the following description: threshold type
-     * for
-     *  graduated feature colour
-     *  
-     * 
-     * @param threshstate the value of field 'threshstate'.
-     */
-    public void setThreshstate(
-            final int threshstate) {
-        this._threshstate = threshstate;
-        this._has_threshstate = true;
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Settin
-     */
-    public static jalview.schemabinding.version2.Setting unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Setting implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  /**
+   * Field _display.
+   */
+  private boolean _display;
+
+  /**
+   * keeps track of state for field: _display
+   */
+  private boolean _has_display;
+
+  /**
+   * Field _order.
+   */
+  private float _order;
+
+  /**
+   * keeps track of state for field: _order
+   */
+  private boolean _has_order;
+
+  /**
+   * Optional minimum colour for graduated feature colour
+   * 
+   */
+  private int _mincolour;
+
+  /**
+   * keeps track of state for field: _mincolour
+   */
+  private boolean _has_mincolour;
+
+  /**
+   * threshold value for graduated feature colour
+   * 
+   */
+  private float _threshold;
+
+  /**
+   * keeps track of state for field: _threshold
+   */
+  private boolean _has_threshold;
+
+  /**
+   * threshold type for graduated feature colour
+   * 
+   */
+  private int _threshstate;
+
+  /**
+   * keeps track of state for field: _threshstate
+   */
+  private boolean _has_threshstate;
+
+  /**
+   * Field _max.
+   */
+  private float _max;
+
+  /**
+   * keeps track of state for field: _max
+   */
+  private boolean _has_max;
+
+  /**
+   * Field _min.
+   */
+  private float _min;
+
+  /**
+   * keeps track of state for field: _min
+   */
+  private boolean _has_min;
+
+  /**
+   * Field _colourByLabel.
+   */
+  private boolean _colourByLabel;
+
+  /**
+   * keeps track of state for field: _colourByLabel
+   */
+  private boolean _has_colourByLabel;
+
+  /**
+   * Field _autoScale.
+   */
+  private boolean _autoScale;
+
+  /**
+   * keeps track of state for field: _autoScale
+   */
+  private boolean _has_autoScale;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Setting()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteAutoScale()
+  {
+    this._has_autoScale = false;
+  }
+
+  /**
+     */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+     */
+  public void deleteColourByLabel()
+  {
+    this._has_colourByLabel = false;
+  }
+
+  /**
+     */
+  public void deleteDisplay()
+  {
+    this._has_display = false;
+  }
+
+  /**
+     */
+  public void deleteMax()
+  {
+    this._has_max = false;
+  }
+
+  /**
+     */
+  public void deleteMin()
+  {
+    this._has_min = false;
+  }
+
+  /**
+     */
+  public void deleteMincolour()
+  {
+    this._has_mincolour = false;
+  }
+
+  /**
+     */
+  public void deleteOrder()
+  {
+    this._has_order = false;
+  }
+
+  /**
+     */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  }
+
+  /**
+     */
+  public void deleteThreshstate()
+  {
+    this._has_threshstate = false;
+  }
+
+  /**
+   * Returns the value of field 'autoScale'.
+   * 
+   * @return the value of field 'AutoScale'.
+   */
+  public boolean getAutoScale()
+  {
+    return this._autoScale;
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'colourByLabel'.
+   * 
+   * @return the value of field 'ColourByLabel'.
+   */
+  public boolean getColourByLabel()
+  {
+    return this._colourByLabel;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean getDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Returns the value of field 'max'.
+   * 
+   * @return the value of field 'Max'.
+   */
+  public float getMax()
+  {
+    return this._max;
+  }
+
+  /**
+   * Returns the value of field 'min'.
+   * 
+   * @return the value of field 'Min'.
+   */
+  public float getMin()
+  {
+    return this._min;
+  }
+
+  /**
+   * Returns the value of field 'mincolour'. The field 'mincolour' has the
+   * following description: Optional minimum colour for graduated feature colour
+   * 
+   * 
+   * @return the value of field 'Mincolour'.
+   */
+  public int getMincolour()
+  {
+    return this._mincolour;
+  }
+
+  /**
+   * Returns the value of field 'order'.
+   * 
+   * @return the value of field 'Order'.
+   */
+  public float getOrder()
+  {
+    return this._order;
+  }
+
+  /**
+   * Returns the value of field 'threshold'. The field 'threshold' has the
+   * following description: threshold value for graduated feature colour
+   * 
+   * 
+   * @return the value of field 'Threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  }
+
+  /**
+   * Returns the value of field 'threshstate'. The field 'threshstate' has the
+   * following description: threshold type for graduated feature colour
+   * 
+   * 
+   * @return the value of field 'Threshstate'.
+   */
+  public int getThreshstate()
+  {
+    return this._threshstate;
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method hasAutoScale.
+   * 
+   * @return true if at least one AutoScale has been added
+   */
+  public boolean hasAutoScale()
+  {
+    return this._has_autoScale;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasColourByLabel.
+   * 
+   * @return true if at least one ColourByLabel has been added
+   */
+  public boolean hasColourByLabel()
+  {
+    return this._has_colourByLabel;
+  }
+
+  /**
+   * Method hasDisplay.
+   * 
+   * @return true if at least one Display has been added
+   */
+  public boolean hasDisplay()
+  {
+    return this._has_display;
+  }
+
+  /**
+   * Method hasMax.
+   * 
+   * @return true if at least one Max has been added
+   */
+  public boolean hasMax()
+  {
+    return this._has_max;
+  }
+
+  /**
+   * Method hasMin.
+   * 
+   * @return true if at least one Min has been added
+   */
+  public boolean hasMin()
+  {
+    return this._has_min;
+  }
+
+  /**
+   * Method hasMincolour.
+   * 
+   * @return true if at least one Mincolour has been added
+   */
+  public boolean hasMincolour()
+  {
+    return this._has_mincolour;
+  }
+
+  /**
+   * Method hasOrder.
+   * 
+   * @return true if at least one Order has been added
+   */
+  public boolean hasOrder()
+  {
+    return this._has_order;
+  }
+
+  /**
+   * Method hasThreshold.
+   * 
+   * @return true if at least one Threshold has been added
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  }
+
+  /**
+   * Method hasThreshstate.
+   * 
+   * @return true if at least one Threshstate has been added
+   */
+  public boolean hasThreshstate()
+  {
+    return this._has_threshstate;
+  }
+
+  /**
+   * Returns the value of field 'autoScale'.
+   * 
+   * @return the value of field 'AutoScale'.
+   */
+  public boolean isAutoScale()
+  {
+    return this._autoScale;
+  }
+
+  /**
+   * Returns the value of field 'colourByLabel'.
+   * 
+   * @return the value of field 'ColourByLabel'.
+   */
+  public boolean isColourByLabel()
+  {
+    return this._colourByLabel;
+  }
+
+  /**
+   * Returns the value of field 'display'.
+   * 
+   * @return the value of field 'Display'.
+   */
+  public boolean isDisplay()
+  {
+    return this._display;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'autoScale'.
+   * 
+   * @param autoScale
+   *          the value of field 'autoScale'.
+   */
+  public void setAutoScale(final boolean autoScale)
+  {
+    this._autoScale = autoScale;
+    this._has_autoScale = true;
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *          the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'colourByLabel'.
+   * 
+   * @param colourByLabel
+   *          the value of field 'colourByLabel'.
+   */
+  public void setColourByLabel(final boolean colourByLabel)
+  {
+    this._colourByLabel = colourByLabel;
+    this._has_colourByLabel = true;
+  }
+
+  /**
+   * Sets the value of field 'display'.
+   * 
+   * @param display
+   *          the value of field 'display'.
+   */
+  public void setDisplay(final boolean display)
+  {
+    this._display = display;
+    this._has_display = true;
+  }
+
+  /**
+   * Sets the value of field 'max'.
+   * 
+   * @param max
+   *          the value of field 'max'.
+   */
+  public void setMax(final float max)
+  {
+    this._max = max;
+    this._has_max = true;
+  }
+
+  /**
+   * Sets the value of field 'min'.
+   * 
+   * @param min
+   *          the value of field 'min'.
+   */
+  public void setMin(final float min)
+  {
+    this._min = min;
+    this._has_min = true;
+  }
+
+  /**
+   * Sets the value of field 'mincolour'. The field 'mincolour' has the
+   * following description: Optional minimum colour for graduated feature colour
+   * 
+   * 
+   * @param mincolour
+   *          the value of field 'mincolour'.
+   */
+  public void setMincolour(final int mincolour)
+  {
+    this._mincolour = mincolour;
+    this._has_mincolour = true;
+  }
+
+  /**
+   * Sets the value of field 'order'.
+   * 
+   * @param order
+   *          the value of field 'order'.
+   */
+  public void setOrder(final float order)
+  {
+    this._order = order;
+    this._has_order = true;
+  }
+
+  /**
+   * Sets the value of field 'threshold'. The field 'threshold' has the
+   * following description: threshold value for graduated feature colour
+   * 
+   * 
+   * @param threshold
+   *          the value of field 'threshold'.
+   */
+  public void setThreshold(final float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  }
+
+  /**
+   * Sets the value of field 'threshstate'. The field 'threshstate' has the
+   * following description: threshold type for graduated feature colour
+   * 
+   * 
+   * @param threshstate
+   *          the value of field 'threshstate'.
+   */
+  public void setThreshstate(final int threshstate)
+  {
+    this._threshstate = threshstate;
+    this._has_threshstate = true;
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *          the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Settin
+   */
+  public static jalview.schemabinding.version2.Setting unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Setting.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index fe7c95d..186e4e6 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,1089 +19,688 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class StructureState implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * internal content storage
-     */
-    private java.lang.String _content = "";
-
-    /**
-     * Field _visible.
-     */
-    private boolean _visible;
-
-    /**
-     * keeps track of state for field: _visible
-     */
-    private boolean _has_visible;
-
-    /**
-     * additional
-     *  identifier
-     *  which
-     *  properly
-     *  disambiguates
-     *  the
-     *  structure
-     *  view
-     *  from
-     *  any
-     *  other
-     *  view
-     *  with
-     *  the
-     *  same
-     *  attributes.
-     *  This
-     *  is
-     *  not
-     *  an
-     *  ID,
-     *  because
-     *  it
-     *  is
-     *  possible
-     *  to
-     *  have
-     *  many
-     *  references
-     *  to
-     *  the
-     *  same
-     *  physical
-     *  structure
-     *  view
-     *  from
-     *  different
-     *  sequences
-     *  in
-     *  an
-     *  alignment.
-     *  A
-     *  structureState
-     *  element
-     *  citing
-     *  the
-     *  same
-     *  viewId
-     *  will
-     *  appear
-     *  for
-     *  each
-     *  instance.
-     *  
-     */
-    private java.lang.String _viewId;
-
-    /**
-     * Flag
-     *  set
-     *  if
-     *  the
-     *  alignment
-     *  panel
-     *  containing
-     *  this
-     *  JSeq
-     *  should
-     *  be
-     *  included
-     *  in
-     *  those
-     *  used
-     *  to
-     *  perform
-     *  a
-     *  structure
-     *  superposition
-     *  (since
-     *  Jalview
-     *  2.7).
-     *  
-     */
-    private boolean _alignwithAlignPanel = true;
-
-    /**
-     * keeps track of state for field: _alignwithAlignPanel
-     */
-    private boolean _has_alignwithAlignPanel;
-
-    /**
-     * Flag
-     *  set
-     *  if
-     *  the
-     *  alignment
-     *  panel
-     *  containing
-     *  this
-     *  JSeq
-     *  should
-     *  be
-     *  included
-     *  in
-     *  those
-     *  used
-     *  to
-     *  colour
-     *  its
-     *  associated
-     *  sequences
-     *  in
-     *  this
-     *  structureState(since
-     *  Jalview
-     *  2.7).
-     *  
-     */
-    private boolean _colourwithAlignPanel = false;
-
-    /**
-     * keeps track of state for field: _colourwithAlignPanel
-     */
-    private boolean _has_colourwithAlignPanel;
-
-    /**
-     * Flag
-     *  set
-     *  if
-     *  the
-     *  structure
-     *  display
-     *  is
-     *  coloured
-     *  by
-     *  the
-     *  Jmol
-     *  state,
-     *  rather
-     *  than
-     *  by
-     *  one
-     *  or
-     *  more
-     *  linked
-     *  alignment
-     *  views.
-     *  
-     */
-    private boolean _colourByJmol = true;
-
-    /**
-     * keeps track of state for field: _colourByJmol
-     */
-    private boolean _has_colourByJmol;
-
-    /**
-     * An
-     *  identifier
-     *  for
-     *  the
-     *  viewer
-     *  type,
-     *  currently
-     *  either
-     *  JMOL
-     *  or
-     *  CHIMERA
-     *  
-     */
-    private java.lang.String _type;
-
-    /**
-     * 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;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public StructureState() {
-        super();
-        setContent("");
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteAlignwithAlignPanel(
-    ) {
-        this._has_alignwithAlignPanel= false;
-    }
-
-    /**
-     */
-    public void deleteColourByJmol(
-    ) {
-        this._has_colourByJmol= false;
-    }
-
-    /**
-     */
-    public void deleteColourwithAlignPanel(
-    ) {
-        this._has_colourwithAlignPanel= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deleteVisible(
-    ) {
-        this._has_visible= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Returns the value of field 'alignwithAlignPanel'. The field
-     * 'alignwithAlignPanel' has the following description: Flag
-     *  set
-     *  if
-     *  the
-     *  alignment
-     *  panel
-     *  containing
-     *  this
-     *  JSeq
-     *  should
-     *  be
-     *  included
-     *  in
-     *  those
-     *  used
-     *  to
-     *  perform
-     *  a
-     *  structure
-     *  superposition
-     *  (since
-     *  Jalview
-     *  2.7).
-     *  
-     * 
-     * @return the value of field 'AlignwithAlignPanel'.
-     */
-    public boolean getAlignwithAlignPanel(
-    ) {
-        return this._alignwithAlignPanel;
-    }
-
-    /**
-     * Returns the value of field 'colourByJmol'. The field
-     * 'colourByJmol' has the following description: Flag
-     *  set
-     *  if
-     *  the
-     *  structure
-     *  display
-     *  is
-     *  coloured
-     *  by
-     *  the
-     *  Jmol
-     *  state,
-     *  rather
-     *  than
-     *  by
-     *  one
-     *  or
-     *  more
-     *  linked
-     *  alignment
-     *  views.
-     *  
-     * 
-     * @return the value of field 'ColourByJmol'.
-     */
-    public boolean getColourByJmol(
-    ) {
-        return this._colourByJmol;
-    }
-
-    /**
-     * Returns the value of field 'colourwithAlignPanel'. The field
-     * 'colourwithAlignPanel' has the following description: Flag
-     *  set
-     *  if
-     *  the
-     *  alignment
-     *  panel
-     *  containing
-     *  this
-     *  JSeq
-     *  should
-     *  be
-     *  included
-     *  in
-     *  those
-     *  used
-     *  to
-     *  colour
-     *  its
-     *  associated
-     *  sequences
-     *  in
-     *  this
-     *  structureState(since
-     *  Jalview
-     *  2.7).
-     *  
-     * 
-     * @return the value of field 'ColourwithAlignPanel'.
-     */
-    public boolean getColourwithAlignPanel(
-    ) {
-        return this._colourwithAlignPanel;
-    }
-
-    /**
-     * Returns the value of field 'content'. The field 'content'
-     * has the following description: internal content storage
-     * 
-     * @return the value of field 'Content'.
-     */
-    public java.lang.String getContent(
-    ) {
-        return this._content;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Returns the value of field 'type'. The field 'type' has the
-     * following description: An
-     *  identifier
-     *  for
-     *  the
-     *  viewer
-     *  type,
-     *  currently
-     *  either
-     *  JMOL
-     *  or
-     *  CHIMERA
-     *  
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Returns the value of field 'viewId'. The field 'viewId' has
-     * the following description: additional
-     *  identifier
-     *  which
-     *  properly
-     *  disambiguates
-     *  the
-     *  structure
-     *  view
-     *  from
-     *  any
-     *  other
-     *  view
-     *  with
-     *  the
-     *  same
-     *  attributes.
-     *  This
-     *  is
-     *  not
-     *  an
-     *  ID,
-     *  because
-     *  it
-     *  is
-     *  possible
-     *  to
-     *  have
-     *  many
-     *  references
-     *  to
-     *  the
-     *  same
-     *  physical
-     *  structure
-     *  view
-     *  from
-     *  different
-     *  sequences
-     *  in
-     *  an
-     *  alignment.
-     *  A
-     *  structureState
-     *  element
-     *  citing
-     *  the
-     *  same
-     *  viewId
-     *  will
-     *  appear
-     *  for
-     *  each
-     *  instance.
-     *  
-     * 
-     * @return the value of field 'ViewId'.
-     */
-    public java.lang.String getViewId(
-    ) {
-        return this._viewId;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean getVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasAlignwithAlignPanel.
-     * 
-     * @return true if at least one AlignwithAlignPanel has been
-     * added
-     */
-    public boolean hasAlignwithAlignPanel(
-    ) {
-        return this._has_alignwithAlignPanel;
-    }
-
-    /**
-     * Method hasColourByJmol.
-     * 
-     * @return true if at least one ColourByJmol has been added
-     */
-    public boolean hasColourByJmol(
-    ) {
-        return this._has_colourByJmol;
-    }
-
-    /**
-     * Method hasColourwithAlignPanel.
-     * 
-     * @return true if at least one ColourwithAlignPanel has been
-     * added
-     */
-    public boolean hasColourwithAlignPanel(
-    ) {
-        return this._has_colourwithAlignPanel;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasVisible.
-     * 
-     * @return true if at least one Visible has been added
-     */
-    public boolean hasVisible(
-    ) {
-        return this._has_visible;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Returns the value of field 'alignwithAlignPanel'. The field
-     * 'alignwithAlignPanel' has the following description: Flag
-     *  set
-     *  if
-     *  the
-     *  alignment
-     *  panel
-     *  containing
-     *  this
-     *  JSeq
-     *  should
-     *  be
-     *  included
-     *  in
-     *  those
-     *  used
-     *  to
-     *  perform
-     *  a
-     *  structure
-     *  superposition
-     *  (since
-     *  Jalview
-     *  2.7).
-     *  
-     * 
-     * @return the value of field 'AlignwithAlignPanel'.
-     */
-    public boolean isAlignwithAlignPanel(
-    ) {
-        return this._alignwithAlignPanel;
-    }
-
-    /**
-     * Returns the value of field 'colourByJmol'. The field
-     * 'colourByJmol' has the following description: Flag
-     *  set
-     *  if
-     *  the
-     *  structure
-     *  display
-     *  is
-     *  coloured
-     *  by
-     *  the
-     *  Jmol
-     *  state,
-     *  rather
-     *  than
-     *  by
-     *  one
-     *  or
-     *  more
-     *  linked
-     *  alignment
-     *  views.
-     *  
-     * 
-     * @return the value of field 'ColourByJmol'.
-     */
-    public boolean isColourByJmol(
-    ) {
-        return this._colourByJmol;
-    }
-
-    /**
-     * Returns the value of field 'colourwithAlignPanel'. The field
-     * 'colourwithAlignPanel' has the following description: Flag
-     *  set
-     *  if
-     *  the
-     *  alignment
-     *  panel
-     *  containing
-     *  this
-     *  JSeq
-     *  should
-     *  be
-     *  included
-     *  in
-     *  those
-     *  used
-     *  to
-     *  colour
-     *  its
-     *  associated
-     *  sequences
-     *  in
-     *  this
-     *  structureState(since
-     *  Jalview
-     *  2.7).
-     *  
-     * 
-     * @return the value of field 'ColourwithAlignPanel'.
-     */
-    public boolean isColourwithAlignPanel(
-    ) {
-        return this._colourwithAlignPanel;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean isVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'alignwithAlignPanel'. The field
-     * 'alignwithAlignPanel' has the following description: Flag
-     *  set
-     *  if
-     *  the
-     *  alignment
-     *  panel
-     *  containing
-     *  this
-     *  JSeq
-     *  should
-     *  be
-     *  included
-     *  in
-     *  those
-     *  used
-     *  to
-     *  perform
-     *  a
-     *  structure
-     *  superposition
-     *  (since
-     *  Jalview
-     *  2.7).
-     *  
-     * 
-     * @param alignwithAlignPanel the value of field
-     * 'alignwithAlignPanel'.
-     */
-    public void setAlignwithAlignPanel(
-            final boolean alignwithAlignPanel) {
-        this._alignwithAlignPanel = alignwithAlignPanel;
-        this._has_alignwithAlignPanel = true;
-    }
-
-    /**
-     * Sets the value of field 'colourByJmol'. The field
-     * 'colourByJmol' has the following description: Flag
-     *  set
-     *  if
-     *  the
-     *  structure
-     *  display
-     *  is
-     *  coloured
-     *  by
-     *  the
-     *  Jmol
-     *  state,
-     *  rather
-     *  than
-     *  by
-     *  one
-     *  or
-     *  more
-     *  linked
-     *  alignment
-     *  views.
-     *  
-     * 
-     * @param colourByJmol the value of field 'colourByJmol'.
-     */
-    public void setColourByJmol(
-            final boolean colourByJmol) {
-        this._colourByJmol = colourByJmol;
-        this._has_colourByJmol = true;
-    }
-
-    /**
-     * Sets the value of field 'colourwithAlignPanel'. The field
-     * 'colourwithAlignPanel' has the following description: Flag
-     *  set
-     *  if
-     *  the
-     *  alignment
-     *  panel
-     *  containing
-     *  this
-     *  JSeq
-     *  should
-     *  be
-     *  included
-     *  in
-     *  those
-     *  used
-     *  to
-     *  colour
-     *  its
-     *  associated
-     *  sequences
-     *  in
-     *  this
-     *  structureState(since
-     *  Jalview
-     *  2.7).
-     *  
-     * 
-     * @param colourwithAlignPanel the value of field
-     * 'colourwithAlignPanel'.
-     */
-    public void setColourwithAlignPanel(
-            final boolean colourwithAlignPanel) {
-        this._colourwithAlignPanel = colourwithAlignPanel;
-        this._has_colourwithAlignPanel = true;
-    }
-
-    /**
-     * Sets the value of field 'content'. The field 'content' has
-     * the following description: internal content storage
-     * 
-     * @param content the value of field 'content'.
-     */
-    public void setContent(
-            final java.lang.String content) {
-        this._content = content;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * Sets the value of field 'type'. The field 'type' has the
-     * following description: An
-     *  identifier
-     *  for
-     *  the
-     *  viewer
-     *  type,
-     *  currently
-     *  either
-     *  JMOL
-     *  or
-     *  CHIMERA
-     *  
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
-    }
-
-    /**
-     * Sets the value of field 'viewId'. The field 'viewId' has the
-     * following description: additional
-     *  identifier
-     *  which
-     *  properly
-     *  disambiguates
-     *  the
-     *  structure
-     *  view
-     *  from
-     *  any
-     *  other
-     *  view
-     *  with
-     *  the
-     *  same
-     *  attributes.
-     *  This
-     *  is
-     *  not
-     *  an
-     *  ID,
-     *  because
-     *  it
-     *  is
-     *  possible
-     *  to
-     *  have
-     *  many
-     *  references
-     *  to
-     *  the
-     *  same
-     *  physical
-     *  structure
-     *  view
-     *  from
-     *  different
-     *  sequences
-     *  in
-     *  an
-     *  alignment.
-     *  A
-     *  structureState
-     *  element
-     *  citing
-     *  the
-     *  same
-     *  viewId
-     *  will
-     *  appear
-     *  for
-     *  each
-     *  instance.
-     *  
-     * 
-     * @param viewId the value of field 'viewId'.
-     */
-    public void setViewId(
-            final java.lang.String viewId) {
-        this._viewId = viewId;
-    }
-
-    /**
-     * Sets the value of field 'visible'.
-     * 
-     * @param visible the value of field 'visible'.
-     */
-    public void setVisible(
-            final boolean visible) {
-        this._visible = visible;
-        this._has_visible = true;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.StructureState
-     */
-    public static jalview.schemabinding.version2.StructureState unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class StructureState implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * internal content storage
+   */
+  private java.lang.String _content = "";
+
+  /**
+   * Field _visible.
+   */
+  private boolean _visible;
+
+  /**
+   * keeps track of state for field: _visible
+   */
+  private boolean _has_visible;
+
+  /**
+   * additional identifier which properly disambiguates the structure view from
+   * any other view with the same attributes. This is not an ID, because it is
+   * possible to have many references to the same physical structure view from
+   * different sequences in an alignment. A structureState element citing the
+   * same viewId will appear for each instance.
+   * 
+   */
+  private java.lang.String _viewId;
+
+  /**
+   * Flag set if the alignment panel containing this JSeq should be included in
+   * those used to perform a structure superposition (since Jalview 2.7).
+   * 
+   */
+  private boolean _alignwithAlignPanel = true;
+
+  /**
+   * keeps track of state for field: _alignwithAlignPanel
+   */
+  private boolean _has_alignwithAlignPanel;
+
+  /**
+   * Flag set if the alignment panel containing this JSeq should be included in
+   * those used to colour its associated sequences in this structureState(since
+   * Jalview 2.7).
+   * 
+   */
+  private boolean _colourwithAlignPanel = false;
+
+  /**
+   * keeps track of state for field: _colourwithAlignPanel
+   */
+  private boolean _has_colourwithAlignPanel;
+
+  /**
+   * Flag set if the structure display is coloured by the Jmol state, rather
+   * than by one or more linked alignment views.
+   * 
+   */
+  private boolean _colourByJmol = true;
+
+  /**
+   * keeps track of state for field: _colourByJmol
+   */
+  private boolean _has_colourByJmol;
+
+  /**
+   * An identifier for the viewer type, currently either JMOL or CHIMERA
+   * 
+   */
+  private java.lang.String _type;
+
+  /**
+   * 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;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public StructureState()
+  {
+    super();
+    setContent("");
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteAlignwithAlignPanel()
+  {
+    this._has_alignwithAlignPanel = false;
+  }
+
+  /**
+     */
+  public void deleteColourByJmol()
+  {
+    this._has_colourByJmol = false;
+  }
+
+  /**
+     */
+  public void deleteColourwithAlignPanel()
+  {
+    this._has_colourwithAlignPanel = false;
+  }
+
+  /**
+     */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+     */
+  public void deleteVisible()
+  {
+    this._has_visible = false;
+  }
+
+  /**
+     */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+     */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+     */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Returns the value of field 'alignwithAlignPanel'. The field
+   * 'alignwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * perform a structure superposition (since Jalview 2.7).
+   * 
+   * 
+   * @return the value of field 'AlignwithAlignPanel'.
+   */
+  public boolean getAlignwithAlignPanel()
+  {
+    return this._alignwithAlignPanel;
+  }
+
+  /**
+   * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
+   * following description: Flag set if the structure display is coloured by the
+   * Jmol state, rather than by one or more linked alignment views.
+   * 
+   * 
+   * @return the value of field 'ColourByJmol'.
+   */
+  public boolean getColourByJmol()
+  {
+    return this._colourByJmol;
+  }
+
+  /**
+   * Returns the value of field 'colourwithAlignPanel'. The field
+   * 'colourwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * colour its associated sequences in this structureState(since Jalview 2.7).
+   * 
+   * 
+   * @return the value of field 'ColourwithAlignPanel'.
+   */
+  public boolean getColourwithAlignPanel()
+  {
+    return this._colourwithAlignPanel;
+  }
+
+  /**
+   * Returns the value of field 'content'. The field 'content' has the following
+   * description: internal content storage
+   * 
+   * @return the value of field 'Content'.
+   */
+  public java.lang.String getContent()
+  {
+    return this._content;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Returns the value of field 'type'. The field 'type' has the following
+   * description: An identifier for the viewer type, currently either JMOL or
+   * CHIMERA
+   * 
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Returns the value of field 'viewId'. The field 'viewId' has the following
+   * description: additional identifier which properly disambiguates the
+   * structure view from any other view with the same attributes. This is not an
+   * ID, because it is possible to have many references to the same physical
+   * structure view from different sequences in an alignment. A structureState
+   * element citing the same viewId will appear for each instance.
+   * 
+   * 
+   * @return the value of field 'ViewId'.
+   */
+  public java.lang.String getViewId()
+  {
+    return this._viewId;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean getVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasAlignwithAlignPanel.
+   * 
+   * @return true if at least one AlignwithAlignPanel has been added
+   */
+  public boolean hasAlignwithAlignPanel()
+  {
+    return this._has_alignwithAlignPanel;
+  }
+
+  /**
+   * Method hasColourByJmol.
+   * 
+   * @return true if at least one ColourByJmol has been added
+   */
+  public boolean hasColourByJmol()
+  {
+    return this._has_colourByJmol;
+  }
+
+  /**
+   * Method hasColourwithAlignPanel.
+   * 
+   * @return true if at least one ColourwithAlignPanel has been added
+   */
+  public boolean hasColourwithAlignPanel()
+  {
+    return this._has_colourwithAlignPanel;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasVisible.
+   * 
+   * @return true if at least one Visible has been added
+   */
+  public boolean hasVisible()
+  {
+    return this._has_visible;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'alignwithAlignPanel'. The field
+   * 'alignwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * perform a structure superposition (since Jalview 2.7).
+   * 
+   * 
+   * @return the value of field 'AlignwithAlignPanel'.
+   */
+  public boolean isAlignwithAlignPanel()
+  {
+    return this._alignwithAlignPanel;
+  }
+
+  /**
+   * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
+   * following description: Flag set if the structure display is coloured by the
+   * Jmol state, rather than by one or more linked alignment views.
+   * 
+   * 
+   * @return the value of field 'ColourByJmol'.
+   */
+  public boolean isColourByJmol()
+  {
+    return this._colourByJmol;
+  }
+
+  /**
+   * Returns the value of field 'colourwithAlignPanel'. The field
+   * 'colourwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * colour its associated sequences in this structureState(since Jalview 2.7).
+   * 
+   * 
+   * @return the value of field 'ColourwithAlignPanel'.
+   */
+  public boolean isColourwithAlignPanel()
+  {
+    return this._colourwithAlignPanel;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean isVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'alignwithAlignPanel'. The field
+   * 'alignwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * perform a structure superposition (since Jalview 2.7).
+   * 
+   * 
+   * @param alignwithAlignPanel
+   *          the value of field 'alignwithAlignPanel'.
+   */
+  public void setAlignwithAlignPanel(final boolean alignwithAlignPanel)
+  {
+    this._alignwithAlignPanel = alignwithAlignPanel;
+    this._has_alignwithAlignPanel = true;
+  }
+
+  /**
+   * Sets the value of field 'colourByJmol'. The field 'colourByJmol' has the
+   * following description: Flag set if the structure display is coloured by the
+   * Jmol state, rather than by one or more linked alignment views.
+   * 
+   * 
+   * @param colourByJmol
+   *          the value of field 'colourByJmol'.
+   */
+  public void setColourByJmol(final boolean colourByJmol)
+  {
+    this._colourByJmol = colourByJmol;
+    this._has_colourByJmol = true;
+  }
+
+  /**
+   * Sets the value of field 'colourwithAlignPanel'. The field
+   * 'colourwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * colour its associated sequences in this structureState(since Jalview 2.7).
+   * 
+   * 
+   * @param colourwithAlignPanel
+   *          the value of field 'colourwithAlignPanel'.
+   */
+  public void setColourwithAlignPanel(final boolean colourwithAlignPanel)
+  {
+    this._colourwithAlignPanel = colourwithAlignPanel;
+    this._has_colourwithAlignPanel = true;
+  }
+
+  /**
+   * Sets the value of field 'content'. The field 'content' has the following
+   * description: internal content storage
+   * 
+   * @param content
+   *          the value of field 'content'.
+   */
+  public void setContent(final java.lang.String content)
+  {
+    this._content = content;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *          the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * Sets the value of field 'type'. The field 'type' has the following
+   * description: An identifier for the viewer type, currently either JMOL or
+   * CHIMERA
+   * 
+   * 
+   * @param type
+   *          the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * Sets the value of field 'viewId'. The field 'viewId' has the following
+   * description: additional identifier which properly disambiguates the
+   * structure view from any other view with the same attributes. This is not an
+   * ID, because it is possible to have many references to the same physical
+   * structure view from different sequences in an alignment. A structureState
+   * element citing the same viewId will appear for each instance.
+   * 
+   * 
+   * @param viewId
+   *          the value of field 'viewId'.
+   */
+  public void setViewId(final java.lang.String viewId)
+  {
+    this._viewId = viewId;
+  }
+
+  /**
+   * Sets the value of field 'visible'.
+   * 
+   * @param visible
+   *          the value of field 'visible'.
+   */
+  public void setVisible(final boolean visible)
+  {
+    this._visible = visible;
+    this._has_visible = true;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *          the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *          the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *          the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.StructureState
+   */
+  public static jalview.schemabinding.version2.StructureState unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.StructureState) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.StructureState.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java
index 31affa2..d70d855 100644
--- a/src/jalview/schemabinding/version2/ThresholdLine.java
+++ b/src/jalview/schemabinding/version2/ThresholdLine.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,223 +19,235 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class ThresholdLine implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _label.
-     */
-    private java.lang.String _label;
-
-    /**
-     * Field _value.
-     */
-    private float _value;
-
-    /**
-     * keeps track of state for field: _value
-     */
-    private boolean _has_value;
-
-    /**
-     * Field _colour.
-     */
-    private int _colour;
-
-    /**
-     * keeps track of state for field: _colour
-     */
-    private boolean _has_colour;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ThresholdLine() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteColour(
-    ) {
-        this._has_colour= false;
-    }
-
-    /**
-     */
-    public void deleteValue(
-    ) {
-        this._has_value= false;
-    }
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return the value of field 'Colour'.
-     */
-    public int getColour(
-    ) {
-        return this._colour;
-    }
-
-    /**
-     * Returns the value of field 'label'.
-     * 
-     * @return the value of field 'Label'.
-     */
-    public java.lang.String getLabel(
-    ) {
-        return this._label;
-    }
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return the value of field 'Value'.
-     */
-    public float getValue(
-    ) {
-        return this._value;
-    }
-
-    /**
-     * Method hasColour.
-     * 
-     * @return true if at least one Colour has been added
-     */
-    public boolean hasColour(
-    ) {
-        return this._has_colour;
-    }
-
-    /**
-     * Method hasValue.
-     * 
-     * @return true if at least one Value has been added
-     */
-    public boolean hasValue(
-    ) {
-        return this._has_value;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(
-            final int colour) {
-        this._colour = colour;
-        this._has_colour = true;
-    }
-
-    /**
-     * Sets the value of field 'label'.
-     * 
-     * @param label the value of field 'label'.
-     */
-    public void setLabel(
-            final java.lang.String label) {
-        this._label = label;
-    }
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(
-            final float value) {
-        this._value = value;
-        this._has_value = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.ThresholdLine
-     */
-    public static jalview.schemabinding.version2.ThresholdLine unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class ThresholdLine implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _label.
+   */
+  private java.lang.String _label;
+
+  /**
+   * Field _value.
+   */
+  private float _value;
+
+  /**
+   * keeps track of state for field: _value
+   */
+  private boolean _has_value;
+
+  /**
+   * Field _colour.
+   */
+  private int _colour;
+
+  /**
+   * keeps track of state for field: _colour
+   */
+  private boolean _has_colour;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public ThresholdLine()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  }
+
+  /**
+     */
+  public void deleteValue()
+  {
+    this._has_value = false;
+  }
+
+  /**
+   * Returns the value of field 'colour'.
+   * 
+   * @return the value of field 'Colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  }
+
+  /**
+   * Returns the value of field 'label'.
+   * 
+   * @return the value of field 'Label'.
+   */
+  public java.lang.String getLabel()
+  {
+    return this._label;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public float getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method hasColour.
+   * 
+   * @return true if at least one Colour has been added
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  }
+
+  /**
+   * Method hasValue.
+   * 
+   * @return true if at least one Value has been added
+   */
+  public boolean hasValue()
+  {
+    return this._has_value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'colour'.
+   * 
+   * @param colour
+   *          the value of field 'colour'.
+   */
+  public void setColour(final int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  }
+
+  /**
+   * Sets the value of field 'label'.
+   * 
+   * @param label
+   *          the value of field 'label'.
+   */
+  public void setLabel(final java.lang.String label)
+  {
+    this._label = label;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *          the value of field 'value'.
+   */
+  public void setValue(final float value)
+  {
+    this._value = value;
+    this._has_value = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.ThresholdLine
+   */
+  public static jalview.schemabinding.version2.ThresholdLine unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.ThresholdLine.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java
index b147498..19b3eb1 100644
--- a/src/jalview/schemabinding/version2/Tree.java
+++ b/src/jalview/schemabinding/version2/Tree.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,841 +19,860 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Tree implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * 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;
-
-    /**
-     * Tree ID added for binding tree
-     *  visualization
-     *  settings to vamsas
-     *  document trees in jalview 2.4.1
-     *  
-     */
-    private java.lang.String _id;
-
-    /**
-     * 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 _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * Field _newick.
-     */
-    private java.lang.String _newick;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Tree() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteCurrentTree(
-    ) {
-        this._has_currentTree= false;
-    }
-
-    /**
-     */
-    public void deleteFitToWindow(
-    ) {
-        this._has_fitToWindow= false;
-    }
-
-    /**
-     */
-    public void deleteFontSize(
-    ) {
-        this._has_fontSize= false;
-    }
-
-    /**
-     */
-    public void deleteFontStyle(
-    ) {
-        this._has_fontStyle= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deleteMarkUnlinked(
-    ) {
-        this._has_markUnlinked= false;
-    }
-
-    /**
-     */
-    public void deleteShowBootstrap(
-    ) {
-        this._has_showBootstrap= false;
-    }
-
-    /**
-     */
-    public void deleteShowDistances(
-    ) {
-        this._has_showDistances= false;
-    }
-
-    /**
-     */
-    public void deleteThreshold(
-    ) {
-        this._has_threshold= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Returns the value of field 'currentTree'.
-     * 
-     * @return the value of field 'CurrentTree'.
-     */
-    public boolean getCurrentTree(
-    ) {
-        return this._currentTree;
-    }
-
-    /**
-     * Returns the value of field 'fitToWindow'.
-     * 
-     * @return the value of field 'FitToWindow'.
-     */
-    public boolean getFitToWindow(
-    ) {
-        return this._fitToWindow;
-    }
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return the value of field 'FontName'.
-     */
-    public java.lang.String getFontName(
-    ) {
-        return this._fontName;
-    }
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return the value of field 'FontSize'.
-     */
-    public int getFontSize(
-    ) {
-        return this._fontSize;
-    }
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return the value of field 'FontStyle'.
-     */
-    public int getFontStyle(
-    ) {
-        return this._fontStyle;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Returns the value of field 'id'. The field 'id' has the
-     * following description: Tree ID added for binding tree
-     *  visualization
-     *  settings to vamsas
-     *  document trees in jalview 2.4.1
-     *  
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'markUnlinked'.
-     * 
-     * @return the value of field 'MarkUnlinked'.
-     */
-    public boolean getMarkUnlinked(
-    ) {
-        return this._markUnlinked;
-    }
-
-    /**
-     * Returns the value of field 'newick'.
-     * 
-     * @return the value of field 'Newick'.
-     */
-    public java.lang.String getNewick(
-    ) {
-        return this._newick;
-    }
-
-    /**
-     * Returns the value of field 'showBootstrap'.
-     * 
-     * @return the value of field 'ShowBootstrap'.
-     */
-    public boolean getShowBootstrap(
-    ) {
-        return this._showBootstrap;
-    }
-
-    /**
-     * Returns the value of field 'showDistances'.
-     * 
-     * @return the value of field 'ShowDistances'.
-     */
-    public boolean getShowDistances(
-    ) {
-        return this._showDistances;
-    }
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return the value of field 'Threshold'.
-     */
-    public float getThreshold(
-    ) {
-        return this._threshold;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasCurrentTree.
-     * 
-     * @return true if at least one CurrentTree has been added
-     */
-    public boolean hasCurrentTree(
-    ) {
-        return this._has_currentTree;
-    }
-
-    /**
-     * Method hasFitToWindow.
-     * 
-     * @return true if at least one FitToWindow has been added
-     */
-    public boolean hasFitToWindow(
-    ) {
-        return this._has_fitToWindow;
-    }
-
-    /**
-     * Method hasFontSize.
-     * 
-     * @return true if at least one FontSize has been added
-     */
-    public boolean hasFontSize(
-    ) {
-        return this._has_fontSize;
-    }
-
-    /**
-     * Method hasFontStyle.
-     * 
-     * @return true if at least one FontStyle has been added
-     */
-    public boolean hasFontStyle(
-    ) {
-        return this._has_fontStyle;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasMarkUnlinked.
-     * 
-     * @return true if at least one MarkUnlinked has been added
-     */
-    public boolean hasMarkUnlinked(
-    ) {
-        return this._has_markUnlinked;
-    }
-
-    /**
-     * Method hasShowBootstrap.
-     * 
-     * @return true if at least one ShowBootstrap has been added
-     */
-    public boolean hasShowBootstrap(
-    ) {
-        return this._has_showBootstrap;
-    }
-
-    /**
-     * Method hasShowDistances.
-     * 
-     * @return true if at least one ShowDistances has been added
-     */
-    public boolean hasShowDistances(
-    ) {
-        return this._has_showDistances;
-    }
-
-    /**
-     * Method hasThreshold.
-     * 
-     * @return true if at least one Threshold has been added
-     */
-    public boolean hasThreshold(
-    ) {
-        return this._has_threshold;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Returns the value of field 'currentTree'.
-     * 
-     * @return the value of field 'CurrentTree'.
-     */
-    public boolean isCurrentTree(
-    ) {
-        return this._currentTree;
-    }
-
-    /**
-     * Returns the value of field 'fitToWindow'.
-     * 
-     * @return the value of field 'FitToWindow'.
-     */
-    public boolean isFitToWindow(
-    ) {
-        return this._fitToWindow;
-    }
-
-    /**
-     * Returns the value of field 'markUnlinked'.
-     * 
-     * @return the value of field 'MarkUnlinked'.
-     */
-    public boolean isMarkUnlinked(
-    ) {
-        return this._markUnlinked;
-    }
-
-    /**
-     * Returns the value of field 'showBootstrap'.
-     * 
-     * @return the value of field 'ShowBootstrap'.
-     */
-    public boolean isShowBootstrap(
-    ) {
-        return this._showBootstrap;
-    }
-
-    /**
-     * Returns the value of field 'showDistances'.
-     * 
-     * @return the value of field 'ShowDistances'.
-     */
-    public boolean isShowDistances(
-    ) {
-        return this._showDistances;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'currentTree'.
-     * 
-     * @param currentTree the value of field 'currentTree'.
-     */
-    public void setCurrentTree(
-            final boolean currentTree) {
-        this._currentTree = currentTree;
-        this._has_currentTree = true;
-    }
-
-    /**
-     * Sets the value of field 'fitToWindow'.
-     * 
-     * @param fitToWindow the value of field 'fitToWindow'.
-     */
-    public void setFitToWindow(
-            final boolean fitToWindow) {
-        this._fitToWindow = fitToWindow;
-        this._has_fitToWindow = true;
-    }
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(
-            final java.lang.String fontName) {
-        this._fontName = fontName;
-    }
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(
-            final int fontSize) {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    }
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(
-            final int fontStyle) {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * Sets the value of field 'id'. The field 'id' has the
-     * following description: Tree ID added for binding tree
-     *  visualization
-     *  settings to vamsas
-     *  document trees in jalview 2.4.1
-     *  
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'markUnlinked'.
-     * 
-     * @param markUnlinked the value of field 'markUnlinked'.
-     */
-    public void setMarkUnlinked(
-            final boolean markUnlinked) {
-        this._markUnlinked = markUnlinked;
-        this._has_markUnlinked = true;
-    }
-
-    /**
-     * Sets the value of field 'newick'.
-     * 
-     * @param newick the value of field 'newick'.
-     */
-    public void setNewick(
-            final java.lang.String newick) {
-        this._newick = newick;
-    }
-
-    /**
-     * Sets the value of field 'showBootstrap'.
-     * 
-     * @param showBootstrap the value of field 'showBootstrap'.
-     */
-    public void setShowBootstrap(
-            final boolean showBootstrap) {
-        this._showBootstrap = showBootstrap;
-        this._has_showBootstrap = true;
-    }
-
-    /**
-     * Sets the value of field 'showDistances'.
-     * 
-     * @param showDistances the value of field 'showDistances'.
-     */
-    public void setShowDistances(
-            final boolean showDistances) {
-        this._showDistances = showDistances;
-        this._has_showDistances = true;
-    }
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(
-            final float threshold) {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.Tree
-     */
-    public static jalview.schemabinding.version2.Tree unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+public class Tree implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _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;
+
+  /**
+   * Tree ID added for binding tree visualization settings to vamsas document
+   * trees in jalview 2.4.1
+   * 
+   */
+  private java.lang.String _id;
+
+  /**
+   * 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 _title.
+   */
+  private java.lang.String _title;
+
+  /**
+   * Field _newick.
+   */
+  private java.lang.String _newick;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Tree()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteCurrentTree()
+  {
+    this._has_currentTree = false;
+  }
+
+  /**
+     */
+  public void deleteFitToWindow()
+  {
+    this._has_fitToWindow = false;
+  }
+
+  /**
+     */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  }
+
+  /**
+     */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  }
+
+  /**
+     */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+     */
+  public void deleteMarkUnlinked()
+  {
+    this._has_markUnlinked = false;
+  }
+
+  /**
+     */
+  public void deleteShowBootstrap()
+  {
+    this._has_showBootstrap = false;
+  }
+
+  /**
+     */
+  public void deleteShowDistances()
+  {
+    this._has_showDistances = false;
+  }
+
+  /**
+     */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  }
+
+  /**
+     */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+     */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+     */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Returns the value of field 'currentTree'.
+   * 
+   * @return the value of field 'CurrentTree'.
+   */
+  public boolean getCurrentTree()
+  {
+    return this._currentTree;
+  }
+
+  /**
+   * Returns the value of field 'fitToWindow'.
+   * 
+   * @return the value of field 'FitToWindow'.
+   */
+  public boolean getFitToWindow()
+  {
+    return this._fitToWindow;
+  }
+
+  /**
+   * Returns the value of field 'fontName'.
+   * 
+   * @return the value of field 'FontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  }
+
+  /**
+   * Returns the value of field 'fontSize'.
+   * 
+   * @return the value of field 'FontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  }
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   * 
+   * @return the value of field 'FontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Returns the value of field 'id'. The field 'id' has the following
+   * description: Tree ID added for binding tree visualization settings to
+   * vamsas document trees in jalview 2.4.1
+   * 
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'markUnlinked'.
+   * 
+   * @return the value of field 'MarkUnlinked'.
+   */
+  public boolean getMarkUnlinked()
+  {
+    return this._markUnlinked;
+  }
+
+  /**
+   * Returns the value of field 'newick'.
+   * 
+   * @return the value of field 'Newick'.
+   */
+  public java.lang.String getNewick()
+  {
+    return this._newick;
+  }
+
+  /**
+   * Returns the value of field 'showBootstrap'.
+   * 
+   * @return the value of field 'ShowBootstrap'.
+   */
+  public boolean getShowBootstrap()
+  {
+    return this._showBootstrap;
+  }
+
+  /**
+   * Returns the value of field 'showDistances'.
+   * 
+   * @return the value of field 'ShowDistances'.
+   */
+  public boolean getShowDistances()
+  {
+    return this._showDistances;
+  }
+
+  /**
+   * Returns the value of field 'threshold'.
+   * 
+   * @return the value of field 'Threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasCurrentTree.
+   * 
+   * @return true if at least one CurrentTree has been added
+   */
+  public boolean hasCurrentTree()
+  {
+    return this._has_currentTree;
+  }
+
+  /**
+   * Method hasFitToWindow.
+   * 
+   * @return true if at least one FitToWindow has been added
+   */
+  public boolean hasFitToWindow()
+  {
+    return this._has_fitToWindow;
+  }
+
+  /**
+   * Method hasFontSize.
+   * 
+   * @return true if at least one FontSize has been added
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  }
+
+  /**
+   * Method hasFontStyle.
+   * 
+   * @return true if at least one FontStyle has been added
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasMarkUnlinked.
+   * 
+   * @return true if at least one MarkUnlinked has been added
+   */
+  public boolean hasMarkUnlinked()
+  {
+    return this._has_markUnlinked;
+  }
+
+  /**
+   * Method hasShowBootstrap.
+   * 
+   * @return true if at least one ShowBootstrap has been added
+   */
+  public boolean hasShowBootstrap()
+  {
+    return this._has_showBootstrap;
+  }
+
+  /**
+   * Method hasShowDistances.
+   * 
+   * @return true if at least one ShowDistances has been added
+   */
+  public boolean hasShowDistances()
+  {
+    return this._has_showDistances;
+  }
+
+  /**
+   * Method hasThreshold.
+   * 
+   * @return true if at least one Threshold has been added
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'currentTree'.
+   * 
+   * @return the value of field 'CurrentTree'.
+   */
+  public boolean isCurrentTree()
+  {
+    return this._currentTree;
+  }
+
+  /**
+   * Returns the value of field 'fitToWindow'.
+   * 
+   * @return the value of field 'FitToWindow'.
+   */
+  public boolean isFitToWindow()
+  {
+    return this._fitToWindow;
+  }
+
+  /**
+   * Returns the value of field 'markUnlinked'.
+   * 
+   * @return the value of field 'MarkUnlinked'.
+   */
+  public boolean isMarkUnlinked()
+  {
+    return this._markUnlinked;
+  }
+
+  /**
+   * Returns the value of field 'showBootstrap'.
+   * 
+   * @return the value of field 'ShowBootstrap'.
+   */
+  public boolean isShowBootstrap()
+  {
+    return this._showBootstrap;
+  }
+
+  /**
+   * Returns the value of field 'showDistances'.
+   * 
+   * @return the value of field 'ShowDistances'.
+   */
+  public boolean isShowDistances()
+  {
+    return this._showDistances;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'currentTree'.
+   * 
+   * @param currentTree
+   *          the value of field 'currentTree'.
+   */
+  public void setCurrentTree(final boolean currentTree)
+  {
+    this._currentTree = currentTree;
+    this._has_currentTree = true;
+  }
+
+  /**
+   * Sets the value of field 'fitToWindow'.
+   * 
+   * @param fitToWindow
+   *          the value of field 'fitToWindow'.
+   */
+  public void setFitToWindow(final boolean fitToWindow)
+  {
+    this._fitToWindow = fitToWindow;
+    this._has_fitToWindow = true;
+  }
+
+  /**
+   * Sets the value of field 'fontName'.
+   * 
+   * @param fontName
+   *          the value of field 'fontName'.
+   */
+  public void setFontName(final java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  }
+
+  /**
+   * Sets the value of field 'fontSize'.
+   * 
+   * @param fontSize
+   *          the value of field 'fontSize'.
+   */
+  public void setFontSize(final int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  }
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   * 
+   * @param fontStyle
+   *          the value of field 'fontStyle'.
+   */
+  public void setFontStyle(final int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *          the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * Sets the value of field 'id'. The field 'id' has the following description:
+   * Tree ID added for binding tree visualization settings to vamsas document
+   * trees in jalview 2.4.1
+   * 
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'markUnlinked'.
+   * 
+   * @param markUnlinked
+   *          the value of field 'markUnlinked'.
+   */
+  public void setMarkUnlinked(final boolean markUnlinked)
+  {
+    this._markUnlinked = markUnlinked;
+    this._has_markUnlinked = true;
+  }
+
+  /**
+   * Sets the value of field 'newick'.
+   * 
+   * @param newick
+   *          the value of field 'newick'.
+   */
+  public void setNewick(final java.lang.String newick)
+  {
+    this._newick = newick;
+  }
+
+  /**
+   * Sets the value of field 'showBootstrap'.
+   * 
+   * @param showBootstrap
+   *          the value of field 'showBootstrap'.
+   */
+  public void setShowBootstrap(final boolean showBootstrap)
+  {
+    this._showBootstrap = showBootstrap;
+    this._has_showBootstrap = true;
+  }
+
+  /**
+   * Sets the value of field 'showDistances'.
+   * 
+   * @param showDistances
+   *          the value of field 'showDistances'.
+   */
+  public void setShowDistances(final boolean showDistances)
+  {
+    this._showDistances = showDistances;
+    this._has_showDistances = true;
+  }
+
+  /**
+   * Sets the value of field 'threshold'.
+   * 
+   * @param threshold
+   *          the value of field 'threshold'.
+   */
+  public void setThreshold(final float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *          the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *          the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *          the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *          the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Tree
+   */
+  public static jalview.schemabinding.version2.Tree unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.Tree.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java
index de531a8..e4983bd 100644
--- a/src/jalview/schemabinding/version2/UserColourScheme.java
+++ b/src/jalview/schemabinding/version2/UserColourScheme.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,99 +19,109 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColourScheme extends JalviewUserColours 
-implements java.io.Serializable
+public class UserColourScheme extends JalviewUserColours implements
+        java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColourScheme() {
-        super();
-    }
-
+  public UserColourScheme()
+  {
+    super();
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.JalviewUserColours
-     */
-    public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours
+   */
+  public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.UserColourScheme.class,
+                    reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java
index 8c56e0c..b02d0cd 100644
--- a/src/jalview/schemabinding/version2/UserColours.java
+++ b/src/jalview/schemabinding/version2/UserColours.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,152 +19,164 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _userColourScheme.
-     */
-    private jalview.schemabinding.version2.UserColourScheme _userColourScheme;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColours() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'userColourScheme'.
-     * 
-     * @return the value of field 'UserColourScheme'.
-     */
-    public jalview.schemabinding.version2.UserColourScheme getUserColourScheme(
-    ) {
-        return this._userColourScheme;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'userColourScheme'.
-     * 
-     * @param userColourScheme the value of field 'userColourScheme'
-     */
-    public void setUserColourScheme(
-            final jalview.schemabinding.version2.UserColourScheme userColourScheme) {
-        this._userColourScheme = userColourScheme;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.UserColours
-     */
-    public static jalview.schemabinding.version2.UserColours unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+public class UserColours implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _userColourScheme.
+   */
+  private jalview.schemabinding.version2.UserColourScheme _userColourScheme;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public UserColours()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'userColourScheme'.
+   * 
+   * @return the value of field 'UserColourScheme'.
+   */
+  public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()
+  {
+    return this._userColourScheme;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'userColourScheme'.
+   * 
+   * @param userColourScheme
+   *          the value of field 'userColourScheme'
+   */
+  public void setUserColourScheme(
+          final jalview.schemabinding.version2.UserColourScheme userColourScheme)
+  {
+    this._userColourScheme = userColourScheme;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.UserColours
+   */
+  public static jalview.schemabinding.version2.UserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.UserColours) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.UserColours.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index 8605dc5..d025824 100644
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,411 +19,436 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class VAMSAS implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _treeList.
-     */
-    private java.util.Vector _treeList;
-
-    /**
-     * Field _sequenceSetList.
-     */
-    private java.util.Vector _sequenceSetList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VAMSAS() {
-        super();
-        this._treeList = new java.util.Vector();
-        this._sequenceSetList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSet(
-            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetList.addElement(vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSequenceSet(
-            final int index,
-            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        this._sequenceSetList.add(index, vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.addElement(vTree);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addTree(
-            final int index,
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        this._treeList.add(index, vTree);
-    }
-
-    /**
-     * Method enumerateSequenceSet.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.SequenceSet elements
-     */
-    public java.util.Enumeration enumerateSequenceSet(
-    ) {
-        return this._sequenceSetList.elements();
-    }
-
-    /**
-     * Method enumerateTree.
-     * 
-     * @return an Enumeration over all java.lang.String elements
-     */
-    public java.util.Enumeration enumerateTree(
-    ) {
-        return this._treeList.elements();
-    }
-
-    /**
-     * Method getSequenceSet.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.SequenceSet at the given index
-     */
-    public jalview.schemabinding.version2.SequenceSet getSequenceSet(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetList.size()) {
-            throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.get(index);
-    }
-
-    /**
-     * Method getSequenceSet.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.SequenceSet[] getSequenceSet(
-    ) {
-        jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
-        return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array);
-    }
-
-    /**
-     * Method getSequenceSetCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSequenceSetCount(
-    ) {
-        return this._sequenceSetList.size();
-    }
-
-    /**
-     * Method getTree.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the java.lang.String at the given index
-     */
-    public java.lang.String getTree(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        return (java.lang.String) _treeList.get(index);
-    }
-
-    /**
-     * Method getTree.Returns the contents of the collection in an
-     * Array.  
Note:  Just in case the collection contents are
-     * changing in another thread, we pass a 0-length Array of the
-     * correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public java.lang.String[] getTree(
-    ) {
-        java.lang.String[] array = new java.lang.String[0];
-        return (java.lang.String[]) this._treeList.toArray(array);
-    }
-
-    /**
-     * Method getTreeCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getTreeCount(
-    ) {
-        return this._treeList.size();
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllSequenceSet(
-    ) {
-        this._sequenceSetList.clear();
+public class VAMSAS implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _treeList.
+   */
+  private java.util.Vector _treeList;
+
+  /**
+   * Field _sequenceSetList.
+   */
+  private java.util.Vector _sequenceSetList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public VAMSAS()
+  {
+    super();
+    this._treeList = new java.util.Vector();
+    this._sequenceSetList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSet(
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetList.addElement(vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addSequenceSet(final int index,
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._sequenceSetList.add(index, vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.addElement(vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._treeList.add(index, vTree);
+  }
+
+  /**
+   * Method enumerateSequenceSet.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.SequenceSet
+   *         elements
+   */
+  public java.util.Enumeration enumerateSequenceSet()
+  {
+    return this._sequenceSetList.elements();
+  }
+
+  /**
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return this._treeList.elements();
+  }
+
+  /**
+   * Method getSequenceSet.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.SequenceSet at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.SequenceSet getSequenceSet(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
+    {
+      throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
     }
 
-    /**
-     */
-    public void removeAllTree(
-    ) {
-        this._treeList.clear();
-    }
-
-    /**
-     * Method removeSequenceSet.
-     * 
-     * @param vSequenceSet
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSequenceSet(
-            final jalview.schemabinding.version2.SequenceSet vSequenceSet) {
-        boolean removed = _sequenceSetList.remove(vSequenceSet);
-        return removed;
-    }
-
-    /**
-     * Method removeSequenceSetAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
-            final int index) {
-        java.lang.Object obj = this._sequenceSetList.remove(index);
-        return (jalview.schemabinding.version2.SequenceSet) obj;
-    }
-
-    /**
-     * Method removeTree.
-     * 
-     * @param vTree
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeTree(
-            final java.lang.String vTree) {
-        boolean removed = _treeList.remove(vTree);
-        return removed;
+    return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList
+            .get(index);
+  }
+
+  /**
+   * Method getSequenceSet.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
+  {
+    jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0];
+    return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList
+            .toArray(array);
+  }
+
+  /**
+   * Method getSequenceSetCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSequenceSetCount()
+  {
+    return this._sequenceSetList.size();
+  }
+
+  /**
+   * Method getTree.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeTreeAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public java.lang.String removeTreeAt(
-            final int index) {
-        java.lang.Object obj = this._treeList.remove(index);
-        return (java.lang.String) obj;
+    return (java.lang.String) _treeList.get(index);
+  }
+
+  /**
+   * Method getTree.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getTree()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._treeList.toArray(array);
+  }
+
+  /**
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getTreeCount()
+  {
+    return this._treeList.size();
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSequenceSet(
-            final int index,
-            final jalview.schemabinding.version2.SequenceSet vSequenceSet)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._sequenceSetList.size()) {
-            throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
-        }
-        
-        this._sequenceSetList.set(index, vSequenceSet);
-    }
-
-    /**
-     * 
-     * 
-     * @param vSequenceSetArray
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
      */
-    public void setSequenceSet(
-            final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) {
-        //-- copy array
-        _sequenceSetList.clear();
-        
-        for (int i = 0; i < vSequenceSetArray.length; i++) {
-                this._sequenceSetList.add(vSequenceSetArray[i]);
-        }
-    }
+  public void removeAllSequenceSet()
+  {
+    this._sequenceSetList.clear();
+  }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vTree
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
+  /**
      */
-    public void setTree(
-            final int index,
-            final java.lang.String vTree)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._treeList.size()) {
-            throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
-        }
-        
-        this._treeList.set(index, vTree);
+  public void removeAllTree()
+  {
+    this._treeList.clear();
+  }
+
+  /**
+   * Method removeSequenceSet.
+   * 
+   * @param vSequenceSet
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSequenceSet(
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+  {
+    boolean removed = _sequenceSetList.remove(vSequenceSet);
+    return removed;
+  }
+
+  /**
+   * Method removeSequenceSetAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(
+          final int index)
+  {
+    java.lang.Object obj = this._sequenceSetList.remove(index);
+    return (jalview.schemabinding.version2.SequenceSet) obj;
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final java.lang.String vTree)
+  {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
+
+  /**
+   * Method removeTreeAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeTreeAt(final int index)
+  {
+    java.lang.Object obj = this._treeList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSequenceSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setSequenceSet(final int index,
+          final jalview.schemabinding.version2.SequenceSet vSequenceSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._sequenceSetList.size())
+    {
+      throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param vTreeArray
-     */
-    public void setTree(
-            final java.lang.String[] vTreeArray) {
-        //-- copy array
-        _treeList.clear();
-        
-        for (int i = 0; i < vTreeArray.length; i++) {
-                this._treeList.add(vTreeArray[i]);
-        }
+    this._sequenceSetList.set(index, vSequenceSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vSequenceSetArray
+   */
+  public void setSequenceSet(
+          final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray)
+  {
+    // -- copy array
+    _sequenceSetList.clear();
+
+    for (int i = 0; i < vSequenceSetArray.length; i++)
+    {
+      this._sequenceSetList.add(vSequenceSetArray[i]);
     }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
-     */
-    public static jalview.schemabinding.version2.VAMSAS unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setTree(final int index, final java.lang.String vTree)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
+    {
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._treeList.set(index, vTree);
+  }
+
+  /**
+   * 
+   * 
+   * @param vTreeArray
+   */
+  public void setTree(final java.lang.String[] vTreeArray)
+  {
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
+    {
+      this._treeList.add(vTreeArray[i]);
     }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
+   */
+  public static jalview.schemabinding.version2.VAMSAS unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.VAMSAS.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java
index 245bd3d..d3fe796 100644
--- a/src/jalview/schemabinding/version2/VamsasModel.java
+++ b/src/jalview/schemabinding/version2/VamsasModel.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,98 +19,106 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class VamsasModel extends VAMSAS 
-implements java.io.Serializable
+public class VamsasModel extends VAMSAS implements java.io.Serializable
 {
 
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VamsasModel() {
-        super();
-    }
-
+  public VamsasModel()
+  {
+    super();
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
+    return true;
+  }
 
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
 
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
 
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
-     */
-    public static jalview.schemabinding.version2.VAMSAS unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader);
-    }
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.VAMSAS
+   */
+  public static jalview.schemabinding.version2.VAMSAS unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(
+            jalview.schemabinding.version2.VamsasModel.class, reader);
+  }
 
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index e3a19de..159f7ae 100644
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,2732 +19,2785 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Viewport implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _conservationSelected.
-     */
-    private boolean _conservationSelected;
-
-    /**
-     * keeps track of state for field: _conservationSelected
-     */
-    private boolean _has_conservationSelected;
-
-    /**
-     * Field _pidSelected.
-     */
-    private boolean _pidSelected;
-
-    /**
-     * keeps track of state for field: _pidSelected
-     */
-    private boolean _has_pidSelected;
-
-    /**
-     * Field _bgColour.
-     */
-    private java.lang.String _bgColour;
-
-    /**
-     * Field _consThreshold.
-     */
-    private int _consThreshold;
-
-    /**
-     * keeps track of state for field: _consThreshold
-     */
-    private boolean _has_consThreshold;
-
-    /**
-     * Field _pidThreshold.
-     */
-    private int _pidThreshold;
-
-    /**
-     * keeps track of state for field: _pidThreshold
-     */
-    private boolean _has_pidThreshold;
-
-    /**
-     * Field _title.
-     */
-    private java.lang.String _title;
-
-    /**
-     * Field _showFullId.
-     */
-    private boolean _showFullId;
-
-    /**
-     * keeps track of state for field: _showFullId
-     */
-    private boolean _has_showFullId;
-
-    /**
-     * Field _rightAlignIds.
-     */
-    private boolean _rightAlignIds;
-
-    /**
-     * keeps track of state for field: _rightAlignIds
-     */
-    private boolean _has_rightAlignIds;
-
-    /**
-     * Field _showText.
-     */
-    private boolean _showText;
-
-    /**
-     * keeps track of state for field: _showText
-     */
-    private boolean _has_showText;
-
-    /**
-     * Field _showColourText.
-     */
-    private boolean _showColourText;
-
-    /**
-     * keeps track of state for field: _showColourText
-     */
-    private boolean _has_showColourText;
-
-    /**
-     * Field _showUnconserved.
-     */
-    private boolean _showUnconserved = false;
-
-    /**
-     * keeps track of state for field: _showUnconserved
-     */
-    private boolean _has_showUnconserved;
-
-    /**
-     * 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 _showNPfeatureTooltip.
-     */
-    private boolean _showNPfeatureTooltip;
-
-    /**
-     * keeps track of state for field: _showNPfeatureTooltip
-     */
-    private boolean _has_showNPfeatureTooltip;
-
-    /**
-     * Field _showDbRefTooltip.
-     */
-    private boolean _showDbRefTooltip;
-
-    /**
-     * keeps track of state for field: _showDbRefTooltip
-     */
-    private boolean _has_showDbRefTooltip;
-
-    /**
-     * Field _followHighlight.
-     */
-    private boolean _followHighlight = true;
-
-    /**
-     * keeps track of state for field: _followHighlight
-     */
-    private boolean _has_followHighlight;
-
-    /**
-     * Field _followSelection.
-     */
-    private boolean _followSelection = true;
-
-    /**
-     * keeps track of state for field: _followSelection
-     */
-    private boolean _has_followSelection;
-
-    /**
-     * Field _showAnnotation.
-     */
-    private boolean _showAnnotation;
-
-    /**
-     * keeps track of state for field: _showAnnotation
-     */
-    private boolean _has_showAnnotation;
-
-    /**
-     * Field _centreColumnLabels.
-     */
-    private boolean _centreColumnLabels = false;
-
-    /**
-     * keeps track of state for field: _centreColumnLabels
-     */
-    private boolean _has_centreColumnLabels;
-
-    /**
-     * Field _showGroupConservation.
-     */
-    private boolean _showGroupConservation = false;
-
-    /**
-     * keeps track of state for field: _showGroupConservation
-     */
-    private boolean _has_showGroupConservation;
-
-    /**
-     * Field _showGroupConsensus.
-     */
-    private boolean _showGroupConsensus = false;
-
-    /**
-     * keeps track of state for field: _showGroupConsensus
-     */
-    private boolean _has_showGroupConsensus;
-
-    /**
-     * Field _showConsensusHistogram.
-     */
-    private boolean _showConsensusHistogram = true;
-
-    /**
-     * keeps track of state for field: _showConsensusHistogram
-     */
-    private boolean _has_showConsensusHistogram;
-
-    /**
-     * Field _showSequenceLogo.
-     */
-    private boolean _showSequenceLogo = false;
-
-    /**
-     * keeps track of state for field: _showSequenceLogo
-     */
-    private boolean _has_showSequenceLogo;
-
-    /**
-     * Field _normaliseSequenceLogo.
-     */
-    private boolean _normaliseSequenceLogo = false;
-
-    /**
-     * keeps track of state for field: _normaliseSequenceLogo
-     */
-    private boolean _has_normaliseSequenceLogo;
-
-    /**
-     * Field _ignoreGapsinConsensus.
-     */
-    private boolean _ignoreGapsinConsensus = true;
-
-    /**
-     * keeps track of state for field: _ignoreGapsinConsensus
-     */
-    private boolean _has_ignoreGapsinConsensus;
-
-    /**
-     * 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 _scaleProteinAsCdna.
-     */
-    private boolean _scaleProteinAsCdna = true;
-
-    /**
-     * keeps track of state for field: _scaleProteinAsCdna
-     */
-    private boolean _has_scaleProteinAsCdna;
-
-    /**
-     * 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;
-
-    /**
-     * unique id used by jalview to
-     *  synchronize
-     *  between stored and
-     *  instantiated views
-     *  
-     */
-    private java.lang.String _id;
-
-    /**
-     * The viewport id of this viewport's
-     *  (cdna/protein) coding complement, if any
-     *  
-     */
-    private java.lang.String _complementId;
-
-    /**
-     * 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 _annotationColours.
-     */
-    private jalview.schemabinding.version2.AnnotationColours _annotationColours;
-
-    /**
-     * Field _hiddenColumnsList.
-     */
-    private java.util.Vector _hiddenColumnsList;
-
-    /**
-     * Field _calcIdParamList.
-     */
-    private java.util.Vector _calcIdParamList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Viewport() {
-        super();
-        this._hiddenColumnsList = new java.util.Vector();
-        this._calcIdParamList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vCalcIdParam
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addCalcIdParam(
-            final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
-    throws java.lang.IndexOutOfBoundsException {
-        this._calcIdParamList.addElement(vCalcIdParam);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vCalcIdParam
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addCalcIdParam(
-            final int index,
-            final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
-    throws java.lang.IndexOutOfBoundsException {
-        this._calcIdParamList.add(index, vCalcIdParam);
-    }
-
-    /**
-     * 
-     * 
-     * @param vHiddenColumns
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addHiddenColumns(
-            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-    throws java.lang.IndexOutOfBoundsException {
-        this._hiddenColumnsList.addElement(vHiddenColumns);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vHiddenColumns
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addHiddenColumns(
-            final int index,
-            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-    throws java.lang.IndexOutOfBoundsException {
-        this._hiddenColumnsList.add(index, vHiddenColumns);
-    }
+public 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 _showUnconserved.
+   */
+  private boolean _showUnconserved = false;
+
+  /**
+   * keeps track of state for field: _showUnconserved
+   */
+  private boolean _has_showUnconserved;
+
+  /**
+   * 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 _showNPfeatureTooltip.
+   */
+  private boolean _showNPfeatureTooltip;
+
+  /**
+   * keeps track of state for field: _showNPfeatureTooltip
+   */
+  private boolean _has_showNPfeatureTooltip;
+
+  /**
+   * Field _showDbRefTooltip.
+   */
+  private boolean _showDbRefTooltip;
+
+  /**
+   * keeps track of state for field: _showDbRefTooltip
+   */
+  private boolean _has_showDbRefTooltip;
+
+  /**
+   * Field _followHighlight.
+   */
+  private boolean _followHighlight = true;
+
+  /**
+   * keeps track of state for field: _followHighlight
+   */
+  private boolean _has_followHighlight;
+
+  /**
+   * Field _followSelection.
+   */
+  private boolean _followSelection = true;
+
+  /**
+   * keeps track of state for field: _followSelection
+   */
+  private boolean _has_followSelection;
+
+  /**
+   * Field _showAnnotation.
+   */
+  private boolean _showAnnotation;
+
+  /**
+   * keeps track of state for field: _showAnnotation
+   */
+  private boolean _has_showAnnotation;
+
+  /**
+   * Field _centreColumnLabels.
+   */
+  private boolean _centreColumnLabels = false;
+
+  /**
+   * keeps track of state for field: _centreColumnLabels
+   */
+  private boolean _has_centreColumnLabels;
+
+  /**
+   * Field _showGroupConservation.
+   */
+  private boolean _showGroupConservation = false;
+
+  /**
+   * keeps track of state for field: _showGroupConservation
+   */
+  private boolean _has_showGroupConservation;
+
+  /**
+   * Field _showGroupConsensus.
+   */
+  private boolean _showGroupConsensus = false;
+
+  /**
+   * keeps track of state for field: _showGroupConsensus
+   */
+  private boolean _has_showGroupConsensus;
+
+  /**
+   * Field _showConsensusHistogram.
+   */
+  private boolean _showConsensusHistogram = true;
+
+  /**
+   * keeps track of state for field: _showConsensusHistogram
+   */
+  private boolean _has_showConsensusHistogram;
+
+  /**
+   * Field _showSequenceLogo.
+   */
+  private boolean _showSequenceLogo = false;
+
+  /**
+   * keeps track of state for field: _showSequenceLogo
+   */
+  private boolean _has_showSequenceLogo;
+
+  /**
+   * Field _normaliseSequenceLogo.
+   */
+  private boolean _normaliseSequenceLogo = false;
+
+  /**
+   * keeps track of state for field: _normaliseSequenceLogo
+   */
+  private boolean _has_normaliseSequenceLogo;
+
+  /**
+   * Field _ignoreGapsinConsensus.
+   */
+  private boolean _ignoreGapsinConsensus = true;
+
+  /**
+   * keeps track of state for field: _ignoreGapsinConsensus
+   */
+  private boolean _has_ignoreGapsinConsensus;
+
+  /**
+   * 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 _scaleProteinAsCdna.
+   */
+  private boolean _scaleProteinAsCdna = true;
+
+  /**
+   * keeps track of state for field: _scaleProteinAsCdna
+   */
+  private boolean _has_scaleProteinAsCdna;
+
+  /**
+   * 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;
+
+  /**
+   * unique id used by jalview to synchronize between stored and instantiated
+   * views
+   * 
+   */
+  private java.lang.String _id;
+
+  /**
+   * The viewport id of this viewport's (cdna/protein) coding complement, if any
+   * 
+   */
+  private java.lang.String _complementId;
+
+  /**
+   * 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 _annotationColours.
+   */
+  private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+  /**
+   * Field _hiddenColumnsList.
+   */
+  private java.util.Vector _hiddenColumnsList;
+
+  /**
+   * Field _calcIdParamList.
+   */
+  private java.util.Vector _calcIdParamList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Viewport()
+  {
+    super();
+    this._hiddenColumnsList = new java.util.Vector();
+    this._calcIdParamList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vCalcIdParam
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addCalcIdParam(
+          final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._calcIdParamList.addElement(vCalcIdParam);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vCalcIdParam
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addCalcIdParam(final int index,
+          final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._calcIdParamList.add(index, vCalcIdParam);
+  }
+
+  /**
+   * 
+   * 
+   * @param vHiddenColumns
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addHiddenColumns(
+          final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenColumnsList.addElement(vHiddenColumns);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenColumns
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addHiddenColumns(final int index,
+          final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._hiddenColumnsList.add(index, vHiddenColumns);
+  }
+
+  /**
+     */
+  public void deleteCentreColumnLabels()
+  {
+    this._has_centreColumnLabels = false;
+  }
+
+  /**
+     */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  }
+
+  /**
+     */
+  public void deleteConservationSelected()
+  {
+    this._has_conservationSelected = false;
+  }
+
+  /**
+     */
+  public void deleteFollowHighlight()
+  {
+    this._has_followHighlight = false;
+  }
+
+  /**
+     */
+  public void deleteFollowSelection()
+  {
+    this._has_followSelection = false;
+  }
+
+  /**
+     */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  }
+
+  /**
+     */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  }
+
+  /**
+     */
+  public void deleteGatheredViews()
+  {
+    this._has_gatheredViews = false;
+  }
+
+  /**
+     */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteCentreColumnLabels(
-    ) {
-        this._has_centreColumnLabels= false;
-    }
-
-    /**
-     */
-    public void deleteConsThreshold(
-    ) {
-        this._has_consThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteConservationSelected(
-    ) {
-        this._has_conservationSelected= false;
-    }
-
-    /**
-     */
-    public void deleteFollowHighlight(
-    ) {
-        this._has_followHighlight= false;
-    }
-
-    /**
-     */
-    public void deleteFollowSelection(
-    ) {
-        this._has_followSelection= false;
-    }
-
-    /**
-     */
-    public void deleteFontSize(
-    ) {
-        this._has_fontSize= false;
-    }
-
-    /**
-     */
-    public void deleteFontStyle(
-    ) {
-        this._has_fontStyle= false;
-    }
-
-    /**
-     */
-    public void deleteGatheredViews(
-    ) {
-        this._has_gatheredViews= false;
-    }
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deleteIgnoreGapsinConsensus(
-    ) {
-        this._has_ignoreGapsinConsensus= false;
-    }
-
-    /**
-     */
-    public void deleteNormaliseSequenceLogo(
-    ) {
-        this._has_normaliseSequenceLogo= false;
-    }
-
-    /**
-     */
-    public void deletePidSelected(
-    ) {
-        this._has_pidSelected= false;
-    }
-
-    /**
-     */
-    public void deletePidThreshold(
-    ) {
-        this._has_pidThreshold= false;
-    }
-
-    /**
-     */
-    public void deleteRenderGaps(
-    ) {
-        this._has_renderGaps= false;
-    }
+  public void deleteIgnoreGapsinConsensus()
+  {
+    this._has_ignoreGapsinConsensus = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteRightAlignIds(
-    ) {
-        this._has_rightAlignIds= false;
-    }
-
-    /**
-     */
-    public void deleteScaleProteinAsCdna(
-    ) {
-        this._has_scaleProteinAsCdna= false;
-    }
+  public void deleteNormaliseSequenceLogo()
+  {
+    this._has_normaliseSequenceLogo = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowAnnotation(
-    ) {
-        this._has_showAnnotation= false;
-    }
+  public void deletePidSelected()
+  {
+    this._has_pidSelected = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowBoxes(
-    ) {
-        this._has_showBoxes= false;
-    }
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowColourText(
-    ) {
-        this._has_showColourText= false;
-    }
+  public void deleteRenderGaps()
+  {
+    this._has_renderGaps = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowConsensusHistogram(
-    ) {
-        this._has_showConsensusHistogram= false;
-    }
+  public void deleteRightAlignIds()
+  {
+    this._has_rightAlignIds = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowDbRefTooltip(
-    ) {
-        this._has_showDbRefTooltip= false;
-    }
+  public void deleteScaleProteinAsCdna()
+  {
+    this._has_scaleProteinAsCdna = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowFullId(
-    ) {
-        this._has_showFullId= false;
-    }
+  public void deleteShowAnnotation()
+  {
+    this._has_showAnnotation = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowGroupConsensus(
-    ) {
-        this._has_showGroupConsensus= false;
-    }
+  public void deleteShowBoxes()
+  {
+    this._has_showBoxes = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowGroupConservation(
-    ) {
-        this._has_showGroupConservation= false;
-    }
+  public void deleteShowColourText()
+  {
+    this._has_showColourText = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowNPfeatureTooltip(
-    ) {
-        this._has_showNPfeatureTooltip= false;
-    }
+  public void deleteShowConsensusHistogram()
+  {
+    this._has_showConsensusHistogram = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowSequenceFeatures(
-    ) {
-        this._has_showSequenceFeatures= false;
-    }
+  public void deleteShowDbRefTooltip()
+  {
+    this._has_showDbRefTooltip = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowSequenceLogo(
-    ) {
-        this._has_showSequenceLogo= false;
-    }
+  public void deleteShowFullId()
+  {
+    this._has_showFullId = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowText(
-    ) {
-        this._has_showText= false;
-    }
+  public void deleteShowGroupConsensus()
+  {
+    this._has_showGroupConsensus = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteShowUnconserved(
-    ) {
-        this._has_showUnconserved= false;
-    }
+  public void deleteShowGroupConservation()
+  {
+    this._has_showGroupConservation = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteStartRes(
-    ) {
-        this._has_startRes= false;
-    }
+  public void deleteShowNPfeatureTooltip()
+  {
+    this._has_showNPfeatureTooltip = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteStartSeq(
-    ) {
-        this._has_startSeq= false;
-    }
+  public void deleteShowSequenceFeatures()
+  {
+    this._has_showSequenceFeatures = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteTextCol1(
-    ) {
-        this._has_textCol1= false;
-    }
+  public void deleteShowSequenceLogo()
+  {
+    this._has_showSequenceLogo = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteTextCol2(
-    ) {
-        this._has_textCol2= false;
-    }
+  public void deleteShowText()
+  {
+    this._has_showText = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteTextColThreshold(
-    ) {
-        this._has_textColThreshold= false;
-    }
+  public void deleteShowUnconserved()
+  {
+    this._has_showUnconserved = false;
+  }
 
-    /**
+  /**
      */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteWrapAlignment(
-    ) {
-        this._has_wrapAlignment= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Method enumerateCalcIdParam.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.CalcIdParam elements
-     */
-    public java.util.Enumeration enumerateCalcIdParam(
-    ) {
-        return this._calcIdParamList.elements();
-    }
-
-    /**
-     * Method enumerateHiddenColumns.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.HiddenColumns elements
-     */
-    public java.util.Enumeration enumerateHiddenColumns(
-    ) {
-        return this._hiddenColumnsList.elements();
-    }
-
-    /**
-     * Returns the value of field 'annotationColours'.
-     * 
-     * @return the value of field 'AnnotationColours'.
-     */
-    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
-    ) {
-        return this._annotationColours;
-    }
-
-    /**
-     * Returns the value of field 'bgColour'.
-     * 
-     * @return the value of field 'BgColour'.
-     */
-    public java.lang.String getBgColour(
-    ) {
-        return this._bgColour;
-    }
-
-    /**
-     * Method getCalcIdParam.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.CalcIdParam at the given index
-     */
-    public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._calcIdParamList.size()) {
-            throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
-    }
-
-    /**
-     * Method getCalcIdParam.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam(
-    ) {
-        jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
-        return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
-    }
-
-    /**
-     * Method getCalcIdParamCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getCalcIdParamCount(
-    ) {
-        return this._calcIdParamList.size();
-    }
-
-    /**
-     * Returns the value of field 'centreColumnLabels'.
-     * 
-     * @return the value of field 'CentreColumnLabels'.
-     */
-    public boolean getCentreColumnLabels(
-    ) {
-        return this._centreColumnLabels;
-    }
-
-    /**
-     * Returns the value of field 'complementId'. The field
-     * 'complementId' has the following description: The viewport
-     * id of this viewport's
-     *  (cdna/protein) coding complement, if any
-     *  
-     * 
-     * @return the value of field 'ComplementId'.
-     */
-    public java.lang.String getComplementId(
-    ) {
-        return this._complementId;
-    }
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return the value of field 'ConsThreshold'.
-     */
-    public int getConsThreshold(
-    ) {
-        return this._consThreshold;
-    }
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return the value of field 'ConservationSelected'.
-     */
-    public boolean getConservationSelected(
-    ) {
-        return this._conservationSelected;
-    }
-
-    /**
-     * Returns the value of field 'followHighlight'.
-     * 
-     * @return the value of field 'FollowHighlight'.
-     */
-    public boolean getFollowHighlight(
-    ) {
-        return this._followHighlight;
-    }
-
-    /**
-     * Returns the value of field 'followSelection'.
-     * 
-     * @return the value of field 'FollowSelection'.
-     */
-    public boolean getFollowSelection(
-    ) {
-        return this._followSelection;
-    }
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return the value of field 'FontName'.
-     */
-    public java.lang.String getFontName(
-    ) {
-        return this._fontName;
-    }
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return the value of field 'FontSize'.
-     */
-    public int getFontSize(
-    ) {
-        return this._fontSize;
-    }
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return the value of field 'FontStyle'.
-     */
-    public int getFontStyle(
-    ) {
-        return this._fontStyle;
-    }
-
-    /**
-     * Returns the value of field 'gatheredViews'.
-     * 
-     * @return the value of field 'GatheredViews'.
-     */
-    public boolean getGatheredViews(
-    ) {
-        return this._gatheredViews;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Method getHiddenColumns.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the
-     * jalview.schemabinding.version2.HiddenColumns at the given
-     * index
-     */
-    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._hiddenColumnsList.size()) {
-            throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
-        }
-        
-        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index);
-    }
-
-    /**
-     * Method getHiddenColumns.Returns the contents of the
-     * collection in an Array.  
Note:  Just in case the
-     * collection contents are changing in another thread, we pass
-     * a 0-length Array of the correct type into the API call. 
-     * This way we know that the Array returned is of
-     * exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns(
-    ) {
-        jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
-        return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array);
-    }
-
-    /**
-     * Method getHiddenColumnsCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getHiddenColumnsCount(
-    ) {
-        return this._hiddenColumnsList.size();
-    }
-
-    /**
-     * Returns the value of field 'id'. The field 'id' has the
-     * following description: unique id used by jalview to
-     *  synchronize
-     *  between stored and
-     *  instantiated views
-     *  
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'ignoreGapsinConsensus'.
-     * 
-     * @return the value of field 'IgnoreGapsinConsensus'.
-     */
-    public boolean getIgnoreGapsinConsensus(
-    ) {
-        return this._ignoreGapsinConsensus;
-    }
-
-    /**
-     * Returns the value of field 'normaliseSequenceLogo'.
-     * 
-     * @return the value of field 'NormaliseSequenceLogo'.
-     */
-    public boolean getNormaliseSequenceLogo(
-    ) {
-        return this._normaliseSequenceLogo;
-    }
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return the value of field 'PidSelected'.
-     */
-    public boolean getPidSelected(
-    ) {
-        return this._pidSelected;
-    }
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return the value of field 'PidThreshold'.
-     */
-    public int getPidThreshold(
-    ) {
-        return this._pidThreshold;
-    }
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return the value of field 'RenderGaps'.
-     */
-    public boolean getRenderGaps(
-    ) {
-        return this._renderGaps;
-    }
-
-    /**
-     * Returns the value of field 'rightAlignIds'.
-     * 
-     * @return the value of field 'RightAlignIds'.
-     */
-    public boolean getRightAlignIds(
-    ) {
-        return this._rightAlignIds;
-    }
-
-    /**
-     * Returns the value of field 'scaleProteinAsCdna'.
-     * 
-     * @return the value of field 'ScaleProteinAsCdna'.
-     */
-    public boolean getScaleProteinAsCdna(
-    ) {
-        return this._scaleProteinAsCdna;
-    }
-
-    /**
-     * Returns the value of field 'sequenceSetId'.
-     * 
-     * @return the value of field 'SequenceSetId'.
-     */
-    public java.lang.String getSequenceSetId(
-    ) {
-        return this._sequenceSetId;
-    }
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return the value of field 'ShowAnnotation'.
-     */
-    public boolean getShowAnnotation(
-    ) {
-        return this._showAnnotation;
-    }
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return the value of field 'ShowBoxes'.
-     */
-    public boolean getShowBoxes(
-    ) {
-        return this._showBoxes;
-    }
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return the value of field 'ShowColourText'.
-     */
-    public boolean getShowColourText(
-    ) {
-        return this._showColourText;
-    }
-
-    /**
-     * Returns the value of field 'showConsensusHistogram'.
-     * 
-     * @return the value of field 'ShowConsensusHistogram'.
-     */
-    public boolean getShowConsensusHistogram(
-    ) {
-        return this._showConsensusHistogram;
-    }
-
-    /**
-     * Returns the value of field 'showDbRefTooltip'.
-     * 
-     * @return the value of field 'ShowDbRefTooltip'.
-     */
-    public boolean getShowDbRefTooltip(
-    ) {
-        return this._showDbRefTooltip;
-    }
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return the value of field 'ShowFullId'.
-     */
-    public boolean getShowFullId(
-    ) {
-        return this._showFullId;
-    }
-
-    /**
-     * Returns the value of field 'showGroupConsensus'.
-     * 
-     * @return the value of field 'ShowGroupConsensus'.
-     */
-    public boolean getShowGroupConsensus(
-    ) {
-        return this._showGroupConsensus;
-    }
-
-    /**
-     * Returns the value of field 'showGroupConservation'.
-     * 
-     * @return the value of field 'ShowGroupConservation'.
-     */
-    public boolean getShowGroupConservation(
-    ) {
-        return this._showGroupConservation;
-    }
-
-    /**
-     * Returns the value of field 'showNPfeatureTooltip'.
-     * 
-     * @return the value of field 'ShowNPfeatureTooltip'.
-     */
-    public boolean getShowNPfeatureTooltip(
-    ) {
-        return this._showNPfeatureTooltip;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return the value of field 'ShowSequenceFeatures'.
-     */
-    public boolean getShowSequenceFeatures(
-    ) {
-        return this._showSequenceFeatures;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceLogo'.
-     * 
-     * @return the value of field 'ShowSequenceLogo'.
-     */
-    public boolean getShowSequenceLogo(
-    ) {
-        return this._showSequenceLogo;
-    }
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return the value of field 'ShowText'.
-     */
-    public boolean getShowText(
-    ) {
-        return this._showText;
-    }
-
-    /**
-     * Returns the value of field 'showUnconserved'.
-     * 
-     * @return the value of field 'ShowUnconserved'.
-     */
-    public boolean getShowUnconserved(
-    ) {
-        return this._showUnconserved;
-    }
-
-    /**
-     * Returns the value of field 'startRes'.
-     * 
-     * @return the value of field 'StartRes'.
-     */
-    public int getStartRes(
-    ) {
-        return this._startRes;
-    }
-
-    /**
-     * Returns the value of field 'startSeq'.
-     * 
-     * @return the value of field 'StartSeq'.
-     */
-    public int getStartSeq(
-    ) {
-        return this._startSeq;
-    }
-
-    /**
-     * Returns the value of field 'textCol1'.
-     * 
-     * @return the value of field 'TextCol1'.
-     */
-    public int getTextCol1(
-    ) {
-        return this._textCol1;
-    }
-
-    /**
-     * Returns the value of field 'textCol2'.
-     * 
-     * @return the value of field 'TextCol2'.
-     */
-    public int getTextCol2(
-    ) {
-        return this._textCol2;
-    }
-
-    /**
-     * Returns the value of field 'textColThreshold'.
-     * 
-     * @return the value of field 'TextColThreshold'.
-     */
-    public int getTextColThreshold(
-    ) {
-        return this._textColThreshold;
-    }
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return the value of field 'Title'.
-     */
-    public java.lang.String getTitle(
-    ) {
-        return this._title;
-    }
-
-    /**
-     * Returns the value of field 'viewName'.
-     * 
-     * @return the value of field 'ViewName'.
-     */
-    public java.lang.String getViewName(
-    ) {
-        return this._viewName;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return the value of field 'WrapAlignment'.
-     */
-    public boolean getWrapAlignment(
-    ) {
-        return this._wrapAlignment;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasCentreColumnLabels.
-     * 
-     * @return true if at least one CentreColumnLabels has been adde
-     */
-    public boolean hasCentreColumnLabels(
-    ) {
-        return this._has_centreColumnLabels;
-    }
-
-    /**
-     * Method hasConsThreshold.
-     * 
-     * @return true if at least one ConsThreshold has been added
-     */
-    public boolean hasConsThreshold(
-    ) {
-        return this._has_consThreshold;
-    }
-
-    /**
-     * Method hasConservationSelected.
-     * 
-     * @return true if at least one ConservationSelected has been
-     * added
-     */
-    public boolean hasConservationSelected(
-    ) {
-        return this._has_conservationSelected;
-    }
-
-    /**
-     * Method hasFollowHighlight.
-     * 
-     * @return true if at least one FollowHighlight has been added
-     */
-    public boolean hasFollowHighlight(
-    ) {
-        return this._has_followHighlight;
-    }
-
-    /**
-     * Method hasFollowSelection.
-     * 
-     * @return true if at least one FollowSelection has been added
-     */
-    public boolean hasFollowSelection(
-    ) {
-        return this._has_followSelection;
-    }
-
-    /**
-     * Method hasFontSize.
-     * 
-     * @return true if at least one FontSize has been added
-     */
-    public boolean hasFontSize(
-    ) {
-        return this._has_fontSize;
-    }
-
-    /**
-     * Method hasFontStyle.
-     * 
-     * @return true if at least one FontStyle has been added
-     */
-    public boolean hasFontStyle(
-    ) {
-        return this._has_fontStyle;
-    }
-
-    /**
-     * Method hasGatheredViews.
-     * 
-     * @return true if at least one GatheredViews has been added
-     */
-    public boolean hasGatheredViews(
-    ) {
-        return this._has_gatheredViews;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasIgnoreGapsinConsensus.
-     * 
-     * @return true if at least one IgnoreGapsinConsensus has been
-     * added
-     */
-    public boolean hasIgnoreGapsinConsensus(
-    ) {
-        return this._has_ignoreGapsinConsensus;
-    }
-
-    /**
-     * Method hasNormaliseSequenceLogo.
-     * 
-     * @return true if at least one NormaliseSequenceLogo has been
-     * added
-     */
-    public boolean hasNormaliseSequenceLogo(
-    ) {
-        return this._has_normaliseSequenceLogo;
-    }
-
-    /**
-     * Method hasPidSelected.
-     * 
-     * @return true if at least one PidSelected has been added
-     */
-    public boolean hasPidSelected(
-    ) {
-        return this._has_pidSelected;
-    }
-
-    /**
-     * Method hasPidThreshold.
-     * 
-     * @return true if at least one PidThreshold has been added
-     */
-    public boolean hasPidThreshold(
-    ) {
-        return this._has_pidThreshold;
-    }
-
-    /**
-     * Method hasRenderGaps.
-     * 
-     * @return true if at least one RenderGaps has been added
-     */
-    public boolean hasRenderGaps(
-    ) {
-        return this._has_renderGaps;
-    }
-
-    /**
-     * Method hasRightAlignIds.
-     * 
-     * @return true if at least one RightAlignIds has been added
-     */
-    public boolean hasRightAlignIds(
-    ) {
-        return this._has_rightAlignIds;
-    }
-
-    /**
-     * Method hasScaleProteinAsCdna.
-     * 
-     * @return true if at least one ScaleProteinAsCdna has been adde
-     */
-    public boolean hasScaleProteinAsCdna(
-    ) {
-        return this._has_scaleProteinAsCdna;
-    }
-
-    /**
-     * Method hasShowAnnotation.
-     * 
-     * @return true if at least one ShowAnnotation has been added
-     */
-    public boolean hasShowAnnotation(
-    ) {
-        return this._has_showAnnotation;
-    }
-
-    /**
-     * Method hasShowBoxes.
-     * 
-     * @return true if at least one ShowBoxes has been added
-     */
-    public boolean hasShowBoxes(
-    ) {
-        return this._has_showBoxes;
-    }
-
-    /**
-     * Method hasShowColourText.
-     * 
-     * @return true if at least one ShowColourText has been added
-     */
-    public boolean hasShowColourText(
-    ) {
-        return this._has_showColourText;
-    }
-
-    /**
-     * Method hasShowConsensusHistogram.
-     * 
-     * @return true if at least one ShowConsensusHistogram has been
-     * added
-     */
-    public boolean hasShowConsensusHistogram(
-    ) {
-        return this._has_showConsensusHistogram;
-    }
-
-    /**
-     * Method hasShowDbRefTooltip.
-     * 
-     * @return true if at least one ShowDbRefTooltip has been added
-     */
-    public boolean hasShowDbRefTooltip(
-    ) {
-        return this._has_showDbRefTooltip;
-    }
-
-    /**
-     * Method hasShowFullId.
-     * 
-     * @return true if at least one ShowFullId has been added
-     */
-    public boolean hasShowFullId(
-    ) {
-        return this._has_showFullId;
-    }
-
-    /**
-     * Method hasShowGroupConsensus.
-     * 
-     * @return true if at least one ShowGroupConsensus has been adde
-     */
-    public boolean hasShowGroupConsensus(
-    ) {
-        return this._has_showGroupConsensus;
-    }
-
-    /**
-     * Method hasShowGroupConservation.
-     * 
-     * @return true if at least one ShowGroupConservation has been
-     * added
-     */
-    public boolean hasShowGroupConservation(
-    ) {
-        return this._has_showGroupConservation;
-    }
-
-    /**
-     * Method hasShowNPfeatureTooltip.
-     * 
-     * @return true if at least one ShowNPfeatureTooltip has been
-     * added
-     */
-    public boolean hasShowNPfeatureTooltip(
-    ) {
-        return this._has_showNPfeatureTooltip;
-    }
-
-    /**
-     * Method hasShowSequenceFeatures.
-     * 
-     * @return true if at least one ShowSequenceFeatures has been
-     * added
-     */
-    public boolean hasShowSequenceFeatures(
-    ) {
-        return this._has_showSequenceFeatures;
-    }
-
-    /**
-     * Method hasShowSequenceLogo.
-     * 
-     * @return true if at least one ShowSequenceLogo has been added
-     */
-    public boolean hasShowSequenceLogo(
-    ) {
-        return this._has_showSequenceLogo;
-    }
-
-    /**
-     * Method hasShowText.
-     * 
-     * @return true if at least one ShowText has been added
-     */
-    public boolean hasShowText(
-    ) {
-        return this._has_showText;
-    }
-
-    /**
-     * Method hasShowUnconserved.
-     * 
-     * @return true if at least one ShowUnconserved has been added
-     */
-    public boolean hasShowUnconserved(
-    ) {
-        return this._has_showUnconserved;
-    }
-
-    /**
-     * Method hasStartRes.
-     * 
-     * @return true if at least one StartRes has been added
-     */
-    public boolean hasStartRes(
-    ) {
-        return this._has_startRes;
-    }
-
-    /**
-     * Method hasStartSeq.
-     * 
-     * @return true if at least one StartSeq has been added
-     */
-    public boolean hasStartSeq(
-    ) {
-        return this._has_startSeq;
-    }
-
-    /**
-     * Method hasTextCol1.
-     * 
-     * @return true if at least one TextCol1 has been added
-     */
-    public boolean hasTextCol1(
-    ) {
-        return this._has_textCol1;
-    }
-
-    /**
-     * Method hasTextCol2.
-     * 
-     * @return true if at least one TextCol2 has been added
-     */
-    public boolean hasTextCol2(
-    ) {
-        return this._has_textCol2;
-    }
-
-    /**
-     * Method hasTextColThreshold.
-     * 
-     * @return true if at least one TextColThreshold has been added
-     */
-    public boolean hasTextColThreshold(
-    ) {
-        return this._has_textColThreshold;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasWrapAlignment.
-     * 
-     * @return true if at least one WrapAlignment has been added
-     */
-    public boolean hasWrapAlignment(
-    ) {
-        return this._has_wrapAlignment;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * Returns the value of field 'centreColumnLabels'.
-     * 
-     * @return the value of field 'CentreColumnLabels'.
-     */
-    public boolean isCentreColumnLabels(
-    ) {
-        return this._centreColumnLabels;
-    }
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return the value of field 'ConservationSelected'.
-     */
-    public boolean isConservationSelected(
-    ) {
-        return this._conservationSelected;
-    }
-
-    /**
-     * Returns the value of field 'followHighlight'.
-     * 
-     * @return the value of field 'FollowHighlight'.
-     */
-    public boolean isFollowHighlight(
-    ) {
-        return this._followHighlight;
-    }
-
-    /**
-     * Returns the value of field 'followSelection'.
-     * 
-     * @return the value of field 'FollowSelection'.
-     */
-    public boolean isFollowSelection(
-    ) {
-        return this._followSelection;
-    }
-
-    /**
-     * Returns the value of field 'gatheredViews'.
-     * 
-     * @return the value of field 'GatheredViews'.
-     */
-    public boolean isGatheredViews(
-    ) {
-        return this._gatheredViews;
-    }
-
-    /**
-     * Returns the value of field 'ignoreGapsinConsensus'.
-     * 
-     * @return the value of field 'IgnoreGapsinConsensus'.
-     */
-    public boolean isIgnoreGapsinConsensus(
-    ) {
-        return this._ignoreGapsinConsensus;
-    }
-
-    /**
-     * Returns the value of field 'normaliseSequenceLogo'.
-     * 
-     * @return the value of field 'NormaliseSequenceLogo'.
-     */
-    public boolean isNormaliseSequenceLogo(
-    ) {
-        return this._normaliseSequenceLogo;
-    }
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return the value of field 'PidSelected'.
-     */
-    public boolean isPidSelected(
-    ) {
-        return this._pidSelected;
-    }
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return the value of field 'RenderGaps'.
-     */
-    public boolean isRenderGaps(
-    ) {
-        return this._renderGaps;
-    }
-
-    /**
-     * Returns the value of field 'rightAlignIds'.
-     * 
-     * @return the value of field 'RightAlignIds'.
-     */
-    public boolean isRightAlignIds(
-    ) {
-        return this._rightAlignIds;
-    }
-
-    /**
-     * Returns the value of field 'scaleProteinAsCdna'.
-     * 
-     * @return the value of field 'ScaleProteinAsCdna'.
-     */
-    public boolean isScaleProteinAsCdna(
-    ) {
-        return this._scaleProteinAsCdna;
-    }
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return the value of field 'ShowAnnotation'.
-     */
-    public boolean isShowAnnotation(
-    ) {
-        return this._showAnnotation;
-    }
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return the value of field 'ShowBoxes'.
-     */
-    public boolean isShowBoxes(
-    ) {
-        return this._showBoxes;
-    }
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return the value of field 'ShowColourText'.
-     */
-    public boolean isShowColourText(
-    ) {
-        return this._showColourText;
-    }
-
-    /**
-     * Returns the value of field 'showConsensusHistogram'.
-     * 
-     * @return the value of field 'ShowConsensusHistogram'.
-     */
-    public boolean isShowConsensusHistogram(
-    ) {
-        return this._showConsensusHistogram;
-    }
-
-    /**
-     * Returns the value of field 'showDbRefTooltip'.
-     * 
-     * @return the value of field 'ShowDbRefTooltip'.
-     */
-    public boolean isShowDbRefTooltip(
-    ) {
-        return this._showDbRefTooltip;
-    }
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return the value of field 'ShowFullId'.
-     */
-    public boolean isShowFullId(
-    ) {
-        return this._showFullId;
-    }
-
-    /**
-     * Returns the value of field 'showGroupConsensus'.
-     * 
-     * @return the value of field 'ShowGroupConsensus'.
-     */
-    public boolean isShowGroupConsensus(
-    ) {
-        return this._showGroupConsensus;
-    }
-
-    /**
-     * Returns the value of field 'showGroupConservation'.
-     * 
-     * @return the value of field 'ShowGroupConservation'.
-     */
-    public boolean isShowGroupConservation(
-    ) {
-        return this._showGroupConservation;
-    }
-
-    /**
-     * Returns the value of field 'showNPfeatureTooltip'.
-     * 
-     * @return the value of field 'ShowNPfeatureTooltip'.
-     */
-    public boolean isShowNPfeatureTooltip(
-    ) {
-        return this._showNPfeatureTooltip;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return the value of field 'ShowSequenceFeatures'.
-     */
-    public boolean isShowSequenceFeatures(
-    ) {
-        return this._showSequenceFeatures;
-    }
-
-    /**
-     * Returns the value of field 'showSequenceLogo'.
-     * 
-     * @return the value of field 'ShowSequenceLogo'.
-     */
-    public boolean isShowSequenceLogo(
-    ) {
-        return this._showSequenceLogo;
-    }
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return the value of field 'ShowText'.
-     */
-    public boolean isShowText(
-    ) {
-        return this._showText;
-    }
-
-    /**
-     * Returns the value of field 'showUnconserved'.
-     * 
-     * @return the value of field 'ShowUnconserved'.
-     */
-    public boolean isShowUnconserved(
-    ) {
-        return this._showUnconserved;
-    }
-
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return the value of field 'WrapAlignment'.
-     */
-    public boolean isWrapAlignment(
-    ) {
-        return this._wrapAlignment;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllCalcIdParam(
-    ) {
-        this._calcIdParamList.clear();
-    }
-
-    /**
-     */
-    public void removeAllHiddenColumns(
-    ) {
-        this._hiddenColumnsList.clear();
-    }
-
-    /**
-     * Method removeCalcIdParam.
-     * 
-     * @param vCalcIdParam
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeCalcIdParam(
-            final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
-        boolean removed = _calcIdParamList.remove(vCalcIdParam);
-        return removed;
-    }
-
-    /**
-     * Method removeCalcIdParamAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
-            final int index) {
-        java.lang.Object obj = this._calcIdParamList.remove(index);
-        return (jalview.schemabinding.version2.CalcIdParam) obj;
-    }
-
-    /**
-     * Method removeHiddenColumns.
-     * 
-     * @param vHiddenColumns
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeHiddenColumns(
-            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) {
-        boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
-        return removed;
-    }
-
-    /**
-     * Method removeHiddenColumnsAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
-            final int index) {
-        java.lang.Object obj = this._hiddenColumnsList.remove(index);
-        return (jalview.schemabinding.version2.HiddenColumns) obj;
-    }
-
-    /**
-     * Sets the value of field 'annotationColours'.
-     * 
-     * @param annotationColours the value of field
-     * 'annotationColours'.
-     */
-    public void setAnnotationColours(
-            final jalview.schemabinding.version2.AnnotationColours annotationColours) {
-        this._annotationColours = annotationColours;
-    }
-
-    /**
-     * Sets the value of field 'bgColour'.
-     * 
-     * @param bgColour the value of field 'bgColour'.
-     */
-    public void setBgColour(
-            final java.lang.String bgColour) {
-        this._bgColour = bgColour;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vCalcIdParam
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setCalcIdParam(
-            final int index,
-            final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._calcIdParamList.size()) {
-            throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
-        }
-        
-        this._calcIdParamList.set(index, vCalcIdParam);
-    }
-
-    /**
-     * 
-     * 
-     * @param vCalcIdParamArray
-     */
-    public void setCalcIdParam(
-            final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
-        //-- copy array
-        _calcIdParamList.clear();
-        
-        for (int i = 0; i < vCalcIdParamArray.length; i++) {
-                this._calcIdParamList.add(vCalcIdParamArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'centreColumnLabels'.
-     * 
-     * @param centreColumnLabels the value of field
-     * 'centreColumnLabels'.
-     */
-    public void setCentreColumnLabels(
-            final boolean centreColumnLabels) {
-        this._centreColumnLabels = centreColumnLabels;
-        this._has_centreColumnLabels = true;
-    }
-
-    /**
-     * Sets the value of field 'complementId'. The field
-     * 'complementId' has the following description: The viewport
-     * id of this viewport's
-     *  (cdna/protein) coding complement, if any
-     *  
-     * 
-     * @param complementId the value of field 'complementId'.
-     */
-    public void setComplementId(
-            final java.lang.String complementId) {
-        this._complementId = complementId;
-    }
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(
-            final int consThreshold) {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'conservationSelected'.
-     * 
-     * @param conservationSelected the value of field
-     * 'conservationSelected'.
-     */
-    public void setConservationSelected(
-            final boolean conservationSelected) {
-        this._conservationSelected = conservationSelected;
-        this._has_conservationSelected = true;
-    }
-
-    /**
-     * Sets the value of field 'followHighlight'.
-     * 
-     * @param followHighlight the value of field 'followHighlight'.
-     */
-    public void setFollowHighlight(
-            final boolean followHighlight) {
-        this._followHighlight = followHighlight;
-        this._has_followHighlight = true;
-    }
-
-    /**
-     * Sets the value of field 'followSelection'.
-     * 
-     * @param followSelection the value of field 'followSelection'.
-     */
-    public void setFollowSelection(
-            final boolean followSelection) {
-        this._followSelection = followSelection;
-        this._has_followSelection = true;
-    }
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(
-            final java.lang.String fontName) {
-        this._fontName = fontName;
-    }
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(
-            final int fontSize) {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    }
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(
-            final int fontStyle) {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    }
-
-    /**
-     * Sets the value of field 'gatheredViews'.
-     * 
-     * @param gatheredViews the value of field 'gatheredViews'.
-     */
-    public void setGatheredViews(
-            final boolean gatheredViews) {
-        this._gatheredViews = gatheredViews;
-        this._has_gatheredViews = true;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vHiddenColumns
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setHiddenColumns(
-            final int index,
-            final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._hiddenColumnsList.size()) {
-            throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]");
-        }
-        
-        this._hiddenColumnsList.set(index, vHiddenColumns);
-    }
-
-    /**
-     * 
-     * 
-     * @param vHiddenColumnsArray
-     */
-    public void setHiddenColumns(
-            final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) {
-        //-- copy array
-        _hiddenColumnsList.clear();
-        
-        for (int i = 0; i < vHiddenColumnsArray.length; i++) {
-                this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'id'. The field 'id' has the
-     * following description: unique id used by jalview to
-     *  synchronize
-     *  between stored and
-     *  instantiated views
-     *  
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * Sets the value of field 'ignoreGapsinConsensus'.
-     * 
-     * @param ignoreGapsinConsensus the value of field
-     * 'ignoreGapsinConsensus'.
-     */
-    public void setIgnoreGapsinConsensus(
-            final boolean ignoreGapsinConsensus) {
-        this._ignoreGapsinConsensus = ignoreGapsinConsensus;
-        this._has_ignoreGapsinConsensus = true;
-    }
-
-    /**
-     * Sets the value of field 'normaliseSequenceLogo'.
-     * 
-     * @param normaliseSequenceLogo the value of field
-     * 'normaliseSequenceLogo'.
-     */
-    public void setNormaliseSequenceLogo(
-            final boolean normaliseSequenceLogo) {
-        this._normaliseSequenceLogo = normaliseSequenceLogo;
-        this._has_normaliseSequenceLogo = true;
-    }
-
-    /**
-     * Sets the value of field 'pidSelected'.
-     * 
-     * @param pidSelected the value of field 'pidSelected'.
-     */
-    public void setPidSelected(
-            final boolean pidSelected) {
-        this._pidSelected = pidSelected;
-        this._has_pidSelected = true;
-    }
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(
-            final int pidThreshold) {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'renderGaps'.
-     * 
-     * @param renderGaps the value of field 'renderGaps'.
-     */
-    public void setRenderGaps(
-            final boolean renderGaps) {
-        this._renderGaps = renderGaps;
-        this._has_renderGaps = true;
-    }
-
-    /**
-     * Sets the value of field 'rightAlignIds'.
-     * 
-     * @param rightAlignIds the value of field 'rightAlignIds'.
-     */
-    public void setRightAlignIds(
-            final boolean rightAlignIds) {
-        this._rightAlignIds = rightAlignIds;
-        this._has_rightAlignIds = true;
-    }
-
-    /**
-     * Sets the value of field 'scaleProteinAsCdna'.
-     * 
-     * @param scaleProteinAsCdna the value of field
-     * 'scaleProteinAsCdna'.
-     */
-    public void setScaleProteinAsCdna(
-            final boolean scaleProteinAsCdna) {
-        this._scaleProteinAsCdna = scaleProteinAsCdna;
-        this._has_scaleProteinAsCdna = true;
-    }
-
-    /**
-     * Sets the value of field 'sequenceSetId'.
-     * 
-     * @param sequenceSetId the value of field 'sequenceSetId'.
-     */
-    public void setSequenceSetId(
-            final java.lang.String sequenceSetId) {
-        this._sequenceSetId = sequenceSetId;
-    }
-
-    /**
-     * Sets the value of field 'showAnnotation'.
-     * 
-     * @param showAnnotation the value of field 'showAnnotation'.
-     */
-    public void setShowAnnotation(
-            final boolean showAnnotation) {
-        this._showAnnotation = showAnnotation;
-        this._has_showAnnotation = true;
-    }
-
-    /**
-     * Sets the value of field 'showBoxes'.
-     * 
-     * @param showBoxes the value of field 'showBoxes'.
-     */
-    public void setShowBoxes(
-            final boolean showBoxes) {
-        this._showBoxes = showBoxes;
-        this._has_showBoxes = true;
-    }
-
-    /**
-     * Sets the value of field 'showColourText'.
-     * 
-     * @param showColourText the value of field 'showColourText'.
-     */
-    public void setShowColourText(
-            final boolean showColourText) {
-        this._showColourText = showColourText;
-        this._has_showColourText = true;
-    }
-
-    /**
-     * Sets the value of field 'showConsensusHistogram'.
-     * 
-     * @param showConsensusHistogram the value of field
-     * 'showConsensusHistogram'.
-     */
-    public void setShowConsensusHistogram(
-            final boolean showConsensusHistogram) {
-        this._showConsensusHistogram = showConsensusHistogram;
-        this._has_showConsensusHistogram = true;
-    }
-
-    /**
-     * Sets the value of field 'showDbRefTooltip'.
-     * 
-     * @param showDbRefTooltip the value of field 'showDbRefTooltip'
-     */
-    public void setShowDbRefTooltip(
-            final boolean showDbRefTooltip) {
-        this._showDbRefTooltip = showDbRefTooltip;
-        this._has_showDbRefTooltip = true;
-    }
-
-    /**
-     * Sets the value of field 'showFullId'.
-     * 
-     * @param showFullId the value of field 'showFullId'.
-     */
-    public void setShowFullId(
-            final boolean showFullId) {
-        this._showFullId = showFullId;
-        this._has_showFullId = true;
-    }
-
-    /**
-     * Sets the value of field 'showGroupConsensus'.
-     * 
-     * @param showGroupConsensus the value of field
-     * 'showGroupConsensus'.
-     */
-    public void setShowGroupConsensus(
-            final boolean showGroupConsensus) {
-        this._showGroupConsensus = showGroupConsensus;
-        this._has_showGroupConsensus = true;
-    }
-
-    /**
-     * Sets the value of field 'showGroupConservation'.
-     * 
-     * @param showGroupConservation the value of field
-     * 'showGroupConservation'.
-     */
-    public void setShowGroupConservation(
-            final boolean showGroupConservation) {
-        this._showGroupConservation = showGroupConservation;
-        this._has_showGroupConservation = true;
-    }
-
-    /**
-     * Sets the value of field 'showNPfeatureTooltip'.
-     * 
-     * @param showNPfeatureTooltip the value of field
-     * 'showNPfeatureTooltip'.
-     */
-    public void setShowNPfeatureTooltip(
-            final boolean showNPfeatureTooltip) {
-        this._showNPfeatureTooltip = showNPfeatureTooltip;
-        this._has_showNPfeatureTooltip = true;
-    }
-
-    /**
-     * Sets the value of field 'showSequenceFeatures'.
-     * 
-     * @param showSequenceFeatures the value of field
-     * 'showSequenceFeatures'.
-     */
-    public void setShowSequenceFeatures(
-            final boolean showSequenceFeatures) {
-        this._showSequenceFeatures = showSequenceFeatures;
-        this._has_showSequenceFeatures = true;
-    }
-
-    /**
-     * Sets the value of field 'showSequenceLogo'.
-     * 
-     * @param showSequenceLogo the value of field 'showSequenceLogo'
-     */
-    public void setShowSequenceLogo(
-            final boolean showSequenceLogo) {
-        this._showSequenceLogo = showSequenceLogo;
-        this._has_showSequenceLogo = true;
-    }
-
-    /**
-     * Sets the value of field 'showText'.
-     * 
-     * @param showText the value of field 'showText'.
-     */
-    public void setShowText(
-            final boolean showText) {
-        this._showText = showText;
-        this._has_showText = true;
-    }
-
-    /**
-     * Sets the value of field 'showUnconserved'.
-     * 
-     * @param showUnconserved the value of field 'showUnconserved'.
-     */
-    public void setShowUnconserved(
-            final boolean showUnconserved) {
-        this._showUnconserved = showUnconserved;
-        this._has_showUnconserved = true;
-    }
-
-    /**
-     * Sets the value of field 'startRes'.
-     * 
-     * @param startRes the value of field 'startRes'.
-     */
-    public void setStartRes(
-            final int startRes) {
-        this._startRes = startRes;
-        this._has_startRes = true;
-    }
-
-    /**
-     * Sets the value of field 'startSeq'.
-     * 
-     * @param startSeq the value of field 'startSeq'.
-     */
-    public void setStartSeq(
-            final int startSeq) {
-        this._startSeq = startSeq;
-        this._has_startSeq = true;
-    }
-
-    /**
-     * Sets the value of field 'textCol1'.
-     * 
-     * @param textCol1 the value of field 'textCol1'.
-     */
-    public void setTextCol1(
-            final int textCol1) {
-        this._textCol1 = textCol1;
-        this._has_textCol1 = true;
-    }
-
-    /**
-     * Sets the value of field 'textCol2'.
-     * 
-     * @param textCol2 the value of field 'textCol2'.
-     */
-    public void setTextCol2(
-            final int textCol2) {
-        this._textCol2 = textCol2;
-        this._has_textCol2 = true;
-    }
-
-    /**
-     * Sets the value of field 'textColThreshold'.
-     * 
-     * @param textColThreshold the value of field 'textColThreshold'
-     */
-    public void setTextColThreshold(
-            final int textColThreshold) {
-        this._textColThreshold = textColThreshold;
-        this._has_textColThreshold = true;
-    }
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(
-            final java.lang.String title) {
-        this._title = title;
-    }
-
-    /**
-     * Sets the value of field 'viewName'.
-     * 
-     * @param viewName the value of field 'viewName'.
-     */
-    public void setViewName(
-            final java.lang.String viewName) {
-        this._viewName = viewName;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'wrapAlignment'.
-     * 
-     * @param wrapAlignment the value of field 'wrapAlignment'.
-     */
-    public void setWrapAlignment(
-            final boolean wrapAlignment) {
-        this._wrapAlignment = wrapAlignment;
-        this._has_wrapAlignment = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.Viewport
-     */
-    public static jalview.schemabinding.version2.Viewport unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    }
+  public void deleteStartRes()
+  {
+    this._has_startRes = false;
+  }
+
+  /**
+     */
+  public void deleteStartSeq()
+  {
+    this._has_startSeq = false;
+  }
+
+  /**
+     */
+  public void deleteTextCol1()
+  {
+    this._has_textCol1 = false;
+  }
+
+  /**
+     */
+  public void deleteTextCol2()
+  {
+    this._has_textCol2 = false;
+  }
+
+  /**
+     */
+  public void deleteTextColThreshold()
+  {
+    this._has_textColThreshold = false;
+  }
+
+  /**
+     */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+     */
+  public void deleteWrapAlignment()
+  {
+    this._has_wrapAlignment = false;
+  }
+
+  /**
+     */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+     */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Method enumerateCalcIdParam.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.CalcIdParam
+   *         elements
+   */
+  public java.util.Enumeration enumerateCalcIdParam()
+  {
+    return this._calcIdParamList.elements();
+  }
+
+  /**
+   * Method enumerateHiddenColumns.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.HiddenColumns elements
+   */
+  public java.util.Enumeration enumerateHiddenColumns()
+  {
+    return this._hiddenColumnsList.elements();
+  }
+
+  /**
+   * Returns the value of field 'annotationColours'.
+   * 
+   * @return the value of field 'AnnotationColours'.
+   */
+  public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+  {
+    return this._annotationColours;
+  }
+
+  /**
+   * Returns the value of field 'bgColour'.
+   * 
+   * @return the value of field 'BgColour'.
+   */
+  public java.lang.String getBgColour()
+  {
+    return this._bgColour;
+  }
+
+  /**
+   * Method getCalcIdParam.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.CalcIdParam at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._calcIdParamList.size())
+    {
+      throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
+              + index + "' not in range [0.."
+              + (this._calcIdParamList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
+            .get(index);
+  }
+
+  /**
+   * Method getCalcIdParam.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam()
+  {
+    jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
+    return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList
+            .toArray(array);
+  }
+
+  /**
+   * Method getCalcIdParamCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getCalcIdParamCount()
+  {
+    return this._calcIdParamList.size();
+  }
+
+  /**
+   * Returns the value of field 'centreColumnLabels'.
+   * 
+   * @return the value of field 'CentreColumnLabels'.
+   */
+  public boolean getCentreColumnLabels()
+  {
+    return this._centreColumnLabels;
+  }
+
+  /**
+   * Returns the value of field 'complementId'. The field 'complementId' has the
+   * following description: The viewport id of this viewport's (cdna/protein)
+   * coding complement, if any
+   * 
+   * 
+   * @return the value of field 'ComplementId'.
+   */
+  public java.lang.String getComplementId()
+  {
+    return this._complementId;
+  }
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   * 
+   * @return the value of field 'ConsThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  }
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   * 
+   * @return the value of field 'ConservationSelected'.
+   */
+  public boolean getConservationSelected()
+  {
+    return this._conservationSelected;
+  }
+
+  /**
+   * Returns the value of field 'followHighlight'.
+   * 
+   * @return the value of field 'FollowHighlight'.
+   */
+  public boolean getFollowHighlight()
+  {
+    return this._followHighlight;
+  }
+
+  /**
+   * Returns the value of field 'followSelection'.
+   * 
+   * @return the value of field 'FollowSelection'.
+   */
+  public boolean getFollowSelection()
+  {
+    return this._followSelection;
+  }
+
+  /**
+   * Returns the value of field 'fontName'.
+   * 
+   * @return the value of field 'FontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  }
+
+  /**
+   * Returns the value of field 'fontSize'.
+   * 
+   * @return the value of field 'FontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  }
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   * 
+   * @return the value of field 'FontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  }
+
+  /**
+   * Returns the value of field 'gatheredViews'.
+   * 
+   * @return the value of field 'GatheredViews'.
+   */
+  public boolean getGatheredViews()
+  {
+    return this._gatheredViews;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Method getHiddenColumns.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.HiddenColumns at
+   *         the given index
+   */
+  public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenColumnsList.size())
+    {
+      throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
+              + index + "' not in range [0.."
+              + (this._hiddenColumnsList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
+            .get(index);
+  }
+
+  /**
+   * Method getHiddenColumns.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
+  {
+    jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0];
+    return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList
+            .toArray(array);
+  }
+
+  /**
+   * Method getHiddenColumnsCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getHiddenColumnsCount()
+  {
+    return this._hiddenColumnsList.size();
+  }
+
+  /**
+   * Returns the value of field 'id'. The field 'id' has the following
+   * description: unique id used by jalview to synchronize between stored and
+   * instantiated views
+   * 
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'ignoreGapsinConsensus'.
+   * 
+   * @return the value of field 'IgnoreGapsinConsensus'.
+   */
+  public boolean getIgnoreGapsinConsensus()
+  {
+    return this._ignoreGapsinConsensus;
+  }
+
+  /**
+   * Returns the value of field 'normaliseSequenceLogo'.
+   * 
+   * @return the value of field 'NormaliseSequenceLogo'.
+   */
+  public boolean getNormaliseSequenceLogo()
+  {
+    return this._normaliseSequenceLogo;
+  }
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   * 
+   * @return the value of field 'PidSelected'.
+   */
+  public boolean getPidSelected()
+  {
+    return this._pidSelected;
+  }
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   * 
+   * @return the value of field 'PidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  }
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   * 
+   * @return the value of field 'RenderGaps'.
+   */
+  public boolean getRenderGaps()
+  {
+    return this._renderGaps;
+  }
+
+  /**
+   * Returns the value of field 'rightAlignIds'.
+   * 
+   * @return the value of field 'RightAlignIds'.
+   */
+  public boolean getRightAlignIds()
+  {
+    return this._rightAlignIds;
+  }
+
+  /**
+   * Returns the value of field 'scaleProteinAsCdna'.
+   * 
+   * @return the value of field 'ScaleProteinAsCdna'.
+   */
+  public boolean getScaleProteinAsCdna()
+  {
+    return this._scaleProteinAsCdna;
+  }
+
+  /**
+   * Returns the value of field 'sequenceSetId'.
+   * 
+   * @return the value of field 'SequenceSetId'.
+   */
+  public java.lang.String getSequenceSetId()
+  {
+    return this._sequenceSetId;
+  }
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   * 
+   * @return the value of field 'ShowAnnotation'.
+   */
+  public boolean getShowAnnotation()
+  {
+    return this._showAnnotation;
+  }
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   * 
+   * @return the value of field 'ShowBoxes'.
+   */
+  public boolean getShowBoxes()
+  {
+    return this._showBoxes;
+  }
+
+  /**
+   * Returns the value of field 'showColourText'.
+   * 
+   * @return the value of field 'ShowColourText'.
+   */
+  public boolean getShowColourText()
+  {
+    return this._showColourText;
+  }
+
+  /**
+   * Returns the value of field 'showConsensusHistogram'.
+   * 
+   * @return the value of field 'ShowConsensusHistogram'.
+   */
+  public boolean getShowConsensusHistogram()
+  {
+    return this._showConsensusHistogram;
+  }
+
+  /**
+   * Returns the value of field 'showDbRefTooltip'.
+   * 
+   * @return the value of field 'ShowDbRefTooltip'.
+   */
+  public boolean getShowDbRefTooltip()
+  {
+    return this._showDbRefTooltip;
+  }
+
+  /**
+   * Returns the value of field 'showFullId'.
+   * 
+   * @return the value of field 'ShowFullId'.
+   */
+  public boolean getShowFullId()
+  {
+    return this._showFullId;
+  }
+
+  /**
+   * Returns the value of field 'showGroupConsensus'.
+   * 
+   * @return the value of field 'ShowGroupConsensus'.
+   */
+  public boolean getShowGroupConsensus()
+  {
+    return this._showGroupConsensus;
+  }
+
+  /**
+   * Returns the value of field 'showGroupConservation'.
+   * 
+   * @return the value of field 'ShowGroupConservation'.
+   */
+  public boolean getShowGroupConservation()
+  {
+    return this._showGroupConservation;
+  }
+
+  /**
+   * Returns the value of field 'showNPfeatureTooltip'.
+   * 
+   * @return the value of field 'ShowNPfeatureTooltip'.
+   */
+  public boolean getShowNPfeatureTooltip()
+  {
+    return this._showNPfeatureTooltip;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   * 
+   * @return the value of field 'ShowSequenceFeatures'.
+   */
+  public boolean getShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceLogo'.
+   * 
+   * @return the value of field 'ShowSequenceLogo'.
+   */
+  public boolean getShowSequenceLogo()
+  {
+    return this._showSequenceLogo;
+  }
+
+  /**
+   * Returns the value of field 'showText'.
+   * 
+   * @return the value of field 'ShowText'.
+   */
+  public boolean getShowText()
+  {
+    return this._showText;
+  }
+
+  /**
+   * Returns the value of field 'showUnconserved'.
+   * 
+   * @return the value of field 'ShowUnconserved'.
+   */
+  public boolean getShowUnconserved()
+  {
+    return this._showUnconserved;
+  }
+
+  /**
+   * Returns the value of field 'startRes'.
+   * 
+   * @return the value of field 'StartRes'.
+   */
+  public int getStartRes()
+  {
+    return this._startRes;
+  }
+
+  /**
+   * Returns the value of field 'startSeq'.
+   * 
+   * @return the value of field 'StartSeq'.
+   */
+  public int getStartSeq()
+  {
+    return this._startSeq;
+  }
+
+  /**
+   * Returns the value of field 'textCol1'.
+   * 
+   * @return the value of field 'TextCol1'.
+   */
+  public int getTextCol1()
+  {
+    return this._textCol1;
+  }
+
+  /**
+   * Returns the value of field 'textCol2'.
+   * 
+   * @return the value of field 'TextCol2'.
+   */
+  public int getTextCol2()
+  {
+    return this._textCol2;
+  }
+
+  /**
+   * Returns the value of field 'textColThreshold'.
+   * 
+   * @return the value of field 'TextColThreshold'.
+   */
+  public int getTextColThreshold()
+  {
+    return this._textColThreshold;
+  }
+
+  /**
+   * Returns the value of field 'title'.
+   * 
+   * @return the value of field 'Title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  }
+
+  /**
+   * Returns the value of field 'viewName'.
+   * 
+   * @return the value of field 'ViewName'.
+   */
+  public java.lang.String getViewName()
+  {
+    return this._viewName;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   * 
+   * @return the value of field 'WrapAlignment'.
+   */
+  public boolean getWrapAlignment()
+  {
+    return this._wrapAlignment;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasCentreColumnLabels.
+   * 
+   * @return true if at least one CentreColumnLabels has been adde
+   */
+  public boolean hasCentreColumnLabels()
+  {
+    return this._has_centreColumnLabels;
+  }
+
+  /**
+   * Method hasConsThreshold.
+   * 
+   * @return true if at least one ConsThreshold has been added
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  }
+
+  /**
+   * Method hasConservationSelected.
+   * 
+   * @return true if at least one ConservationSelected has been added
+   */
+  public boolean hasConservationSelected()
+  {
+    return this._has_conservationSelected;
+  }
+
+  /**
+   * Method hasFollowHighlight.
+   * 
+   * @return true if at least one FollowHighlight has been added
+   */
+  public boolean hasFollowHighlight()
+  {
+    return this._has_followHighlight;
+  }
+
+  /**
+   * Method hasFollowSelection.
+   * 
+   * @return true if at least one FollowSelection has been added
+   */
+  public boolean hasFollowSelection()
+  {
+    return this._has_followSelection;
+  }
+
+  /**
+   * Method hasFontSize.
+   * 
+   * @return true if at least one FontSize has been added
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  }
+
+  /**
+   * Method hasFontStyle.
+   * 
+   * @return true if at least one FontStyle has been added
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  }
+
+  /**
+   * Method hasGatheredViews.
+   * 
+   * @return true if at least one GatheredViews has been added
+   */
+  public boolean hasGatheredViews()
+  {
+    return this._has_gatheredViews;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasIgnoreGapsinConsensus.
+   * 
+   * @return true if at least one IgnoreGapsinConsensus has been added
+   */
+  public boolean hasIgnoreGapsinConsensus()
+  {
+    return this._has_ignoreGapsinConsensus;
+  }
+
+  /**
+   * Method hasNormaliseSequenceLogo.
+   * 
+   * @return true if at least one NormaliseSequenceLogo has been added
+   */
+  public boolean hasNormaliseSequenceLogo()
+  {
+    return this._has_normaliseSequenceLogo;
+  }
+
+  /**
+   * Method hasPidSelected.
+   * 
+   * @return true if at least one PidSelected has been added
+   */
+  public boolean hasPidSelected()
+  {
+    return this._has_pidSelected;
+  }
+
+  /**
+   * Method hasPidThreshold.
+   * 
+   * @return true if at least one PidThreshold has been added
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  }
+
+  /**
+   * Method hasRenderGaps.
+   * 
+   * @return true if at least one RenderGaps has been added
+   */
+  public boolean hasRenderGaps()
+  {
+    return this._has_renderGaps;
+  }
+
+  /**
+   * Method hasRightAlignIds.
+   * 
+   * @return true if at least one RightAlignIds has been added
+   */
+  public boolean hasRightAlignIds()
+  {
+    return this._has_rightAlignIds;
+  }
+
+  /**
+   * Method hasScaleProteinAsCdna.
+   * 
+   * @return true if at least one ScaleProteinAsCdna has been adde
+   */
+  public boolean hasScaleProteinAsCdna()
+  {
+    return this._has_scaleProteinAsCdna;
+  }
+
+  /**
+   * Method hasShowAnnotation.
+   * 
+   * @return true if at least one ShowAnnotation has been added
+   */
+  public boolean hasShowAnnotation()
+  {
+    return this._has_showAnnotation;
+  }
+
+  /**
+   * Method hasShowBoxes.
+   * 
+   * @return true if at least one ShowBoxes has been added
+   */
+  public boolean hasShowBoxes()
+  {
+    return this._has_showBoxes;
+  }
+
+  /**
+   * Method hasShowColourText.
+   * 
+   * @return true if at least one ShowColourText has been added
+   */
+  public boolean hasShowColourText()
+  {
+    return this._has_showColourText;
+  }
+
+  /**
+   * Method hasShowConsensusHistogram.
+   * 
+   * @return true if at least one ShowConsensusHistogram has been added
+   */
+  public boolean hasShowConsensusHistogram()
+  {
+    return this._has_showConsensusHistogram;
+  }
+
+  /**
+   * Method hasShowDbRefTooltip.
+   * 
+   * @return true if at least one ShowDbRefTooltip has been added
+   */
+  public boolean hasShowDbRefTooltip()
+  {
+    return this._has_showDbRefTooltip;
+  }
+
+  /**
+   * Method hasShowFullId.
+   * 
+   * @return true if at least one ShowFullId has been added
+   */
+  public boolean hasShowFullId()
+  {
+    return this._has_showFullId;
+  }
+
+  /**
+   * Method hasShowGroupConsensus.
+   * 
+   * @return true if at least one ShowGroupConsensus has been adde
+   */
+  public boolean hasShowGroupConsensus()
+  {
+    return this._has_showGroupConsensus;
+  }
+
+  /**
+   * Method hasShowGroupConservation.
+   * 
+   * @return true if at least one ShowGroupConservation has been added
+   */
+  public boolean hasShowGroupConservation()
+  {
+    return this._has_showGroupConservation;
+  }
+
+  /**
+   * Method hasShowNPfeatureTooltip.
+   * 
+   * @return true if at least one ShowNPfeatureTooltip has been added
+   */
+  public boolean hasShowNPfeatureTooltip()
+  {
+    return this._has_showNPfeatureTooltip;
+  }
+
+  /**
+   * Method hasShowSequenceFeatures.
+   * 
+   * @return true if at least one ShowSequenceFeatures has been added
+   */
+  public boolean hasShowSequenceFeatures()
+  {
+    return this._has_showSequenceFeatures;
+  }
+
+  /**
+   * Method hasShowSequenceLogo.
+   * 
+   * @return true if at least one ShowSequenceLogo has been added
+   */
+  public boolean hasShowSequenceLogo()
+  {
+    return this._has_showSequenceLogo;
+  }
+
+  /**
+   * Method hasShowText.
+   * 
+   * @return true if at least one ShowText has been added
+   */
+  public boolean hasShowText()
+  {
+    return this._has_showText;
+  }
+
+  /**
+   * Method hasShowUnconserved.
+   * 
+   * @return true if at least one ShowUnconserved has been added
+   */
+  public boolean hasShowUnconserved()
+  {
+    return this._has_showUnconserved;
+  }
+
+  /**
+   * Method hasStartRes.
+   * 
+   * @return true if at least one StartRes has been added
+   */
+  public boolean hasStartRes()
+  {
+    return this._has_startRes;
+  }
+
+  /**
+   * Method hasStartSeq.
+   * 
+   * @return true if at least one StartSeq has been added
+   */
+  public boolean hasStartSeq()
+  {
+    return this._has_startSeq;
+  }
+
+  /**
+   * Method hasTextCol1.
+   * 
+   * @return true if at least one TextCol1 has been added
+   */
+  public boolean hasTextCol1()
+  {
+    return this._has_textCol1;
+  }
+
+  /**
+   * Method hasTextCol2.
+   * 
+   * @return true if at least one TextCol2 has been added
+   */
+  public boolean hasTextCol2()
+  {
+    return this._has_textCol2;
+  }
+
+  /**
+   * Method hasTextColThreshold.
+   * 
+   * @return true if at least one TextColThreshold has been added
+   */
+  public boolean hasTextColThreshold()
+  {
+    return this._has_textColThreshold;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasWrapAlignment.
+   * 
+   * @return true if at least one WrapAlignment has been added
+   */
+  public boolean hasWrapAlignment()
+  {
+    return this._has_wrapAlignment;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'centreColumnLabels'.
+   * 
+   * @return the value of field 'CentreColumnLabels'.
+   */
+  public boolean isCentreColumnLabels()
+  {
+    return this._centreColumnLabels;
+  }
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   * 
+   * @return the value of field 'ConservationSelected'.
+   */
+  public boolean isConservationSelected()
+  {
+    return this._conservationSelected;
+  }
+
+  /**
+   * Returns the value of field 'followHighlight'.
+   * 
+   * @return the value of field 'FollowHighlight'.
+   */
+  public boolean isFollowHighlight()
+  {
+    return this._followHighlight;
+  }
+
+  /**
+   * Returns the value of field 'followSelection'.
+   * 
+   * @return the value of field 'FollowSelection'.
+   */
+  public boolean isFollowSelection()
+  {
+    return this._followSelection;
+  }
+
+  /**
+   * Returns the value of field 'gatheredViews'.
+   * 
+   * @return the value of field 'GatheredViews'.
+   */
+  public boolean isGatheredViews()
+  {
+    return this._gatheredViews;
+  }
+
+  /**
+   * Returns the value of field 'ignoreGapsinConsensus'.
+   * 
+   * @return the value of field 'IgnoreGapsinConsensus'.
+   */
+  public boolean isIgnoreGapsinConsensus()
+  {
+    return this._ignoreGapsinConsensus;
+  }
+
+  /**
+   * Returns the value of field 'normaliseSequenceLogo'.
+   * 
+   * @return the value of field 'NormaliseSequenceLogo'.
+   */
+  public boolean isNormaliseSequenceLogo()
+  {
+    return this._normaliseSequenceLogo;
+  }
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   * 
+   * @return the value of field 'PidSelected'.
+   */
+  public boolean isPidSelected()
+  {
+    return this._pidSelected;
+  }
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   * 
+   * @return the value of field 'RenderGaps'.
+   */
+  public boolean isRenderGaps()
+  {
+    return this._renderGaps;
+  }
+
+  /**
+   * Returns the value of field 'rightAlignIds'.
+   * 
+   * @return the value of field 'RightAlignIds'.
+   */
+  public boolean isRightAlignIds()
+  {
+    return this._rightAlignIds;
+  }
+
+  /**
+   * Returns the value of field 'scaleProteinAsCdna'.
+   * 
+   * @return the value of field 'ScaleProteinAsCdna'.
+   */
+  public boolean isScaleProteinAsCdna()
+  {
+    return this._scaleProteinAsCdna;
+  }
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   * 
+   * @return the value of field 'ShowAnnotation'.
+   */
+  public boolean isShowAnnotation()
+  {
+    return this._showAnnotation;
+  }
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   * 
+   * @return the value of field 'ShowBoxes'.
+   */
+  public boolean isShowBoxes()
+  {
+    return this._showBoxes;
+  }
+
+  /**
+   * Returns the value of field 'showColourText'.
+   * 
+   * @return the value of field 'ShowColourText'.
+   */
+  public boolean isShowColourText()
+  {
+    return this._showColourText;
+  }
+
+  /**
+   * Returns the value of field 'showConsensusHistogram'.
+   * 
+   * @return the value of field 'ShowConsensusHistogram'.
+   */
+  public boolean isShowConsensusHistogram()
+  {
+    return this._showConsensusHistogram;
+  }
+
+  /**
+   * Returns the value of field 'showDbRefTooltip'.
+   * 
+   * @return the value of field 'ShowDbRefTooltip'.
+   */
+  public boolean isShowDbRefTooltip()
+  {
+    return this._showDbRefTooltip;
+  }
+
+  /**
+   * Returns the value of field 'showFullId'.
+   * 
+   * @return the value of field 'ShowFullId'.
+   */
+  public boolean isShowFullId()
+  {
+    return this._showFullId;
+  }
+
+  /**
+   * Returns the value of field 'showGroupConsensus'.
+   * 
+   * @return the value of field 'ShowGroupConsensus'.
+   */
+  public boolean isShowGroupConsensus()
+  {
+    return this._showGroupConsensus;
+  }
+
+  /**
+   * Returns the value of field 'showGroupConservation'.
+   * 
+   * @return the value of field 'ShowGroupConservation'.
+   */
+  public boolean isShowGroupConservation()
+  {
+    return this._showGroupConservation;
+  }
+
+  /**
+   * Returns the value of field 'showNPfeatureTooltip'.
+   * 
+   * @return the value of field 'ShowNPfeatureTooltip'.
+   */
+  public boolean isShowNPfeatureTooltip()
+  {
+    return this._showNPfeatureTooltip;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   * 
+   * @return the value of field 'ShowSequenceFeatures'.
+   */
+  public boolean isShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  }
+
+  /**
+   * Returns the value of field 'showSequenceLogo'.
+   * 
+   * @return the value of field 'ShowSequenceLogo'.
+   */
+  public boolean isShowSequenceLogo()
+  {
+    return this._showSequenceLogo;
+  }
+
+  /**
+   * Returns the value of field 'showText'.
+   * 
+   * @return the value of field 'ShowText'.
+   */
+  public boolean isShowText()
+  {
+    return this._showText;
+  }
+
+  /**
+   * Returns the value of field 'showUnconserved'.
+   * 
+   * @return the value of field 'ShowUnconserved'.
+   */
+  public boolean isShowUnconserved()
+  {
+    return this._showUnconserved;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   * 
+   * @return the value of field 'WrapAlignment'.
+   */
+  public boolean isWrapAlignment()
+  {
+    return this._wrapAlignment;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllCalcIdParam()
+  {
+    this._calcIdParamList.clear();
+  }
+
+  /**
+     */
+  public void removeAllHiddenColumns()
+  {
+    this._hiddenColumnsList.clear();
+  }
+
+  /**
+   * Method removeCalcIdParam.
+   * 
+   * @param vCalcIdParam
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeCalcIdParam(
+          final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+  {
+    boolean removed = _calcIdParamList.remove(vCalcIdParam);
+    return removed;
+  }
+
+  /**
+   * Method removeCalcIdParamAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
+          final int index)
+  {
+    java.lang.Object obj = this._calcIdParamList.remove(index);
+    return (jalview.schemabinding.version2.CalcIdParam) obj;
+  }
+
+  /**
+   * Method removeHiddenColumns.
+   * 
+   * @param vHiddenColumns
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeHiddenColumns(
+          final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+  {
+    boolean removed = _hiddenColumnsList.remove(vHiddenColumns);
+    return removed;
+  }
+
+  /**
+   * Method removeHiddenColumnsAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt(
+          final int index)
+  {
+    java.lang.Object obj = this._hiddenColumnsList.remove(index);
+    return (jalview.schemabinding.version2.HiddenColumns) obj;
+  }
+
+  /**
+   * Sets the value of field 'annotationColours'.
+   * 
+   * @param annotationColours
+   *          the value of field 'annotationColours'.
+   */
+  public void setAnnotationColours(
+          final jalview.schemabinding.version2.AnnotationColours annotationColours)
+  {
+    this._annotationColours = annotationColours;
+  }
+
+  /**
+   * Sets the value of field 'bgColour'.
+   * 
+   * @param bgColour
+   *          the value of field 'bgColour'.
+   */
+  public void setBgColour(final java.lang.String bgColour)
+  {
+    this._bgColour = bgColour;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vCalcIdParam
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setCalcIdParam(final int index,
+          final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._calcIdParamList.size())
+    {
+      throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
+              + index + "' not in range [0.."
+              + (this._calcIdParamList.size() - 1) + "]");
+    }
+
+    this._calcIdParamList.set(index, vCalcIdParam);
+  }
+
+  /**
+   * 
+   * 
+   * @param vCalcIdParamArray
+   */
+  public void setCalcIdParam(
+          final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray)
+  {
+    // -- copy array
+    _calcIdParamList.clear();
+
+    for (int i = 0; i < vCalcIdParamArray.length; i++)
+    {
+      this._calcIdParamList.add(vCalcIdParamArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'centreColumnLabels'.
+   * 
+   * @param centreColumnLabels
+   *          the value of field 'centreColumnLabels'.
+   */
+  public void setCentreColumnLabels(final boolean centreColumnLabels)
+  {
+    this._centreColumnLabels = centreColumnLabels;
+    this._has_centreColumnLabels = true;
+  }
+
+  /**
+   * Sets the value of field 'complementId'. The field 'complementId' has the
+   * following description: The viewport id of this viewport's (cdna/protein)
+   * coding complement, if any
+   * 
+   * 
+   * @param complementId
+   *          the value of field 'complementId'.
+   */
+  public void setComplementId(final java.lang.String complementId)
+  {
+    this._complementId = complementId;
+  }
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   * 
+   * @param consThreshold
+   *          the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(final int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'conservationSelected'.
+   * 
+   * @param conservationSelected
+   *          the value of field 'conservationSelected'.
+   */
+  public void setConservationSelected(final boolean conservationSelected)
+  {
+    this._conservationSelected = conservationSelected;
+    this._has_conservationSelected = true;
+  }
+
+  /**
+   * Sets the value of field 'followHighlight'.
+   * 
+   * @param followHighlight
+   *          the value of field 'followHighlight'.
+   */
+  public void setFollowHighlight(final boolean followHighlight)
+  {
+    this._followHighlight = followHighlight;
+    this._has_followHighlight = true;
+  }
+
+  /**
+   * Sets the value of field 'followSelection'.
+   * 
+   * @param followSelection
+   *          the value of field 'followSelection'.
+   */
+  public void setFollowSelection(final boolean followSelection)
+  {
+    this._followSelection = followSelection;
+    this._has_followSelection = true;
+  }
+
+  /**
+   * Sets the value of field 'fontName'.
+   * 
+   * @param fontName
+   *          the value of field 'fontName'.
+   */
+  public void setFontName(final java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  }
+
+  /**
+   * Sets the value of field 'fontSize'.
+   * 
+   * @param fontSize
+   *          the value of field 'fontSize'.
+   */
+  public void setFontSize(final int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  }
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   * 
+   * @param fontStyle
+   *          the value of field 'fontStyle'.
+   */
+  public void setFontStyle(final int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  }
+
+  /**
+   * Sets the value of field 'gatheredViews'.
+   * 
+   * @param gatheredViews
+   *          the value of field 'gatheredViews'.
+   */
+  public void setGatheredViews(final boolean gatheredViews)
+  {
+    this._gatheredViews = gatheredViews;
+    this._has_gatheredViews = true;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *          the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vHiddenColumns
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setHiddenColumns(final int index,
+          final jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._hiddenColumnsList.size())
+    {
+      throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
+              + index + "' not in range [0.."
+              + (this._hiddenColumnsList.size() - 1) + "]");
+    }
+
+    this._hiddenColumnsList.set(index, vHiddenColumns);
+  }
+
+  /**
+   * 
+   * 
+   * @param vHiddenColumnsArray
+   */
+  public void setHiddenColumns(
+          final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray)
+  {
+    // -- copy array
+    _hiddenColumnsList.clear();
+
+    for (int i = 0; i < vHiddenColumnsArray.length; i++)
+    {
+      this._hiddenColumnsList.add(vHiddenColumnsArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'id'. The field 'id' has the following description:
+   * unique id used by jalview to synchronize between stored and instantiated
+   * views
+   * 
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'ignoreGapsinConsensus'.
+   * 
+   * @param ignoreGapsinConsensus
+   *          the value of field 'ignoreGapsinConsensus'.
+   */
+  public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
+  {
+    this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+    this._has_ignoreGapsinConsensus = true;
+  }
+
+  /**
+   * Sets the value of field 'normaliseSequenceLogo'.
+   * 
+   * @param normaliseSequenceLogo
+   *          the value of field 'normaliseSequenceLogo'.
+   */
+  public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
+  {
+    this._normaliseSequenceLogo = normaliseSequenceLogo;
+    this._has_normaliseSequenceLogo = true;
+  }
+
+  /**
+   * Sets the value of field 'pidSelected'.
+   * 
+   * @param pidSelected
+   *          the value of field 'pidSelected'.
+   */
+  public void setPidSelected(final boolean pidSelected)
+  {
+    this._pidSelected = pidSelected;
+    this._has_pidSelected = true;
+  }
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   * 
+   * @param pidThreshold
+   *          the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(final int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'renderGaps'.
+   * 
+   * @param renderGaps
+   *          the value of field 'renderGaps'.
+   */
+  public void setRenderGaps(final boolean renderGaps)
+  {
+    this._renderGaps = renderGaps;
+    this._has_renderGaps = true;
+  }
+
+  /**
+   * Sets the value of field 'rightAlignIds'.
+   * 
+   * @param rightAlignIds
+   *          the value of field 'rightAlignIds'.
+   */
+  public void setRightAlignIds(final boolean rightAlignIds)
+  {
+    this._rightAlignIds = rightAlignIds;
+    this._has_rightAlignIds = true;
+  }
+
+  /**
+   * Sets the value of field 'scaleProteinAsCdna'.
+   * 
+   * @param scaleProteinAsCdna
+   *          the value of field 'scaleProteinAsCdna'.
+   */
+  public void setScaleProteinAsCdna(final boolean scaleProteinAsCdna)
+  {
+    this._scaleProteinAsCdna = scaleProteinAsCdna;
+    this._has_scaleProteinAsCdna = true;
+  }
+
+  /**
+   * Sets the value of field 'sequenceSetId'.
+   * 
+   * @param sequenceSetId
+   *          the value of field 'sequenceSetId'.
+   */
+  public void setSequenceSetId(final java.lang.String sequenceSetId)
+  {
+    this._sequenceSetId = sequenceSetId;
+  }
+
+  /**
+   * Sets the value of field 'showAnnotation'.
+   * 
+   * @param showAnnotation
+   *          the value of field 'showAnnotation'.
+   */
+  public void setShowAnnotation(final boolean showAnnotation)
+  {
+    this._showAnnotation = showAnnotation;
+    this._has_showAnnotation = true;
+  }
+
+  /**
+   * Sets the value of field 'showBoxes'.
+   * 
+   * @param showBoxes
+   *          the value of field 'showBoxes'.
+   */
+  public void setShowBoxes(final boolean showBoxes)
+  {
+    this._showBoxes = showBoxes;
+    this._has_showBoxes = true;
+  }
+
+  /**
+   * Sets the value of field 'showColourText'.
+   * 
+   * @param showColourText
+   *          the value of field 'showColourText'.
+   */
+  public void setShowColourText(final boolean showColourText)
+  {
+    this._showColourText = showColourText;
+    this._has_showColourText = true;
+  }
+
+  /**
+   * Sets the value of field 'showConsensusHistogram'.
+   * 
+   * @param showConsensusHistogram
+   *          the value of field 'showConsensusHistogram'.
+   */
+  public void setShowConsensusHistogram(final boolean showConsensusHistogram)
+  {
+    this._showConsensusHistogram = showConsensusHistogram;
+    this._has_showConsensusHistogram = true;
+  }
+
+  /**
+   * Sets the value of field 'showDbRefTooltip'.
+   * 
+   * @param showDbRefTooltip
+   *          the value of field 'showDbRefTooltip'
+   */
+  public void setShowDbRefTooltip(final boolean showDbRefTooltip)
+  {
+    this._showDbRefTooltip = showDbRefTooltip;
+    this._has_showDbRefTooltip = true;
+  }
+
+  /**
+   * Sets the value of field 'showFullId'.
+   * 
+   * @param showFullId
+   *          the value of field 'showFullId'.
+   */
+  public void setShowFullId(final boolean showFullId)
+  {
+    this._showFullId = showFullId;
+    this._has_showFullId = true;
+  }
+
+  /**
+   * Sets the value of field 'showGroupConsensus'.
+   * 
+   * @param showGroupConsensus
+   *          the value of field 'showGroupConsensus'.
+   */
+  public void setShowGroupConsensus(final boolean showGroupConsensus)
+  {
+    this._showGroupConsensus = showGroupConsensus;
+    this._has_showGroupConsensus = true;
+  }
+
+  /**
+   * Sets the value of field 'showGroupConservation'.
+   * 
+   * @param showGroupConservation
+   *          the value of field 'showGroupConservation'.
+   */
+  public void setShowGroupConservation(final boolean showGroupConservation)
+  {
+    this._showGroupConservation = showGroupConservation;
+    this._has_showGroupConservation = true;
+  }
+
+  /**
+   * Sets the value of field 'showNPfeatureTooltip'.
+   * 
+   * @param showNPfeatureTooltip
+   *          the value of field 'showNPfeatureTooltip'.
+   */
+  public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip)
+  {
+    this._showNPfeatureTooltip = showNPfeatureTooltip;
+    this._has_showNPfeatureTooltip = true;
+  }
+
+  /**
+   * Sets the value of field 'showSequenceFeatures'.
+   * 
+   * @param showSequenceFeatures
+   *          the value of field 'showSequenceFeatures'.
+   */
+  public void setShowSequenceFeatures(final boolean showSequenceFeatures)
+  {
+    this._showSequenceFeatures = showSequenceFeatures;
+    this._has_showSequenceFeatures = true;
+  }
+
+  /**
+   * Sets the value of field 'showSequenceLogo'.
+   * 
+   * @param showSequenceLogo
+   *          the value of field 'showSequenceLogo'
+   */
+  public void setShowSequenceLogo(final boolean showSequenceLogo)
+  {
+    this._showSequenceLogo = showSequenceLogo;
+    this._has_showSequenceLogo = true;
+  }
+
+  /**
+   * Sets the value of field 'showText'.
+   * 
+   * @param showText
+   *          the value of field 'showText'.
+   */
+  public void setShowText(final boolean showText)
+  {
+    this._showText = showText;
+    this._has_showText = true;
+  }
+
+  /**
+   * Sets the value of field 'showUnconserved'.
+   * 
+   * @param showUnconserved
+   *          the value of field 'showUnconserved'.
+   */
+  public void setShowUnconserved(final boolean showUnconserved)
+  {
+    this._showUnconserved = showUnconserved;
+    this._has_showUnconserved = true;
+  }
+
+  /**
+   * Sets the value of field 'startRes'.
+   * 
+   * @param startRes
+   *          the value of field 'startRes'.
+   */
+  public void setStartRes(final int startRes)
+  {
+    this._startRes = startRes;
+    this._has_startRes = true;
+  }
+
+  /**
+   * Sets the value of field 'startSeq'.
+   * 
+   * @param startSeq
+   *          the value of field 'startSeq'.
+   */
+  public void setStartSeq(final int startSeq)
+  {
+    this._startSeq = startSeq;
+    this._has_startSeq = true;
+  }
+
+  /**
+   * Sets the value of field 'textCol1'.
+   * 
+   * @param textCol1
+   *          the value of field 'textCol1'.
+   */
+  public void setTextCol1(final int textCol1)
+  {
+    this._textCol1 = textCol1;
+    this._has_textCol1 = true;
+  }
+
+  /**
+   * Sets the value of field 'textCol2'.
+   * 
+   * @param textCol2
+   *          the value of field 'textCol2'.
+   */
+  public void setTextCol2(final int textCol2)
+  {
+    this._textCol2 = textCol2;
+    this._has_textCol2 = true;
+  }
+
+  /**
+   * Sets the value of field 'textColThreshold'.
+   * 
+   * @param textColThreshold
+   *          the value of field 'textColThreshold'
+   */
+  public void setTextColThreshold(final int textColThreshold)
+  {
+    this._textColThreshold = textColThreshold;
+    this._has_textColThreshold = true;
+  }
+
+  /**
+   * Sets the value of field 'title'.
+   * 
+   * @param title
+   *          the value of field 'title'.
+   */
+  public void setTitle(final java.lang.String title)
+  {
+    this._title = title;
+  }
+
+  /**
+   * Sets the value of field 'viewName'.
+   * 
+   * @param viewName
+   *          the value of field 'viewName'.
+   */
+  public void setViewName(final java.lang.String viewName)
+  {
+    this._viewName = viewName;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *          the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'wrapAlignment'.
+   * 
+   * @param wrapAlignment
+   *          the value of field 'wrapAlignment'.
+   */
+  public void setWrapAlignment(final boolean wrapAlignment)
+  {
+    this._wrapAlignment = wrapAlignment;
+    this._has_wrapAlignment = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *          the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *          the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Viewport
+   */
+  public static jalview.schemabinding.version2.Viewport unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Viewport) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Viewport.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/WebServiceParameterSet.java b/src/jalview/schemabinding/version2/WebServiceParameterSet.java
index 611c981..72d2f82 100644
--- a/src/jalview/schemabinding/version2/WebServiceParameterSet.java
+++ b/src/jalview/schemabinding/version2/WebServiceParameterSet.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,421 +19,418 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class WebServiceParameterSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * The short name for the parameter set. This will be shown
-     * amongst the
-     *  other presets for the web service.
-     *  
-     */
-    private java.lang.String _name;
-
-    /**
-     * A Jalview Web Service Parameter Set container
-     *  version number.
-     *  Version 1 created for storing Jaba user presets.
-     *  
-     */
-    private java.lang.String _version;
-
-    /**
-     * Short description - as utf8 encoded text. This is
-     *  usually displayed
-     *  in the body of an HTML capable tooltip, so HTML tags may be
-     * embedded
-     *  using standard UTF8 encoding.
-     *  
-     */
-    private java.lang.String _description;
-
-    /**
-     * URL for which the parameter set is valid. Jalview will use
-     * it to
-     *  match up parameter sets to service instances that can parse
-     * the
-     *  parameter set payload.
-     *  
-     */
-    private java.util.Vector _serviceURLList;
-
-    /**
-     * UTF8 encoded string to be processed into a specific web
-     * services'
-     *  parameter set. Note - newlines may be important to the
-     * structure
-     *  of this file.
-     *  
-     */
-    private java.lang.String _parameters;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public WebServiceParameterSet() {
-        super();
-        this._serviceURLList = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vServiceURL
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addServiceURL(
-            final java.lang.String vServiceURL)
-    throws java.lang.IndexOutOfBoundsException {
-        this._serviceURLList.addElement(vServiceURL);
+public class WebServiceParameterSet implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * The short name for the parameter set. This will be shown amongst the other
+   * presets for the web service.
+   * 
+   */
+  private java.lang.String _name;
+
+  /**
+   * A Jalview Web Service Parameter Set container version number. Version 1
+   * created for storing Jaba user presets.
+   * 
+   */
+  private java.lang.String _version;
+
+  /**
+   * Short description - as utf8 encoded text. This is usually displayed in the
+   * body of an HTML capable tooltip, so HTML tags may be embedded using
+   * standard UTF8 encoding.
+   * 
+   */
+  private java.lang.String _description;
+
+  /**
+   * URL for which the parameter set is valid. Jalview will use it to match up
+   * parameter sets to service instances that can parse the parameter set
+   * payload.
+   * 
+   */
+  private java.util.Vector _serviceURLList;
+
+  /**
+   * UTF8 encoded string to be processed into a specific web services' parameter
+   * set. Note - newlines may be important to the structure of this file.
+   * 
+   */
+  private java.lang.String _parameters;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public WebServiceParameterSet()
+  {
+    super();
+    this._serviceURLList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vServiceURL
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addServiceURL(final java.lang.String vServiceURL)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._serviceURLList.addElement(vServiceURL);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vServiceURL
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addServiceURL(final int index,
+          final java.lang.String vServiceURL)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._serviceURLList.add(index, vServiceURL);
+  }
+
+  /**
+   * Method enumerateServiceURL.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateServiceURL()
+  {
+    return this._serviceURLList.elements();
+  }
+
+  /**
+   * Returns the value of field 'description'. The field 'description' has the
+   * following description: Short description - as utf8 encoded text. This is
+   * usually displayed in the body of an HTML capable tooltip, so HTML tags may
+   * be embedded using standard UTF8 encoding.
+   * 
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'name'. The field 'name' has the following
+   * description: The short name for the parameter set. This will be shown
+   * amongst the other presets for the web service.
+   * 
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  }
+
+  /**
+   * Returns the value of field 'parameters'. The field 'parameters' has the
+   * following description: UTF8 encoded string to be processed into a specific
+   * web services' parameter set. Note - newlines may be important to the
+   * structure of this file.
+   * 
+   * 
+   * @return the value of field 'Parameters'.
+   */
+  public java.lang.String getParameters()
+  {
+    return this._parameters;
+  }
+
+  /**
+   * Method getServiceURL.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getServiceURL(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._serviceURLList.size())
+    {
+      throw new IndexOutOfBoundsException("getServiceURL: Index value '"
+              + index + "' not in range [0.."
+              + (this._serviceURLList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vServiceURL
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addServiceURL(
-            final int index,
-            final java.lang.String vServiceURL)
-    throws java.lang.IndexOutOfBoundsException {
-        this._serviceURLList.add(index, vServiceURL);
+    return (java.lang.String) _serviceURLList.get(index);
+  }
+
+  /**
+   * Method getServiceURL.Returns the contents of the collection in an Array.
+   * 

+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * know that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getServiceURL()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._serviceURLList.toArray(array);
+  }
+
+  /**
+   * Method getServiceURLCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getServiceURLCount()
+  {
+    return this._serviceURLList.size();
+  }
+
+  /**
+   * Returns the value of field 'version'. The field 'version' has the following
+   * description: A Jalview Web Service Parameter Set container version number.
+   * Version 1 created for storing Jaba user presets.
+   * 
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
     }
-
-    /**
-     * Method enumerateServiceURL.
-     * 
-     * @return an Enumeration over all java.lang.String elements
-     */
-    public java.util.Enumeration enumerateServiceURL(
-    ) {
-        return this._serviceURLList.elements();
-    }
-
-    /**
-     * Returns the value of field 'description'. The field
-     * 'description' has the following description: Short
-     * description - as utf8 encoded text. This is
-     *  usually displayed
-     *  in the body of an HTML capable tooltip, so HTML tags may be
-     * embedded
-     *  using standard UTF8 encoding.
-     *  
-     * 
-     * @return the value of field 'Description'.
-     */
-    public java.lang.String getDescription(
-    ) {
-        return this._description;
-    }
-
-    /**
-     * Returns the value of field 'name'. The field 'name' has the
-     * following description: The short name for the parameter set.
-     * This will be shown amongst the
-     *  other presets for the web service.
-     *  
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
-
-    /**
-     * Returns the value of field 'parameters'. The field
-     * 'parameters' has the following description: UTF8 encoded
-     * string to be processed into a specific web services'
-     *  parameter set. Note - newlines may be important to the
-     * structure
-     *  of this file.
-     *  
-     * 
-     * @return the value of field 'Parameters'.
-     */
-    public java.lang.String getParameters(
-    ) {
-        return this._parameters;
-    }
-
-    /**
-     * Method getServiceURL.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the java.lang.String at the given index
-     */
-    public java.lang.String getServiceURL(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._serviceURLList.size()) {
-            throw new IndexOutOfBoundsException("getServiceURL: Index value '" + index + "' not in range [0.." + (this._serviceURLList.size() - 1) + "]");
-        }
-        
-        return (java.lang.String) _serviceURLList.get(index);
-    }
-
-    /**
-     * Method getServiceURL.Returns the contents of the collection
-     * in an Array.  
Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we know
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public java.lang.String[] getServiceURL(
-    ) {
-        java.lang.String[] array = new java.lang.String[0];
-        return (java.lang.String[]) this._serviceURLList.toArray(array);
-    }
-
-    /**
-     * Method getServiceURLCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getServiceURLCount(
-    ) {
-        return this._serviceURLList.size();
-    }
-
-    /**
-     * Returns the value of field 'version'. The field 'version'
-     * has the following description: A Jalview Web Service
-     * Parameter Set container
-     *  version number.
-     *  Version 1 created for storing Jaba user presets.
-     *  
-     * 
-     * @return the value of field 'Version'.
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
      */
-    public java.lang.String getVersion(
-    ) {
-        return this._version;
+  public void removeAllServiceURL()
+  {
+    this._serviceURLList.clear();
+  }
+
+  /**
+   * Method removeServiceURL.
+   * 
+   * @param vServiceURL
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeServiceURL(final java.lang.String vServiceURL)
+  {
+    boolean removed = _serviceURLList.remove(vServiceURL);
+    return removed;
+  }
+
+  /**
+   * Method removeServiceURLAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeServiceURLAt(final int index)
+  {
+    java.lang.Object obj = this._serviceURLList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * Sets the value of field 'description'. The field 'description' has the
+   * following description: Short description - as utf8 encoded text. This is
+   * usually displayed in the body of an HTML capable tooltip, so HTML tags may
+   * be embedded using standard UTF8 encoding.
+   * 
+   * 
+   * @param description
+   *          the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'name'. The field 'name' has the following
+   * description: The short name for the parameter set. This will be shown
+   * amongst the other presets for the web service.
+   * 
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name)
+  {
+    this._name = name;
+  }
+
+  /**
+   * Sets the value of field 'parameters'. The field 'parameters' has the
+   * following description: UTF8 encoded string to be processed into a specific
+   * web services' parameter set. Note - newlines may be important to the
+   * structure of this file.
+   * 
+   * 
+   * @param parameters
+   *          the value of field 'parameters'.
+   */
+  public void setParameters(final java.lang.String parameters)
+  {
+    this._parameters = parameters;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vServiceURL
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setServiceURL(final int index,
+          final java.lang.String vServiceURL)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._serviceURLList.size())
+    {
+      throw new IndexOutOfBoundsException("setServiceURL: Index value '"
+              + index + "' not in range [0.."
+              + (this._serviceURLList.size() - 1) + "]");
     }
 
-    /**
-     * Method isValid.
-     * 
-     * @return true if this object is valid according to the schema
-     */
-    public boolean isValid(
-    ) {
-        try {
-            validate();
-        } catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    }
-
-    /**
-     * 
-     * 
-     * @param out
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void marshal(
-            final java.io.Writer out)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, out);
-    }
-
-    /**
-     * 
-     * 
-     * @param handler
-     * @throws java.io.IOException if an IOException occurs during
-     * marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     */
-    public void marshal(
-            final org.xml.sax.ContentHandler handler)
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        Marshaller.marshal(this, handler);
-    }
-
-    /**
-     */
-    public void removeAllServiceURL(
-    ) {
-        this._serviceURLList.clear();
-    }
-
-    /**
-     * Method removeServiceURL.
-     * 
-     * @param vServiceURL
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeServiceURL(
-            final java.lang.String vServiceURL) {
-        boolean removed = _serviceURLList.remove(vServiceURL);
-        return removed;
-    }
-
-    /**
-     * Method removeServiceURLAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public java.lang.String removeServiceURLAt(
-            final int index) {
-        java.lang.Object obj = this._serviceURLList.remove(index);
-        return (java.lang.String) obj;
-    }
-
-    /**
-     * Sets the value of field 'description'. The field
-     * 'description' has the following description: Short
-     * description - as utf8 encoded text. This is
-     *  usually displayed
-     *  in the body of an HTML capable tooltip, so HTML tags may be
-     * embedded
-     *  using standard UTF8 encoding.
-     *  
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(
-            final java.lang.String description) {
-        this._description = description;
-    }
-
-    /**
-     * Sets the value of field 'name'. The field 'name' has the
-     * following description: The short name for the parameter set.
-     * This will be shown amongst the
-     *  other presets for the web service.
-     *  
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
-
-    /**
-     * Sets the value of field 'parameters'. The field 'parameters'
-     * has the following description: UTF8 encoded string to be
-     * processed into a specific web services'
-     *  parameter set. Note - newlines may be important to the
-     * structure
-     *  of this file.
-     *  
-     * 
-     * @param parameters the value of field 'parameters'.
-     */
-    public void setParameters(
-            final java.lang.String parameters) {
-        this._parameters = parameters;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vServiceURL
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setServiceURL(
-            final int index,
-            final java.lang.String vServiceURL)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._serviceURLList.size()) {
-            throw new IndexOutOfBoundsException("setServiceURL: Index value '" + index + "' not in range [0.." + (this._serviceURLList.size() - 1) + "]");
-        }
-        
-        this._serviceURLList.set(index, vServiceURL);
-    }
-
-    /**
-     * 
-     * 
-     * @param vServiceURLArray
-     */
-    public void setServiceURL(
-            final java.lang.String[] vServiceURLArray) {
-        //-- copy array
-        _serviceURLList.clear();
-        
-        for (int i = 0; i < vServiceURLArray.length; i++) {
-                this._serviceURLList.add(vServiceURLArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'version'. The field 'version' has
-     * the following description: A Jalview Web Service Parameter
-     * Set container
-     *  version number.
-     *  Version 1 created for storing Jaba user presets.
-     *  
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(
-            final java.lang.String version) {
-        this._version = version;
-    }
-
-    /**
-     * Method unmarshal.
-     * 
-     * @param reader
-     * @throws org.exolab.castor.xml.MarshalException if object is
-     * null or if any SAXException is thrown during marshaling
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     * @return the unmarshaled
-     * jalview.schemabinding.version2.WebServiceParameterSet
-     */
-    public static jalview.schemabinding.version2.WebServiceParameterSet unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.WebServiceParameterSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.WebServiceParameterSet.class, reader);
-    }
-
-    /**
-     * 
-     * 
-     * @throws org.exolab.castor.xml.ValidationException if this
-     * object is an invalid instance according to the schema
-     */
-    public void validate(
-    )
-    throws org.exolab.castor.xml.ValidationException {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
+    this._serviceURLList.set(index, vServiceURL);
+  }
+
+  /**
+   * 
+   * 
+   * @param vServiceURLArray
+   */
+  public void setServiceURL(final java.lang.String[] vServiceURLArray)
+  {
+    // -- copy array
+    _serviceURLList.clear();
+
+    for (int i = 0; i < vServiceURLArray.length; i++)
+    {
+      this._serviceURLList.add(vServiceURLArray[i]);
     }
+  }
+
+  /**
+   * Sets the value of field 'version'. The field 'version' has the following
+   * description: A Jalview Web Service Parameter Set container version number.
+   * Version 1 created for storing Jaba user presets.
+   * 
+   * 
+   * @param version
+   *          the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled
+   *         jalview.schemabinding.version2.WebServiceParameterSet
+   */
+  public static jalview.schemabinding.version2.WebServiceParameterSet unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.WebServiceParameterSet) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.WebServiceParameterSet.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
index 0d95592..1447978 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.AlcodMap;
@@ -18,217 +18,230 @@ import jalview.schemabinding.version2.AlcodMap;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodMapDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlcodMapDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "alcodMap";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _dnasq
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dnasq", "dnasq", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AlcodMap target = (AlcodMap) object;
-                return target.getDnasq();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AlcodMap target = (AlcodMap) object;
-                    target.setDnasq( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _dnasq
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _mapping
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AlcodMap target = (AlcodMap) object;
-                return target.getMapping();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AlcodMap target = (AlcodMap) object;
-                    target.setMapping( (jalview.schemabinding.version2.Mapping) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Mapping();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapping
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
+public class AlcodMapDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodMapDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "alcodMap";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _dnasq
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_dnasq", "dnasq",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AlcodMap target = (AlcodMap) object;
+        return target.getDnasq();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AlcodMap target = (AlcodMap) object;
+          target.setDnasq((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _dnasq
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.AlcodMap.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _mapping
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Mapping.class, "_mapping",
+            "Mapping", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AlcodMap target = (AlcodMap) object;
+        return target.getMapping();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AlcodMap target = (AlcodMap) object;
+          target.setMapping((jalview.schemabinding.version2.Mapping) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Mapping();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _mapping
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AlcodMap.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
index c6be168..c1a0eab 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Alcodon;
@@ -18,263 +18,296 @@ import jalview.schemabinding.version2.Alcodon;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodonDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlcodonDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "alcodon";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _pos1
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos1", "pos1", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Alcodon target = (Alcodon) object;
-                if (!target.hasPos1()) { return null; }
-                return new java.lang.Long(target.getPos1());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Alcodon target = (Alcodon) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePos1();
-                        return;
-                    }
-                    target.setPos1( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pos1
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _pos2
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos2", "pos2", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Alcodon target = (Alcodon) object;
-                if (!target.hasPos2()) { return null; }
-                return new java.lang.Long(target.getPos2());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Alcodon target = (Alcodon) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePos2();
-                        return;
-                    }
-                    target.setPos2( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pos2
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
+public class AlcodonDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodonDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "alcodon";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _pos1
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_pos1", "pos1",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Alcodon target = (Alcodon) object;
+        if (!target.hasPos1())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _pos3
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos3", "pos3", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Alcodon target = (Alcodon) object;
-                if (!target.hasPos3()) { return null; }
-                return new java.lang.Long(target.getPos3());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Alcodon target = (Alcodon) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePos3();
-                        return;
-                    }
-                    target.setPos3( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pos3
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Long(target.getPos1());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Alcodon target = (Alcodon) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePos1();
+            return;
+          }
+          target.setPos1(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
+    // -- validation code for: _pos1
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pos2
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_pos2", "pos2",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Alcodon target = (Alcodon) object;
+        if (!target.hasPos2())
+        {
+          return null;
+        }
+        return new java.lang.Long(target.getPos2());
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Alcodon target = (Alcodon) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePos2();
+            return;
+          }
+          target.setPos2(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _pos2
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _pos3
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_pos3", "pos3",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Alcodon target = (Alcodon) object;
+        if (!target.hasPos3())
+        {
+          return null;
+        }
+        return new java.lang.Long(target.getPos3());
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Alcodon.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Alcodon target = (Alcodon) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePos3();
+            return;
+          }
+          target.setPos3(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _pos3
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Alcodon.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
index 9d9551a..919941e 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.AlcodonFrame;
@@ -18,227 +18,250 @@ import jalview.schemabinding.version2.AlcodonFrame;
  * 
  * @version $Revision$ $Date$
  */
-public class AlcodonFrameDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AlcodonFrameDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "AlcodonFrame";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _alcodonList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alcodon.class, "_alcodonList", "alcodon", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AlcodonFrame target = (AlcodonFrame) object;
-                return target.getAlcodon();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AlcodonFrame target = (AlcodonFrame) object;
-                    target.addAlcodon( (jalview.schemabinding.version2.Alcodon) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    AlcodonFrame target = (AlcodonFrame) object;
-                    target.removeAllAlcodon();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Alcodon();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _alcodonList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class AlcodonFrameDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AlcodonFrameDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "AlcodonFrame";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _alcodonList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Alcodon.class, "_alcodonList",
+            "alcodon", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AlcodonFrame target = (AlcodonFrame) object;
+        return target.getAlcodon();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AlcodonFrame target = (AlcodonFrame) object;
+          target.addAlcodon((jalview.schemabinding.version2.Alcodon) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _alcodMapList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", "alcodMap", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AlcodonFrame target = (AlcodonFrame) object;
-                return target.getAlcodMap();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AlcodonFrame target = (AlcodonFrame) object;
-                    target.addAlcodMap( (jalview.schemabinding.version2.AlcodMap) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    AlcodonFrame target = (AlcodonFrame) object;
-                    target.removeAllAlcodMap();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.AlcodMap();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _alcodMapList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          AlcodonFrame target = (AlcodonFrame) object;
+          target.removeAllAlcodon();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Alcodon();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _alcodonList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _alcodMapList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList",
+            "alcodMap", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AlcodonFrame target = (AlcodonFrame) object;
+        return target.getAlcodMap();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AlcodonFrame target = (AlcodonFrame) object;
+          target.addAlcodMap((jalview.schemabinding.version2.AlcodMap) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          AlcodonFrame target = (AlcodonFrame) object;
+          target.removeAllAlcodMap();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.AlcodMap();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _alcodMapList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.AlcodonFrame.class;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AlcodonFrame.class;
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java
index e4ab0ca..804b49e 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.AnnotationColourScheme;
@@ -18,468 +18,556 @@ import jalview.schemabinding.version2.AnnotationColourScheme;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationColourSchemeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationColourSchemeDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "AnnotationColourScheme";
-        _elementDefinition = false;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _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
-            {
-                AnnotationColourScheme target = (AnnotationColourScheme) 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 {
-                    AnnotationColourScheme target = (AnnotationColourScheme) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteAboveThreshold();
-                        return;
-                    }
-                    target.setAboveThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _aboveThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _annotation
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColourScheme target = (AnnotationColourScheme) object;
-                return target.getAnnotation();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColourScheme target = (AnnotationColourScheme) object;
-                    target.setAnnotation( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _annotation
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class AnnotationColourSchemeDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationColourSchemeDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "AnnotationColourScheme";
+    _elementDefinition = false;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _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
+      {
+        AnnotationColourScheme target = (AnnotationColourScheme) 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
-            {
-                AnnotationColourScheme target = (AnnotationColourScheme) 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 {
-                    AnnotationColourScheme target = (AnnotationColourScheme) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMinColour();
-                        return;
-                    }
-                    target.setMinColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _minColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getAboveThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColourScheme target = (AnnotationColourScheme) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteAboveThreshold();
+            return;
+          }
+          target.setAboveThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _maxColour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColourScheme target = (AnnotationColourScheme) 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 {
-                    AnnotationColourScheme target = (AnnotationColourScheme) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMaxColour();
-                        return;
-                    }
-                    target.setMaxColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _maxColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _aboveThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _annotation
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_annotation", "annotation",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColourScheme target = (AnnotationColourScheme) object;
+        return target.getAnnotation();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColourScheme target = (AnnotationColourScheme) object;
+          target.setAnnotation((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _colourScheme
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColourScheme target = (AnnotationColourScheme) object;
-                return target.getColourScheme();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColourScheme target = (AnnotationColourScheme) object;
-                    target.setColourScheme( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourScheme
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _annotation
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _minColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_minColour", "minColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColourScheme target = (AnnotationColourScheme) object;
+        if (!target.hasMinColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColourScheme target = (AnnotationColourScheme) 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 {
-                    AnnotationColourScheme target = (AnnotationColourScheme) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteThreshold();
-                        return;
-                    }
-                    target.setThreshold( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Integer(target.getMinColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColourScheme target = (AnnotationColourScheme) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMinColour();
+            return;
+          }
+          target.setMinColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _perSequence
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_perSequence", "perSequence", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColourScheme target = (AnnotationColourScheme) object;
-                if (!target.hasPerSequence()) { return null; }
-                return (target.getPerSequence() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColourScheme target = (AnnotationColourScheme) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePerSequence();
-                        return;
-                    }
-                    target.setPerSequence( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _perSequence
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _minColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _maxColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_maxColour", "maxColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColourScheme target = (AnnotationColourScheme) object;
+        if (!target.hasMaxColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _predefinedColours
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_predefinedColours", "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationColourScheme target = (AnnotationColourScheme) object;
-                if (!target.hasPredefinedColours()) { return null; }
-                return (target.getPredefinedColours() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationColourScheme target = (AnnotationColourScheme) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePredefinedColours();
-                        return;
-                    }
-                    target.setPredefinedColours( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _predefinedColours
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getMaxColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColourScheme target = (AnnotationColourScheme) 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());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _maxColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colourScheme
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_colourScheme", "colourScheme",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColourScheme target = (AnnotationColourScheme) object;
+        return target.getColourScheme();
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColourScheme target = (AnnotationColourScheme) object;
+          target.setColourScheme((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _colourScheme
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _threshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_threshold", "threshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColourScheme target = (AnnotationColourScheme) object;
+        if (!target.hasThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getThreshold());
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.AnnotationColourScheme.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColourScheme target = (AnnotationColourScheme) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteThreshold();
+            return;
+          }
+          target.setThreshold(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _threshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+    // -- _perSequence
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_perSequence", "perSequence",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColourScheme target = (AnnotationColourScheme) object;
+        if (!target.hasPerSequence())
+        {
+          return null;
+        }
+        return (target.getPerSequence() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColourScheme target = (AnnotationColourScheme) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePerSequence();
+            return;
+          }
+          target.setPerSequence(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _perSequence
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _predefinedColours
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_predefinedColours",
+            "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationColourScheme target = (AnnotationColourScheme) object;
+        if (!target.hasPredefinedColours())
+        {
+          return null;
+        }
+        return (target.getPredefinedColours() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationColourScheme target = (AnnotationColourScheme) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePredefinedColours();
+            return;
+          }
+          target.setPredefinedColours(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _predefinedColours
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AnnotationColourScheme.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
index aabd971..f269bdf 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
@@ -7,145 +7,142 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import jalview.schemabinding.version2.AnnotationColours;
 
 /**
  * Class AnnotationColoursDescriptor.
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationColoursDescriptor extends jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationColoursDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "AnnotationColours";
-        _elementDefinition = true;
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.AnnotationColours.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+public class AnnotationColoursDescriptor
+        extends
+        jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationColoursDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "AnnotationColours";
+    _elementDefinition = true;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AnnotationColours.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
index e0a2fd2..e2331f4 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Annotation;
@@ -18,1029 +18,1281 @@ import jalview.schemabinding.version2.Annotation;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "Annotation";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _graph
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasGraph()) { return null; }
-                return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setGraph( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graph
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+public class AnnotationDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "Annotation";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _graph
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_graph", "graph",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasGraph())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _graphType
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasGraphType()) { return null; }
-                return new java.lang.Integer(target.getGraphType());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteGraphType();
-                        return;
-                    }
-                    target.setGraphType( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphType
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (target.getGraph() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setGraph(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _sequenceRef
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getSequenceRef();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setSequenceRef( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceRef
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _graph
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _graphType
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_graphType", "graphType",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasGraphType())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _groupRef
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_groupRef", "groupRef", 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.getGroupRef();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setGroupRef( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _groupRef
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Integer(target.getGraphType());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteGraphType();
+            return;
+          }
+          target.setGraphType(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _graphColour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasGraphColour()) { return null; }
-                return new java.lang.Integer(target.getGraphColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteGraphColour();
-                        return;
-                    }
-                    target.setGraphColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _graphType
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _sequenceRef
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_sequenceRef", "sequenceRef",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getSequenceRef();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setSequenceRef((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _graphGroup
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasGraphGroup()) { return null; }
-                return new java.lang.Integer(target.getGraphGroup());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteGraphGroup();
-                        return;
-                    }
-                    target.setGraphGroup( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphGroup
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _sequenceRef
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _groupRef
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_groupRef", "groupRef",
+            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.getGroupRef();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setGroupRef((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _graphHeight
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphHeight", "graphHeight", 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.hasGraphHeight()) { return null; }
-                return new java.lang.Integer(target.getGraphHeight());
-            }
-            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.deleteGraphHeight();
-                        return;
-                    }
-                    target.setGraphHeight( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphHeight
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _groupRef
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _graphColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_graphColour", "graphColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasGraphColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Integer(target.getGraphColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteGraphColour();
+            return;
+          }
+          target.setGraphColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _scoreOnly
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasScoreOnly()) { return null; }
-                return (target.getScoreOnly() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteScoreOnly();
-                        return;
-                    }
-                    target.setScoreOnly( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _scoreOnly
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _graphColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _graphGroup
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_graphGroup", "graphGroup",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasGraphGroup())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _score
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasScore()) { return null; }
-                return new java.lang.Double(target.getScore());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteScore();
-                        return;
-                    }
-                    target.setScore( ((java.lang.Double) value).doubleValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _score
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.DoubleValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-1.7976931348623157E308);
-            typeValidator.setMaxInclusive(1.7976931348623157E308);
+        return new java.lang.Integer(target.getGraphGroup());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteGraphGroup();
+            return;
+          }
+          target.setGraphGroup(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _visible
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                if (!target.hasVisible()) { return null; }
-                return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteVisible();
-                        return;
-                    }
-                    target.setVisible( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _visible
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _graphGroup
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _graphHeight
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_graphHeight", "graphHeight",
+            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.hasGraphHeight())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _centreColLabels
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", 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.hasCentreColLabels()) { return null; }
-                return (target.getCentreColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteCentreColLabels();
-                        return;
-                    }
-                    target.setCentreColLabels( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _centreColLabels
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getGraphHeight());
+      }
+
+      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.deleteGraphHeight();
+            return;
+          }
+          target.setGraphHeight(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _scaleColLabels
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", 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.hasScaleColLabels()) { return null; }
-                return (target.getScaleColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteScaleColLabels();
-                        return;
-                    }
-                    target.setScaleColLabels( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _scaleColLabels
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _graphHeight
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _showAllColLabels
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAllColLabels", "showAllColLabels", 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.hasShowAllColLabels()) { return null; }
-                return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowAllColLabels();
-                        return;
-                    }
-                    target.setShowAllColLabels( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showAllColLabels
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _scoreOnly
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasScoreOnly())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _autoCalculated
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", 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.hasAutoCalculated()) { return null; }
-                return (target.getAutoCalculated() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteAutoCalculated();
-                        return;
-                    }
-                    target.setAutoCalculated( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _autoCalculated
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.getScoreOnly() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteScoreOnly();
+            return;
+          }
+          target.setScoreOnly(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _belowAlignment
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_belowAlignment", "belowAlignment", 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.hasBelowAlignment()) { return null; }
-                return (target.getBelowAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteBelowAlignment();
-                        return;
-                    }
-                    target.setBelowAlignment( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _belowAlignment
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _scoreOnly
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _score
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Double.TYPE, "_score", "score",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasScore())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _calcId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_calcId", "calcId", 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.getCalcId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setCalcId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _calcId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Double(target.getScore());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteScore();
+            return;
+          }
+          target.setScore(((java.lang.Double) value).doubleValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _annotationElementList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getAnnotationElement();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.removeAllAnnotationElement();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.AnnotationElement();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _annotationElementList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _score
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.DoubleValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-1.7976931348623157E308);
+      typeValidator.setMaxInclusive(1.7976931348623157E308);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _visible
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_visible", "visible",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        if (!target.hasVisible())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _label
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getLabel();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setLabel( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _label
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return (target.getVisible() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteVisible();
+            return;
+          }
+          target.setVisible(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _description
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Annotation target = (Annotation) object;
-                return target.getDescription();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.setDescription( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _visible
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _centreColLabels
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels",
+            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.hasCentreColLabels())
+        {
+          return null;
+        }
+        return (target.getCentreColLabels() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteCentreColLabels();
+            return;
+          }
+          target.setCentreColLabels(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        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
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _centreColLabels
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _scaleColLabels
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels",
+            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.hasScaleColLabels())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _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
-            {
-                Annotation target = (Annotation) object;
-                return target.getProperty();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.addProperty( (jalview.schemabinding.version2.Property) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Annotation target = (Annotation) object;
-                    target.removeAllProperty();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Property();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _propertyList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        return (target.getScaleColLabels() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteScaleColLabels();
+            return;
+          }
+          target.setScaleColLabels(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _scaleColLabels
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _showAllColLabels
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showAllColLabels",
+            "showAllColLabels", 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.hasShowAllColLabels())
+        {
+          return null;
+        }
+        return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowAllColLabels();
+            return;
+          }
+          target.setShowAllColLabels(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+    // -- validation code for: _showAllColLabels
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _autoCalculated
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated",
+            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.hasAutoCalculated())
+        {
+          return null;
+        }
+        return (target.getAutoCalculated() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteAutoCalculated();
+            return;
+          }
+          target.setAutoCalculated(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _autoCalculated
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _belowAlignment
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_belowAlignment", "belowAlignment",
+            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.hasBelowAlignment())
+        {
+          return null;
+        }
+        return (target.getBelowAlignment() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+      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.deleteBelowAlignment();
+            return;
+          }
+          target.setBelowAlignment(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _belowAlignment
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _calcId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_calcId", "calcId",
+            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.getCalcId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setCalcId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Annotation.class;
+    // -- validation code for: _calcId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+    // -- _annotationElementList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.AnnotationElement.class,
+            "_annotationElementList", "annotationElement",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getAnnotationElement();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.addAnnotationElement((jalview.schemabinding.version2.AnnotationElement) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.removeAllAnnotationElement();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.AnnotationElement();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _annotationElementList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _label
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_label", "label",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getLabel();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setLabel((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _label
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _description
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_description", "description",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getDescription();
+      }
+
+      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());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _thresholdLine
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.ThresholdLine.class,
+            "_thresholdLine", "thresholdLine",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Annotation target = (Annotation) object;
+        return target.getThresholdLine();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.setThresholdLine((jalview.schemabinding.version2.ThresholdLine) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.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);
+    // -- _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
+      {
+        Annotation target = (Annotation) object;
+        return target.getProperty();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.addProperty((jalview.schemabinding.version2.Property) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Annotation target = (Annotation) object;
+          target.removeAllProperty();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Property();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _propertyList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Annotation.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
index abc0041..4416bbf 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.AnnotationElement;
@@ -18,388 +18,447 @@ import jalview.schemabinding.version2.AnnotationElement;
  * 
  * @version $Revision$ $Date$
  */
-public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationElementDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "annotationElement";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _position
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                if (!target.hasPosition()) { return null; }
-                return new java.lang.Integer(target.getPosition());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setPosition( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _position
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                if (!target.hasColour()) { return null; }
-                return new java.lang.Integer(target.getColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColour();
-                        return;
-                    }
-                    target.setColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _displayCharacter
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                return target.getDisplayCharacter();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    target.setDisplayCharacter( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _displayCharacter
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class AnnotationElementDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public AnnotationElementDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "annotationElement";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _position
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_position", "position",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        if (!target.hasPosition())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _description
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                return target.getDescription();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    target.setDescription( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Integer(target.getPosition());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setPosition(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _secondaryStructure
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                return target.getSecondaryStructure();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    target.setSecondaryStructure( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _secondaryStructure
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-            typeValidator.setLength(1);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _position
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        if (!target.hasColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                AnnotationElement target = (AnnotationElement) object;
-                if (!target.hasValue()) { return null; }
-                return new java.lang.Float(target.getValue());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    AnnotationElement target = (AnnotationElement) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteValue();
-                        return;
-                    }
-                    target.setValue( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Integer(target.getColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColour();
+            return;
+          }
+          target.setColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
+    // -- _displayCharacter
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_displayCharacter",
+            "displayCharacter", org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        return target.getDisplayCharacter();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          target.setDisplayCharacter((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _displayCharacter
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _description
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_description", "description",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        return target.getDescription();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.AnnotationElement.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          target.setDescription((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _secondaryStructure
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_secondaryStructure",
+            "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        return target.getSecondaryStructure();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          target.setSecondaryStructure((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _secondaryStructure
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+      typeValidator.setLength(1);
     }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_value", "value",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        AnnotationElement target = (AnnotationElement) object;
+        if (!target.hasValue())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getValue());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          AnnotationElement target = (AnnotationElement) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteValue();
+            return;
+          }
+          target.setValue(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AnnotationElement.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java b/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java
index 46e867c..6dbea24 100644
--- a/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.CalcIdParam;
@@ -18,262 +18,296 @@ import jalview.schemabinding.version2.CalcIdParam;
  * 
  * @version $Revision$ $Date$
  */
-public class CalcIdParamDescriptor extends jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public CalcIdParamDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "calcIdParam";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _calcId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_calcId", "calcId", 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
-            {
-                CalcIdParam target = (CalcIdParam) object;
-                return target.getCalcId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    CalcIdParam target = (CalcIdParam) object;
-                    target.setCalcId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _calcId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class CalcIdParamDescriptor
+        extends
+        jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public CalcIdParamDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "calcIdParam";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _calcId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_calcId", "calcId",
+            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
+      {
+        CalcIdParam target = (CalcIdParam) object;
+        return target.getCalcId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          CalcIdParam target = (CalcIdParam) object;
+          target.setCalcId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _needsUpdate
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_needsUpdate", "needsUpdate", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                CalcIdParam target = (CalcIdParam) object;
-                if (!target.hasNeedsUpdate()) { return null; }
-                return (target.getNeedsUpdate() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    CalcIdParam target = (CalcIdParam) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteNeedsUpdate();
-                        return;
-                    }
-                    target.setNeedsUpdate( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _needsUpdate
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _calcId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _needsUpdate
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_needsUpdate", "needsUpdate",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        CalcIdParam target = (CalcIdParam) object;
+        if (!target.hasNeedsUpdate())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _autoUpdate
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoUpdate", "autoUpdate", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                CalcIdParam target = (CalcIdParam) object;
-                if (!target.hasAutoUpdate()) { return null; }
-                return (target.getAutoUpdate() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    CalcIdParam target = (CalcIdParam) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setAutoUpdate( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _autoUpdate
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.getNeedsUpdate() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          CalcIdParam target = (CalcIdParam) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteNeedsUpdate();
+            return;
+          }
+          target.setNeedsUpdate(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _needsUpdate
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _autoUpdate
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_autoUpdate", "autoUpdate",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        CalcIdParam target = (CalcIdParam) object;
+        if (!target.hasAutoUpdate())
+        {
+          return null;
+        }
+        return (target.getAutoUpdate() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          CalcIdParam target = (CalcIdParam) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setAutoUpdate(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _autoUpdate
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.CalcIdParam.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.CalcIdParam.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
index 3f6ae2d..8b1ae9e 100644
--- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Colour;
@@ -18,500 +18,592 @@ import jalview.schemabinding.version2.Colour;
  * 
  * @version $Revision$ $Date$
  */
-public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ColourDescriptor() {
-        super();
-        _xmlName = "colour";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Colour target = (Colour) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _RGB
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Colour target = (Colour) object;
-                return target.getRGB();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    target.setRGB( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _RGB
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class ColourDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public ColourDescriptor()
+  {
+    super();
+    _xmlName = "colour";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "Name",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        return target.getName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _minRGB
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_minRGB", "minRGB", 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.getMinRGB();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    target.setMinRGB( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _minRGB
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _RGB
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_RGB", "RGB",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        return target.getRGB();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          target.setRGB((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshType
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_threshType", "threshType", 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.getThreshType();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    target.setThreshType( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshType
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _RGB
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _minRGB
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_minRGB", "minRGB",
+            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.getMinRGB();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          target.setMinRGB((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Colour target = (Colour) 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 {
-                    Colour target = (Colour) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteThreshold();
-                        return;
-                    }
-                    target.setThreshold( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _minRGB
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _threshType
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_threshType", "threshType",
+            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.getThreshType();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          target.setThreshType((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _max
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Colour target = (Colour) object;
-                if (!target.hasMax()) { return null; }
-                return new java.lang.Float(target.getMax());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMax();
-                        return;
-                    }
-                    target.setMax( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _max
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _threshType
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _threshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_threshold", "threshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        if (!target.hasThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _min
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Colour target = (Colour) object;
-                if (!target.hasMin()) { return null; }
-                return new java.lang.Float(target.getMin());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMin();
-                        return;
-                    }
-                    target.setMin( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _min
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Float(target.getThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteThreshold();
+            return;
+          }
+          target.setThreshold(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _colourByLabel
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Colour target = (Colour) object;
-                if (!target.hasColourByLabel()) { return null; }
-                return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColourByLabel();
-                        return;
-                    }
-                    target.setColourByLabel( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourByLabel
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _threshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _max
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_max", "max",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        if (!target.hasMax())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _autoScale
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Colour target = (Colour) object;
-                if (!target.hasAutoScale()) { return null; }
-                return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Colour target = (Colour) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteAutoScale();
-                        return;
-                    }
-                    target.setAutoScale( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _autoScale
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Float(target.getMax());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMax();
+            return;
+          }
+          target.setMax(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
+    // -- validation code for: _max
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _min
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_min", "min",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        if (!target.hasMin())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getMin());
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMin();
+            return;
+          }
+          target.setMin(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _min
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+    // -- _colourByLabel
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        if (!target.hasColourByLabel())
+        {
+          return null;
+        }
+        return (target.getColourByLabel() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Colour.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColourByLabel();
+            return;
+          }
+          target.setColourByLabel(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _colourByLabel
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _autoScale
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_autoScale", "autoScale",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        if (!target.hasAutoScale())
+        {
+          return null;
+        }
+        return (target.getAutoScale() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteAutoScale();
+            return;
+          }
+          target.setAutoScale(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _autoScale
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Colour.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
index 00f81d2..e896d7a 100644
--- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.DBRef;
@@ -18,287 +18,316 @@ import jalview.schemabinding.version2.DBRef;
  * 
  * @version $Revision$ $Date$
  */
-public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public DBRefDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "DBRef";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _source
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                DBRef target = (DBRef) object;
-                return target.getSource();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    DBRef target = (DBRef) object;
-                    target.setSource( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _source
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _version
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                DBRef target = (DBRef) object;
-                return target.getVersion();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    DBRef target = (DBRef) object;
-                    target.setVersion( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _version
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _accessionId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                DBRef target = (DBRef) object;
-                return target.getAccessionId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    DBRef target = (DBRef) object;
-                    target.setAccessionId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _accessionId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _mapping
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                DBRef target = (DBRef) object;
-                return target.getMapping();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    DBRef target = (DBRef) object;
-                    target.setMapping( (jalview.schemabinding.version2.Mapping) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Mapping();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapping
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-    }
+public class DBRefDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
 
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+  public DBRefDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "DBRef";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _source
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_source", "source",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        DBRef target = (DBRef) object;
+        return target.getSource();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          DBRef target = (DBRef) object;
+          target.setSource((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _source
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _version
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_version", "version",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        DBRef target = (DBRef) object;
+        return target.getVersion();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.DBRef.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          DBRef target = (DBRef) object;
+          target.setVersion((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _version
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _accessionId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_accessionId", "accessionId",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        DBRef target = (DBRef) object;
+        return target.getAccessionId();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          DBRef target = (DBRef) object;
+          target.setAccessionId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _accessionId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _mapping
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Mapping.class, "_mapping",
+            "Mapping", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        DBRef target = (DBRef) object;
+        return target.getMapping();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          DBRef target = (DBRef) object;
+          target.setMapping((jalview.schemabinding.version2.Mapping) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Mapping();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _mapping
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.DBRef.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
index 019c680..64ed3a5 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Feature;
@@ -18,464 +18,547 @@ import jalview.schemabinding.version2.Feature;
  * 
  * @version $Revision$ $Date$
  */
-public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeatureDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "feature";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _begin
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                if (!target.hasBegin()) { return null; }
-                return new java.lang.Integer(target.getBegin());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setBegin( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _begin
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _type
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getType();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.setType( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _description
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getDescription();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.setDescription( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _status
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getStatus();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.setStatus( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _status
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _featureGroup
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getFeatureGroup();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.setFeatureGroup( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _featureGroup
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _score
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                if (!target.hasScore()) { return null; }
-                return new java.lang.Float(target.getScore());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteScore();
-                        return;
-                    }
-                    target.setScore( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _score
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+public class FeatureDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "feature";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _begin
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_begin", "begin",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        if (!target.hasBegin())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _otherDataList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Feature target = (Feature) object;
-                return target.getOtherData();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Feature target = (Feature) object;
-                    target.addOtherData( (jalview.schemabinding.version2.OtherData) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Feature target = (Feature) object;
-                    target.removeAllOtherData();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.OtherData();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _otherDataList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        return new java.lang.Integer(target.getBegin());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setBegin(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _begin
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _type
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_type", "type",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getType();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.setType((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Feature.class;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _description
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_description", "description",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getDescription();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.setDescription((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _status
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_status", "status",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getStatus();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.setStatus((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _status
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _featureGroup
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_featureGroup", "featureGroup",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getFeatureGroup();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.setFeatureGroup((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _featureGroup
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _score
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_score", "score",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        if (!target.hasScore())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getScore());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteScore();
+            return;
+          }
+          target.setScore(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _score
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- _otherDataList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.OtherData.class,
+            "_otherDataList", "otherData",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Feature target = (Feature) object;
+        return target.getOtherData();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.addOtherData((jalview.schemabinding.version2.OtherData) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Feature target = (Feature) object;
+          target.removeAllOtherData();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.OtherData();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _otherDataList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Feature.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
index 69ed769..44bc256 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.FeatureSettings;
@@ -18,227 +18,250 @@ import jalview.schemabinding.version2.FeatureSettings;
  * 
  * @version $Revision$ $Date$
  */
-public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeatureSettingsDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "FeatureSettings";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _settingList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                FeatureSettings target = (FeatureSettings) object;
-                return target.getSetting();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    FeatureSettings target = (FeatureSettings) object;
-                    target.addSetting( (jalview.schemabinding.version2.Setting) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    FeatureSettings target = (FeatureSettings) object;
-                    target.removeAllSetting();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Setting();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _settingList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class FeatureSettingsDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureSettingsDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "FeatureSettings";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _settingList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Setting.class, "_settingList",
+            "setting", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureSettings target = (FeatureSettings) object;
+        return target.getSetting();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureSettings target = (FeatureSettings) object;
+          target.addSetting((jalview.schemabinding.version2.Setting) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _groupList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Group.class, "_groupList", "group", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                FeatureSettings target = (FeatureSettings) object;
-                return target.getGroup();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    FeatureSettings target = (FeatureSettings) object;
-                    target.addGroup( (jalview.schemabinding.version2.Group) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    FeatureSettings target = (FeatureSettings) object;
-                    target.removeAllGroup();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Group();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _groupList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          FeatureSettings target = (FeatureSettings) object;
+          target.removeAllSetting();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Setting();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _settingList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _groupList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Group.class, "_groupList",
+            "group", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureSettings target = (FeatureSettings) object;
+        return target.getGroup();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureSettings target = (FeatureSettings) object;
+          target.addGroup((jalview.schemabinding.version2.Group) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          FeatureSettings target = (FeatureSettings) object;
+          target.removeAllGroup();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Group();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _groupList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.FeatureSettings.class;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.FeatureSettings.class;
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
index b292135..5a5b4a9 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
@@ -7,145 +7,141 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import jalview.schemabinding.version2.Features;
 
 /**
  * Class FeaturesDescriptor.
  * 
  * @version $Revision$ $Date$
  */
-public class FeaturesDescriptor extends jalview.schemabinding.version2.descriptors.FeatureDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeaturesDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "features";
-        _elementDefinition = true;
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Features.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+public class FeaturesDescriptor extends
+        jalview.schemabinding.version2.descriptors.FeatureDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeaturesDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "features";
+    _elementDefinition = true;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Features.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
index 8c03e2e..7aa6203 100644
--- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Group;
@@ -18,220 +18,240 @@ import jalview.schemabinding.version2.Group;
  * 
  * @version $Revision$ $Date$
  */
-public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public GroupDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "group";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Group target = (Group) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Group target = (Group) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _display
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Group target = (Group) object;
-                if (!target.hasDisplay()) { return null; }
-                return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Group target = (Group) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setDisplay( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _display
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+public class GroupDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public GroupDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "group";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "name",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Group target = (Group) object;
+        return target.getName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Group target = (Group) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _display
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_display", "display",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Group target = (Group) object;
+        if (!target.hasDisplay())
+        {
+          return null;
+        }
+        return (target.getDisplay() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Group target = (Group) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setDisplay(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _display
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Group.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Group.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
index 9408f58..a5607b7 100644
--- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.HiddenColumns;
@@ -18,226 +18,247 @@ import jalview.schemabinding.version2.HiddenColumns;
  * 
  * @version $Revision$ $Date$
  */
-public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public HiddenColumnsDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "hiddenColumns";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                HiddenColumns target = (HiddenColumns) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    HiddenColumns target = (HiddenColumns) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteStart();
-                        return;
-                    }
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class HiddenColumnsDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public HiddenColumnsDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "hiddenColumns";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        HiddenColumns target = (HiddenColumns) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                HiddenColumns target = (HiddenColumns) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    HiddenColumns target = (HiddenColumns) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteEnd();
-                        return;
-                    }
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          HiddenColumns target = (HiddenColumns) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteStart();
+            return;
+          }
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        HiddenColumns target = (HiddenColumns) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          HiddenColumns target = (HiddenColumns) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteEnd();
+            return;
+          }
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.HiddenColumns.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.HiddenColumns.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
index 0a7316b..620432f 100644
--- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.JGroup;
@@ -18,1007 +18,1258 @@ import jalview.schemabinding.version2.JGroup;
  * 
  * @version $Revision$ $Date$
  */
-public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JGroupDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "JGroup";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteStart();
-                        return;
-                    }
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class JGroupDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JGroupDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "JGroup";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteEnd();
-                        return;
-                    }
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteStart();
+            return;
+          }
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasEnd())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                return target.getColour();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    target.setColour( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Integer(target.getEnd());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteEnd();
+            return;
+          }
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _consThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasConsThreshold()) { return null; }
-                return new java.lang.Integer(target.getConsThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteConsThreshold();
-                        return;
-                    }
-                    target.setConsThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _consThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "name",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        return target.getName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _pidThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasPidThreshold()) { return null; }
-                return new java.lang.Integer(target.getPidThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePidThreshold();
-                        return;
-                    }
-                    target.setPidThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pidThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        return target.getColour();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          target.setColour((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _outlineColour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasOutlineColour()) { return null; }
-                return new java.lang.Integer(target.getOutlineColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteOutlineColour();
-                        return;
-                    }
-                    target.setOutlineColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _outlineColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _consThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_consThreshold", "consThreshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasConsThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _displayBoxes
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasDisplayBoxes()) { return null; }
-                return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteDisplayBoxes();
-                        return;
-                    }
-                    target.setDisplayBoxes( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _displayBoxes
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getConsThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteConsThreshold();
+            return;
+          }
+          target.setConsThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _displayText
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasDisplayText()) { return null; }
-                return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteDisplayText();
-                        return;
-                    }
-                    target.setDisplayText( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _displayText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _consThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pidThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasPidThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _colourText
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasColourText()) { return null; }
-                return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColourText();
-                        return;
-                    }
-                    target.setColourText( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getPidThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePidThreshold();
+            return;
+          }
+          target.setPidThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _textCol1
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasTextCol1()) { return null; }
-                return new java.lang.Integer(target.getTextCol1());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextCol1();
-                        return;
-                    }
-                    target.setTextCol1( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol1
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _pidThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _outlineColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_outlineColour", "outlineColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasOutlineColour())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getOutlineColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteOutlineColour();
+            return;
+          }
+          target.setOutlineColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _textCol2
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasTextCol2()) { return null; }
-                return new java.lang.Integer(target.getTextCol2());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextCol2();
-                        return;
-                    }
-                    target.setTextCol2( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol2
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _outlineColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _displayBoxes
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasDisplayBoxes())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _textColThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                if (!target.hasTextColThreshold()) { return null; }
-                return new java.lang.Integer(target.getTextColThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextColThreshold();
-                        return;
-                    }
-                    target.setTextColThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textColThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteDisplayBoxes();
+            return;
+          }
+          target.setDisplayBoxes(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _showUnconserved
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", 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.hasShowUnconserved()) { return null; }
-                return (target.getShowUnconserved() ? 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.deleteShowUnconserved();
-                        return;
-                    }
-                    target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showUnconserved
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _displayBoxes
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _displayText
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_displayText", "displayText",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasDisplayText())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _ignoreGapsinConsensus
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", 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.hasIgnoreGapsinConsensus()) { return null; }
-                return (target.getIgnoreGapsinConsensus() ? 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.deleteIgnoreGapsinConsensus();
-                        return;
-                    }
-                    target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ignoreGapsinConsensus
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.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());
         }
-        desc.setValidator(fieldValidator);
-        //-- _showConsensusHistogram
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", 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.hasShowConsensusHistogram()) { return null; }
-                return (target.getShowConsensusHistogram() ? 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.deleteShowConsensusHistogram();
-                        return;
-                    }
-                    target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showConsensusHistogram
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _displayText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colourText
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_colourText", "colourText",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasColourText())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _showSequenceLogo
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", 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.hasShowSequenceLogo()) { return null; }
-                return (target.getShowSequenceLogo() ? 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.deleteShowSequenceLogo();
-                        return;
-                    }
-                    target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showSequenceLogo
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.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());
         }
-        desc.setValidator(fieldValidator);
-        //-- _normaliseSequenceLogo
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_normaliseSequenceLogo", "normaliseSequenceLogo", 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.hasNormaliseSequenceLogo()) { return null; }
-                return (target.getNormaliseSequenceLogo() ? 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.deleteNormaliseSequenceLogo();
-                        return;
-                    }
-                    target.setNormaliseSequenceLogo( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _normaliseSequenceLogo
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colourText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _textCol1
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textCol1", "textCol1",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasTextCol1())
+        {
+          return null;
         }
-        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
-            {
-                JGroup target = (JGroup) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        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());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _seqList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JGroup target = (JGroup) object;
-                return target.getSeq();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) object;
-                    target.addSeq( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JGroup target = (JGroup) object;
-                    target.removeAllSeq();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _seqList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _textCol1
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _textCol2
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textCol2", "textCol2",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasTextCol2())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _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
-            {
-                JGroup target = (JGroup) object;
-                return target.getAnnotationColours();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JGroup target = (JGroup) 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
+        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());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _textCol2
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _textColThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textColThreshold",
+            "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        if (!target.hasTextColThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getTextColThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextColThreshold();
+            return;
+          }
+          target.setTextColThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _textColThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showUnconserved
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved",
+            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.hasShowUnconserved())
+        {
+          return null;
+        }
+        return (target.getShowUnconserved() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowUnconserved();
+            return;
+          }
+          target.setShowUnconserved(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showUnconserved
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _ignoreGapsinConsensus
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_ignoreGapsinConsensus",
+            "ignoreGapsinConsensus",
+            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.hasIgnoreGapsinConsensus())
+        {
+          return null;
+        }
+        return (target.getIgnoreGapsinConsensus() ? 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.deleteIgnoreGapsinConsensus();
+            return;
+          }
+          target.setIgnoreGapsinConsensus(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _ignoreGapsinConsensus
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _showConsensusHistogram
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showConsensusHistogram",
+            "showConsensusHistogram",
+            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.hasShowConsensusHistogram())
+        {
+          return null;
+        }
+        return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JGroup.class;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowConsensusHistogram();
+            return;
+          }
+          target.setShowConsensusHistogram(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showConsensusHistogram
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _showSequenceLogo
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showSequenceLogo",
+            "showSequenceLogo", 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.hasShowSequenceLogo())
+        {
+          return null;
+        }
+        return (target.getShowSequenceLogo() ? 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.deleteShowSequenceLogo();
+            return;
+          }
+          target.setShowSequenceLogo(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showSequenceLogo
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _normaliseSequenceLogo
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_normaliseSequenceLogo",
+            "normaliseSequenceLogo",
+            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.hasNormaliseSequenceLogo())
+        {
+          return null;
+        }
+        return (target.getNormaliseSequenceLogo() ? 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.deleteNormaliseSequenceLogo();
+            return;
+          }
+          target.setNormaliseSequenceLogo(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _normaliseSequenceLogo
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _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
+      {
+        JGroup target = (JGroup) object;
+        return target.getId();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _seqList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_seqList", "seq",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JGroup target = (JGroup) object;
+        return target.getSeq();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          target.addSeq((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) object;
+          target.removeAllSeq();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _seqList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _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
+      {
+        JGroup target = (JGroup) object;
+        return target.getAnnotationColours();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JGroup target = (JGroup) 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);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _annotationColours
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JGroup.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
index 44c8caf..0f000bb 100644
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.JSeq;
@@ -18,528 +18,642 @@ import jalview.schemabinding.version2.JSeq;
  * 
  * @version $Revision$ $Date$
  */
-public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JSeqDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "JSeq";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                if (!target.hasColour()) { return null; }
-                return new java.lang.Integer(target.getColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColour();
-                        return;
-                    }
-                    target.setColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class JSeqDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JSeqDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "JSeq";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColour();
+            return;
+          }
+          target.setColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _hidden
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                if (!target.hasHidden()) { return null; }
-                return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHidden();
-                        return;
-                    }
-                    target.setHidden( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _hidden
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasEnd())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _featuresList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                return target.getFeatures();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.addFeatures( (jalview.schemabinding.version2.Features) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.removeAllFeatures();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Features();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _featuresList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        return new java.lang.Integer(target.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());
         }
-        desc.setValidator(fieldValidator);
-        //-- _pdbidsList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                return target.getPdbids();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.removeAllPdbids();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Pdbids();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pdbidsList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _hiddenSequencesList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JSeq target = (JSeq) object;
-                return target.getHiddenSequences();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.addHiddenSequences( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.removeAllHiddenSequences();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _hiddenSequencesList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _hidden
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_hidden", "hidden",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasHidden())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _rnaViewerList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.RnaViewer.class, "_rnaViewerList", "rnaViewer", 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.getRnaViewer();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.addRnaViewer( (jalview.schemabinding.version2.RnaViewer) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JSeq target = (JSeq) object;
-                    target.removeAllRnaViewer();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.RnaViewer();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _rnaViewerList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        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());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _hidden
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
+    // -- _featuresList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Features.class, "_featuresList",
+            "features", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getFeatures();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.addFeatures((jalview.schemabinding.version2.Features) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllFeatures();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
+      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);
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JSeq.class;
+    // -- validation code for: _featuresList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _pdbidsList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",
+            "pdbids", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getPdbids();
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.addPdbids((jalview.schemabinding.version2.Pdbids) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllPdbids();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.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()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getHiddenSequences();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.addHiddenSequences(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllHiddenSequences();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _hiddenSequencesList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _rnaViewerList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.RnaViewer.class,
+            "_rnaViewerList", "rnaViewer",
+            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.getRnaViewer();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.addRnaViewer((jalview.schemabinding.version2.RnaViewer) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllRnaViewer();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.RnaViewer();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _rnaViewerList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JSeq.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
index d52f02d..f400c2c 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.JalviewModel;
@@ -18,293 +18,324 @@ import jalview.schemabinding.version2.JalviewModel;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "JalviewModel";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _creationDate
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModel target = (JalviewModel) object;
-                return target.getCreationDate();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModel target = (JalviewModel) object;
-                    target.setCreationDate( (java.util.Date) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new java.util.Date();
-            }
-        };
-        handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler);
-        desc.setImmutable(true);
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _creationDate
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.DateTimeValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _version
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModel target = (JalviewModel) object;
-                return target.getVersion();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModel target = (JalviewModel) object;
-                    target.setVersion( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _version
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _vamsasModel
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModel target = (JalviewModel) object;
-                return target.getVamsasModel();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModel target = (JalviewModel) object;
-                    target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.VamsasModel();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _vamsasModel
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-        //-- _jalviewModelSequence
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModel target = (JalviewModel) object;
-                return target.getJalviewModelSequence();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModel target = (JalviewModel) object;
-                    target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.JalviewModelSequence();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setContainer(true);
-        desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _jalviewModelSequence
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
+public class JalviewModelDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModelDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "JalviewModel";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _creationDate
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.util.Date.class, "_creationDate", "creationDate",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModel target = (JalviewModel) object;
+        return target.getCreationDate();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModel target = (JalviewModel) object;
+          target.setCreationDate((java.util.Date) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new java.util.Date();
+      }
+    };
+    handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler);
+    desc.setImmutable(true);
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _creationDate
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.DateTimeValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _version
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_version", "version",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModel target = (JalviewModel) object;
+        return target.getVersion();
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          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);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _version
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _vamsasModel
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.VamsasModel.class,
+            "_vamsasModel", "vamsasModel",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModel target = (JalviewModel) object;
+        return target.getVamsasModel();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JalviewModel.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModel target = (JalviewModel) object;
+          target.setVamsasModel((jalview.schemabinding.version2.VamsasModel) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.VamsasModel();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _vamsasModel
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _jalviewModelSequence
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.JalviewModelSequence.class,
+            "_jalviewModelSequence", "-error-if-this-is-used-",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModel target = (JalviewModel) object;
+        return target.getJalviewModelSequence();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModel target = (JalviewModel) object;
+          target.setJalviewModelSequence((jalview.schemabinding.version2.JalviewModelSequence) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.JalviewModelSequence();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setContainer(true);
+    desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _jalviewModelSequence
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JalviewModel.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
index e74d8dd..e8c4ef4 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.JalviewModelSequence;
@@ -18,385 +18,457 @@ import jalview.schemabinding.version2.JalviewModelSequence;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelSequenceDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _JSeqList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getJSeq();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addJSeq( (jalview.schemabinding.version2.JSeq) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllJSeq();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.JSeq();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _JSeqList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class JalviewModelSequenceDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewModelSequenceDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _JSeqList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getJSeq();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.addJSeq((jalview.schemabinding.version2.JSeq) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _JGroupList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getJGroup();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addJGroup( (jalview.schemabinding.version2.JGroup) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllJGroup();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.JGroup();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _JGroupList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllJSeq();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _viewportList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getViewport();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addViewport( (jalview.schemabinding.version2.Viewport) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllViewport();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Viewport();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _viewportList
-        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.JSeq();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _JSeqList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _JGroupList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.JGroup.class, "_JGroupList",
+            "JGroup", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getJGroup();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.addJGroup((jalview.schemabinding.version2.JGroup) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _userColoursList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getUserColours();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addUserColours( (jalview.schemabinding.version2.UserColours) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllUserColours();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.UserColours();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _userColoursList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllJGroup();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _treeList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getTree();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.addTree( (jalview.schemabinding.version2.Tree) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.removeAllTree();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Tree();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _treeList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.JGroup();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _JGroupList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _viewportList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Viewport.class, "_viewportList",
+            "Viewport", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getViewport();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.addViewport((jalview.schemabinding.version2.Viewport) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _featureSettings
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewModelSequence target = (JalviewModelSequence) object;
-                return target.getFeatureSettings();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewModelSequence target = (JalviewModelSequence) object;
-                    target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.FeatureSettings();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _featureSettings
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllViewport();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Viewport();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _viewportList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _userColoursList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.UserColours.class,
+            "_userColoursList", "UserColours",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getUserColours();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.addUserColours((jalview.schemabinding.version2.UserColours) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllUserColours();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.UserColours();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _userColoursList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _treeList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Tree.class, "_treeList", "tree",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getTree();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JalviewModelSequence.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.addTree((jalview.schemabinding.version2.Tree) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.removeAllTree();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Tree();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+    // -- validation code for: _treeList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _featureSettings
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.FeatureSettings.class,
+            "_featureSettings", "FeatureSettings",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewModelSequence target = (JalviewModelSequence) object;
+        return target.getFeatureSettings();
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewModelSequence target = (JalviewModelSequence) object;
+          target.setFeatureSettings((jalview.schemabinding.version2.FeatureSettings) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.FeatureSettings();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _featureSettings
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JalviewModelSequence.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
index 47d0769..77efa7e 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Colour;
@@ -19,258 +19,284 @@ import jalview.schemabinding.version2.JalviewUserColours;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewUserColoursDescriptor() {
-        super();
-        _nsURI = "www.jalview.org/colours";
-        _xmlName = "JalviewUserColours";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _schemeName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewUserColours target = (JalviewUserColours) object;
-                return target.getSchemeName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewUserColours target = (JalviewUserColours) object;
-                    target.setSchemeName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _schemeName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _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
-            {
-                JalviewUserColours target = (JalviewUserColours) object;
-                return target.getVersion();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewUserColours target = (JalviewUserColours) object;
-                    target.setVersion( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _version
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _colourList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                JalviewUserColours target = (JalviewUserColours) object;
-                return target.getColour();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    JalviewUserColours target = (JalviewUserColours) object;
-                    target.addColour( (Colour) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    JalviewUserColours target = (JalviewUserColours) object;
-                    target.removeAllColour();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new Colour();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class JalviewUserColoursDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public JalviewUserColoursDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org/colours";
+    _xmlName = "JalviewUserColours";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _schemeName
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_schemeName", "schemeName",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewUserColours target = (JalviewUserColours) object;
+        return target.getSchemeName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewUserColours target = (JalviewUserColours) object;
+          target.setSchemeName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _schemeName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
+    // -- _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
+      {
+        JalviewUserColours target = (JalviewUserColours) object;
+        return target.getVersion();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewUserColours target = (JalviewUserColours) object;
+          target.setVersion((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _version
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _colourList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            Colour.class, "_colourList", "colour",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewUserColours target = (JalviewUserColours) object;
+        return target.getColour();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.JalviewUserColours.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewUserColours target = (JalviewUserColours) object;
+          target.addColour((Colour) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JalviewUserColours target = (JalviewUserColours) object;
+          target.removeAllColour();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new Colour();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+    // -- validation code for: _colourList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JalviewUserColours.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
index 91dffbe..529f477 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.MapListFrom;
@@ -18,226 +18,251 @@ import jalview.schemabinding.version2.MapListFrom;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListFromDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListFromDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "mapListFrom";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListFrom target = (MapListFrom) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListFrom target = (MapListFrom) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class MapListFromDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListFromDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "mapListFrom";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListFrom target = (MapListFrom) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListFrom target = (MapListFrom) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListFrom target = (MapListFrom) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListFrom target = (MapListFrom) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListFrom target = (MapListFrom) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListFrom target = (MapListFrom) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.MapListFrom.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MapListFrom.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
index 43a4033..bed082a 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.MapListTo;
@@ -18,226 +18,251 @@ import jalview.schemabinding.version2.MapListTo;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListToDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListToDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "mapListTo";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _start
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListTo target = (MapListTo) object;
-                if (!target.hasStart()) { return null; }
-                return new java.lang.Integer(target.getStart());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListTo target = (MapListTo) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setStart( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class MapListToDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListToDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "mapListTo";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListTo target = (MapListTo) object;
+        if (!target.hasStart())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListTo target = (MapListTo) object;
-                if (!target.hasEnd()) { return null; }
-                return new java.lang.Integer(target.getEnd());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListTo target = (MapListTo) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setEnd( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListTo target = (MapListTo) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListTo target = (MapListTo) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListTo target = (MapListTo) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.MapListTo.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MapListTo.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
index 8b92065..fc24a78 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.MapListType;
@@ -18,311 +18,364 @@ import jalview.schemabinding.version2.MapListType;
  * 
  * @version $Revision$ $Date$
  */
-public class MapListTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MapListTypeDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "mapListType";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _mapFromUnit
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListType target = (MapListType) object;
-                if (!target.hasMapFromUnit()) { return null; }
-                return new java.lang.Long(target.getMapFromUnit());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListType target = (MapListType) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setMapFromUnit( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapFromUnit
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(1L);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _mapToUnit
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListType target = (MapListType) object;
-                if (!target.hasMapToUnit()) { return null; }
-                return new java.lang.Long(target.getMapToUnit());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListType target = (MapListType) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setMapToUnit( ((java.lang.Long) value).longValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapToUnit
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.LongValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.LongValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(1L);
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _mapListFromList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListFrom.class, "_mapListFromList", "mapListFrom", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListType target = (MapListType) object;
-                return target.getMapListFrom();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListType target = (MapListType) object;
-                    target.addMapListFrom( (jalview.schemabinding.version2.MapListFrom) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    MapListType target = (MapListType) object;
-                    target.removeAllMapListFrom();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.MapListFrom();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapListFromList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class MapListTypeDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MapListTypeDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "mapListType";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _mapFromUnit
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListType target = (MapListType) object;
+        if (!target.hasMapFromUnit())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _mapListToList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListTo.class, "_mapListToList", "mapListTo", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MapListType target = (MapListType) object;
-                return target.getMapListTo();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MapListType target = (MapListType) object;
-                    target.addMapListTo( (jalview.schemabinding.version2.MapListTo) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    MapListType target = (MapListType) object;
-                    target.removeAllMapListTo();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.MapListTo();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mapListToList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        return new java.lang.Long(target.getMapFromUnit());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setMapFromUnit(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _mapFromUnit
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(1L);
     }
+    desc.setValidator(fieldValidator);
+    // -- _mapToUnit
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Long.TYPE, "_mapToUnit", "mapToUnit",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListType target = (MapListType) object;
+        if (!target.hasMapToUnit())
+        {
+          return null;
+        }
+        return new java.lang.Long(target.getMapToUnit());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+          target.setMapToUnit(((java.lang.Long) value).longValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _mapToUnit
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.LongValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.LongValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(1L);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.MapListType.class;
-    }
+    // -- _mapListFromList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.MapListFrom.class,
+            "_mapListFromList", "mapListFrom",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListType target = (MapListType) object;
+        return target.getMapListFrom();
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          target.addMapListFrom((jalview.schemabinding.version2.MapListFrom) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          target.removeAllMapListFrom();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.MapListFrom();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _mapListFromList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _mapListToList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.MapListTo.class,
+            "_mapListToList", "mapListTo",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MapListType target = (MapListType) object;
+        return target.getMapListTo();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          target.addMapListTo((jalview.schemabinding.version2.MapListTo) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          MapListType target = (MapListType) object;
+          target.removeAllMapListTo();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.MapListTo();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _mapListToList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MapListType.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
index b0aa8f9..ae460af 100644
--- a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.MappingChoice;
@@ -18,213 +18,226 @@ import jalview.schemabinding.version2.MappingChoice;
  * 
  * @version $Revision$ $Date$
  */
-public class MappingChoiceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MappingChoiceDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsChoice();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _sequence
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequence", "Sequence", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MappingChoice target = (MappingChoice) object;
-                return target.getSequence();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MappingChoice target = (MappingChoice) object;
-                    target.setSequence( (jalview.schemabinding.version2.Sequence) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Sequence();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequence
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-        //-- _dseqFor
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dseqFor", "dseqFor", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                MappingChoice target = (MappingChoice) object;
-                return target.getDseqFor();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    MappingChoice target = (MappingChoice) object;
-                    target.setDseqFor( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _dseqFor
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class MappingChoiceDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MappingChoiceDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsChoice();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _sequence
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Sequence.class, "_sequence",
+            "Sequence", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MappingChoice target = (MappingChoice) object;
+        return target.getSequence();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MappingChoice target = (MappingChoice) object;
+          target.setSequence((jalview.schemabinding.version2.Sequence) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Sequence();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _sequence
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _dseqFor
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_dseqFor", "dseqFor",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        MappingChoice target = (MappingChoice) object;
+        return target.getDseqFor();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          MappingChoice target = (MappingChoice) object;
+          target.setDseqFor((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _dseqFor
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.MappingChoice.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MappingChoice.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
index 45157ff..fab0d2e 100644
--- a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Mapping;
@@ -18,179 +18,185 @@ import jalview.schemabinding.version2.Mapping;
  * 
  * @version $Revision$ $Date$
  */
-public class MappingDescriptor extends jalview.schemabinding.version2.descriptors.MapListTypeDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public MappingDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor());
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "Mapping";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsChoice();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _mappingChoice
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MappingChoice.class, "_mappingChoice", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Mapping target = (Mapping) object;
-                return target.getMappingChoice();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Mapping target = (Mapping) object;
-                    target.setMappingChoice( (jalview.schemabinding.version2.MappingChoice) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.MappingChoice();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setContainer(true);
-        desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor());
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mappingChoice
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
+public class MappingDescriptor extends
+        jalview.schemabinding.version2.descriptors.MapListTypeDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MappingDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor());
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "Mapping";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsChoice();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _mappingChoice
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.MappingChoice.class,
+            "_mappingChoice", "-error-if-this-is-used-",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Mapping target = (Mapping) object;
+        return target.getMappingChoice();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Mapping target = (Mapping) object;
+          target.setMappingChoice((jalview.schemabinding.version2.MappingChoice) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Mapping.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.MappingChoice();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setContainer(true);
+    desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor());
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _mappingChoice
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Mapping.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
index 201f4df..f582311 100644
--- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.OtherData;
@@ -18,218 +18,231 @@ import jalview.schemabinding.version2.OtherData;
  * 
  * @version $Revision$ $Date$
  */
-public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public OtherDataDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "otherData";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _key
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                OtherData target = (OtherData) object;
-                return target.getKey();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    OtherData target = (OtherData) object;
-                    target.setKey( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _key
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                OtherData target = (OtherData) object;
-                return target.getValue();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    OtherData target = (OtherData) object;
-                    target.setValue( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class OtherDataDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public OtherDataDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "otherData";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _key
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_key", "key",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        OtherData target = (OtherData) object;
+        return target.getKey();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          OtherData target = (OtherData) object;
+          target.setKey((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _key
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_value", "value",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        OtherData target = (OtherData) object;
+        return target.getValue();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          OtherData target = (OtherData) object;
+          target.setValue((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.OtherData.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.OtherData.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
index 548be45..f19703a 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Pdbentry;
@@ -18,295 +18,329 @@ import jalview.schemabinding.version2.Pdbentry;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryDescriptor() {
-        super();
-        _xmlName = "pdbentry";
-        _elementDefinition = false;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbentry target = (Pdbentry) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _type
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbentry target = (Pdbentry) object;
-                return target.getType();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.setType( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _file
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbentry target = (Pdbentry) object;
-                return target.getFile();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.setFile( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _file
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _items
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (java.lang.String) null, org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbentry target = (Pdbentry) object;
-                return target.getPdbentryItem();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Pdbentry target = (Pdbentry) object;
-                    target.removeAllPdbentryItem();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.PdbentryItem();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setContainer(true);
-        desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor());
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _items
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-    }
+public class PdbentryDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
 
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+  public PdbentryDescriptor()
+  {
+    super();
+    _xmlName = "pdbentry";
+    _elementDefinition = false;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbentry target = (Pdbentry) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _type
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_type", "type",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbentry target = (Pdbentry) object;
+        return target.getType();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Pdbentry.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target.setType((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _file
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_file", "file",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbentry target = (Pdbentry) object;
+        return target.getFile();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target.setFile((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _file
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _items
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.PdbentryItem.class, "_items",
+            (java.lang.String) null, org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbentry target = (Pdbentry) object;
+        return target.getPdbentryItem();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target.addPdbentryItem((jalview.schemabinding.version2.PdbentryItem) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Pdbentry target = (Pdbentry) object;
+          target.removeAllPdbentryItem();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.PdbentryItem();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setContainer(true);
+    desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor());
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    // -- validation code for: _items
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Pdbentry.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
index cb2b5da..4e2fc87 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.PdbentryItem;
@@ -18,185 +18,195 @@ import jalview.schemabinding.version2.PdbentryItem;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryItemDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "pdbentry";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _propertyList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                PdbentryItem target = (PdbentryItem) object;
-                return target.getProperty();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    PdbentryItem target = (PdbentryItem) object;
-                    target.addProperty( (jalview.schemabinding.version2.Property) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    PdbentryItem target = (PdbentryItem) object;
-                    target.removeAllProperty();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Property();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _propertyList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class PdbentryItemDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PdbentryItemDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "pdbentry";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _propertyList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Property.class, "_propertyList",
+            "property", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        PdbentryItem target = (PdbentryItem) object;
+        return target.getProperty();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          PdbentryItem target = (PdbentryItem) object;
+          target.addProperty((jalview.schemabinding.version2.Property) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.PdbentryItem.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          PdbentryItem target = (PdbentryItem) object;
+          target.removeAllProperty();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Property();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _propertyList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.PdbentryItem.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
index f005ce6..584607d 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Pdbids;
@@ -18,186 +18,197 @@ import jalview.schemabinding.version2.Pdbids;
  * 
  * @version $Revision$ $Date$
  */
-public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors.PdbentryDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbidsDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "pdbids";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _structureStateList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureStateList", "structureState", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Pdbids target = (Pdbids) object;
-                return target.getStructureState();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Pdbids target = (Pdbids) object;
-                    target.addStructureState( (jalview.schemabinding.version2.StructureState) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Pdbids target = (Pdbids) object;
-                    target.removeAllStructureState();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.StructureState();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _structureStateList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+public class PdbidsDescriptor extends
+        jalview.schemabinding.version2.descriptors.PdbentryDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PdbidsDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "pdbids";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _structureStateList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.StructureState.class,
+            "_structureStateList", "structureState",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Pdbids target = (Pdbids) object;
+        return target.getStructureState();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Pdbids target = (Pdbids) object;
+          target.addStructureState((jalview.schemabinding.version2.StructureState) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Pdbids.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Pdbids target = (Pdbids) object;
+          target.removeAllStructureState();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.StructureState();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _structureStateList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Pdbids.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
index b7087d2..60d09b4 100644
--- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Property;
@@ -18,218 +18,231 @@ import jalview.schemabinding.version2.Property;
  * 
  * @version $Revision$ $Date$
  */
-public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PropertyDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "property";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Property target = (Property) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Property target = (Property) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Property target = (Property) object;
-                return target.getValue();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Property target = (Property) object;
-                    target.setValue( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class PropertyDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public PropertyDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "property";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "name",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Property target = (Property) object;
+        return target.getName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Property target = (Property) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_value", "value",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Property target = (Property) object;
+        return target.getValue();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Property target = (Property) object;
+          target.setValue((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Property.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Property.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.java b/src/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.java
index fd824a1..3344050 100644
--- a/src/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/RnaViewerDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.RnaViewer;
@@ -18,518 +18,617 @@ import jalview.schemabinding.version2.RnaViewer;
  * 
  * @version $Revision$ $Date$
  */
-public class RnaViewerDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public RnaViewerDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "rnaViewer";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _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
-            {
-                RnaViewer target = (RnaViewer) object;
-                return target.getTitle();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    RnaViewer target = (RnaViewer) object;
-                    target.setTitle( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _title
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _viewId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewId", "viewId", 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
-            {
-                RnaViewer target = (RnaViewer) object;
-                return target.getViewId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    RnaViewer target = (RnaViewer) object;
-                    target.setViewId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _viewId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class RnaViewerDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public RnaViewerDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "rnaViewer";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _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
+      {
+        RnaViewer target = (RnaViewer) object;
+        return target.getTitle();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) object;
+          target.setTitle((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _dividerLocation
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_dividerLocation", "dividerLocation", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                RnaViewer target = (RnaViewer) object;
-                if (!target.hasDividerLocation()) { return null; }
-                return new java.lang.Integer(target.getDividerLocation());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    RnaViewer target = (RnaViewer) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteDividerLocation();
-                        return;
-                    }
-                    target.setDividerLocation( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _dividerLocation
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _title
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _viewId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_viewId", "viewId",
+            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
+      {
+        RnaViewer target = (RnaViewer) object;
+        return target.getViewId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) object;
+          target.setViewId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _selectedRna
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_selectedRna", "selectedRna", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                RnaViewer target = (RnaViewer) object;
-                if (!target.hasSelectedRna()) { return null; }
-                return new java.lang.Integer(target.getSelectedRna());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    RnaViewer target = (RnaViewer) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteSelectedRna();
-                        return;
-                    }
-                    target.setSelectedRna( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _selectedRna
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _viewId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _dividerLocation
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_dividerLocation", "dividerLocation",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        RnaViewer target = (RnaViewer) object;
+        if (!target.hasDividerLocation())
+        {
+          return null;
         }
-        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
-            {
-                RnaViewer target = (RnaViewer) 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 {
-                    RnaViewer target = (RnaViewer) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWidth();
-                        return;
-                    }
-                    target.setWidth( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getDividerLocation());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteDividerLocation();
+            return;
+          }
+          target.setDividerLocation(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        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
-            {
-                RnaViewer target = (RnaViewer) 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 {
-                    RnaViewer target = (RnaViewer) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHeight();
-                        return;
-                    }
-                    target.setHeight( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _dividerLocation
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _selectedRna
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_selectedRna", "selectedRna",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        RnaViewer target = (RnaViewer) object;
+        if (!target.hasSelectedRna())
+        {
+          return null;
         }
-        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
-            {
-                RnaViewer target = (RnaViewer) 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 {
-                    RnaViewer target = (RnaViewer) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteXpos();
-                        return;
-                    }
-                    target.setXpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Integer(target.getSelectedRna());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteSelectedRna();
+            return;
+          }
+          target.setSelectedRna(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        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
-            {
-                RnaViewer target = (RnaViewer) 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 {
-                    RnaViewer target = (RnaViewer) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteYpos();
-                        return;
-                    }
-                    target.setYpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _selectedRna
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _width
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_width", "width",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        RnaViewer target = (RnaViewer) object;
+        if (!target.hasWidth())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _secondaryStructureList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SecondaryStructure.class, "_secondaryStructureList", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                RnaViewer target = (RnaViewer) object;
-                return target.getSecondaryStructure();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    RnaViewer target = (RnaViewer) object;
-                    target.addSecondaryStructure( (jalview.schemabinding.version2.SecondaryStructure) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    RnaViewer target = (RnaViewer) object;
-                    target.removeAllSecondaryStructure();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.SecondaryStructure();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _secondaryStructureList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
+        return new java.lang.Integer(target.getWidth());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteWidth();
+            return;
+          }
+          target.setWidth(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
+    // -- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _height
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_height", "height",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        RnaViewer target = (RnaViewer) object;
+        if (!target.hasHeight())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getHeight());
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHeight();
+            return;
+          }
+          target.setHeight(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _xpos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_xpos", "xpos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        RnaViewer target = (RnaViewer) object;
+        if (!target.hasXpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getXpos());
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.RnaViewer.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) 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());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _ypos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_ypos", "ypos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        RnaViewer target = (RnaViewer) object;
+        if (!target.hasYpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getYpos());
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteYpos();
+            return;
+          }
+          target.setYpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _secondaryStructureList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.SecondaryStructure.class,
+            "_secondaryStructureList", "secondaryStructure",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        RnaViewer target = (RnaViewer) object;
+        return target.getSecondaryStructure();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) object;
+          target.addSecondaryStructure((jalview.schemabinding.version2.SecondaryStructure) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          RnaViewer target = (RnaViewer) object;
+          target.removeAllSecondaryStructure();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.SecondaryStructure();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _secondaryStructureList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.RnaViewer.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.java
index bc7e4ac..c1e46b8 100644
--- a/src/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SecondaryStructureDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.SecondaryStructure;
@@ -18,294 +18,328 @@ import jalview.schemabinding.version2.SecondaryStructure;
  * 
  * @version $Revision$ $Date$
  */
-public class SecondaryStructureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SecondaryStructureDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "secondaryStructure";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _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
-            {
-                SecondaryStructure target = (SecondaryStructure) object;
-                return target.getTitle();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SecondaryStructure target = (SecondaryStructure) object;
-                    target.setTitle( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _title
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class SecondaryStructureDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SecondaryStructureDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "secondaryStructure";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _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
+      {
+        SecondaryStructure target = (SecondaryStructure) object;
+        return target.getTitle();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SecondaryStructure target = (SecondaryStructure) object;
+          target.setTitle((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _annotationId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotationId", "annotationId", 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
-            {
-                SecondaryStructure target = (SecondaryStructure) object;
-                return target.getAnnotationId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SecondaryStructure target = (SecondaryStructure) object;
-                    target.setAnnotationId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _annotationId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _title
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _annotationId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_annotationId", "annotationId",
+            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
+      {
+        SecondaryStructure target = (SecondaryStructure) object;
+        return target.getAnnotationId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SecondaryStructure target = (SecondaryStructure) object;
+          target.setAnnotationId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _gapped
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gapped", "gapped", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SecondaryStructure target = (SecondaryStructure) object;
-                if (!target.hasGapped()) { return null; }
-                return (target.getGapped() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SecondaryStructure target = (SecondaryStructure) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteGapped();
-                        return;
-                    }
-                    target.setGapped( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _gapped
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _annotationId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _gapped
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_gapped", "gapped",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SecondaryStructure target = (SecondaryStructure) object;
+        if (!target.hasGapped())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _viewerState
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewerState", "viewerState", 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
-            {
-                SecondaryStructure target = (SecondaryStructure) object;
-                return target.getViewerState();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SecondaryStructure target = (SecondaryStructure) object;
-                    target.setViewerState( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _viewerState
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return (target.getGapped() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SecondaryStructure target = (SecondaryStructure) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteGapped();
+            return;
+          }
+          target.setGapped(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _gapped
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _viewerState
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_viewerState", "viewerState",
+            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
+      {
+        SecondaryStructure target = (SecondaryStructure) object;
+        return target.getViewerState();
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SecondaryStructure target = (SecondaryStructure) object;
+          target.setViewerState((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _viewerState
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.SecondaryStructure.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.SecondaryStructure.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
index 2de6b0a..2303e1b 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Sequence;
@@ -18,223 +18,241 @@ import jalview.schemabinding.version2.Sequence;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceDescriptor extends jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "Sequence";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _dsseqid
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dsseqid", "dsseqid", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Sequence target = (Sequence) object;
-                return target.getDsseqid();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Sequence target = (Sequence) object;
-                    target.setDsseqid( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _dsseqid
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _DBRefList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Sequence target = (Sequence) object;
-                return target.getDBRef();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Sequence target = (Sequence) object;
-                    target.addDBRef( (jalview.schemabinding.version2.DBRef) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Sequence target = (Sequence) object;
-                    target.removeAllDBRef();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.DBRef();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _DBRefList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-    }
+public class SequenceDescriptor extends
+        jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
 
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+  public SequenceDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "Sequence";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _dsseqid
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_dsseqid", "dsseqid",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Sequence target = (Sequence) object;
+        return target.getDsseqid();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Sequence target = (Sequence) object;
+          target.setDsseqid((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _dsseqid
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Sequence.class;
-    }
+    // -- _DBRefList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.DBRef.class, "_DBRefList",
+            "DBRef", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Sequence target = (Sequence) object;
+        return target.getDBRef();
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Sequence target = (Sequence) object;
+          target.addDBRef((jalview.schemabinding.version2.DBRef) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Sequence target = (Sequence) object;
+          target.removeAllDBRef();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.DBRef();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _DBRefList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Sequence.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
index 1542223..cd74c6e 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.SequenceSet;
@@ -18,387 +18,455 @@ import jalview.schemabinding.version2.SequenceSet;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSetDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "SequenceSet";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _gapChar
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getGapChar();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.setGapChar( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _gapChar
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class SequenceSetDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSetDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "SequenceSet";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _gapChar
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_gapChar", "gapChar",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getGapChar();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.setGapChar((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _datasetId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getDatasetId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.setDatasetId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _datasetId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _gapChar
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _datasetId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_datasetId", "datasetId",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getDatasetId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.setDatasetId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _sequenceList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getSequence();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.addSequence( (jalview.schemabinding.version2.Sequence) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.removeAllSequence();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Sequence();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _datasetId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _sequenceList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Sequence.class, "_sequenceList",
+            "Sequence", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getSequence();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.addSequence((jalview.schemabinding.version2.Sequence) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _annotationList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getAnnotation();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.removeAllAnnotation();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.Annotation();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _annotationList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.removeAllSequence();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _sequenceSetPropertiesList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getSequenceSetProperties();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.removeAllSequenceSetProperties();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.SequenceSetProperties();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceSetPropertiesList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Sequence();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _sequenceList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _annotationList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Annotation.class,
+            "_annotationList", "Annotation",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getAnnotation();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.addAnnotation((jalview.schemabinding.version2.Annotation) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _alcodonFrameList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                return target.getAlcodonFrame();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    target.removeAllAlcodonFrame();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.AlcodonFrame();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _alcodonFrameList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.removeAllAnnotation();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Annotation();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _annotationList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _sequenceSetPropertiesList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.SequenceSetProperties.class,
+            "_sequenceSetPropertiesList", "sequenceSetProperties",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getSequenceSetProperties();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.removeAllSequenceSetProperties();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.SequenceSetProperties();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _sequenceSetPropertiesList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _alcodonFrameList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.AlcodonFrame.class,
+            "_alcodonFrameList", "AlcodonFrame",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSet target = (SequenceSet) object;
+        return target.getAlcodonFrame();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.SequenceSet.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          SequenceSet target = (SequenceSet) object;
+          target.removeAllAlcodonFrame();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.AlcodonFrame();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+    // -- validation code for: _alcodonFrameList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.SequenceSet.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
index 5c8be83..409abdd 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.SequenceSetProperties;
@@ -18,214 +18,227 @@ import jalview.schemabinding.version2.SequenceSetProperties;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSetPropertiesDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "sequenceSetProperties";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _key
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSetProperties target = (SequenceSetProperties) object;
-                return target.getKey();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSetProperties target = (SequenceSetProperties) object;
-                    target.setKey( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _key
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSetProperties target = (SequenceSetProperties) object;
-                return target.getValue();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSetProperties target = (SequenceSetProperties) object;
-                    target.setValue( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class SequenceSetPropertiesDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceSetPropertiesDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "sequenceSetProperties";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _key
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_key", "key",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSetProperties target = (SequenceSetProperties) object;
+        return target.getKey();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSetProperties target = (SequenceSetProperties) object;
+          target.setKey((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _key
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_value", "value",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceSetProperties target = (SequenceSetProperties) object;
+        return target.getValue();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceSetProperties target = (SequenceSetProperties) object;
+          target.setValue((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.SequenceSetProperties.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.SequenceSetProperties.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
index 27305e7..3ee3fa9 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.SequenceType;
@@ -18,293 +18,322 @@ import jalview.schemabinding.version2.SequenceType;
  * 
  * @version $Revision$ $Date$
  */
-public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceTypeDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "SequenceType";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceType target = (SequenceType) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceType target = (SequenceType) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _description
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceType target = (SequenceType) object;
-                return target.getDescription();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceType target = (SequenceType) object;
-                    target.setDescription( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _sequence
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceType target = (SequenceType) object;
-                return target.getSequence();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceType target = (SequenceType) object;
-                    target.setSequence( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequence
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class SequenceTypeDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SequenceTypeDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "SequenceType";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceType target = (SequenceType) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceType target = (SequenceType) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _name
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceType target = (SequenceType) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceType target = (SequenceType) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _description
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_description", "description",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceType target = (SequenceType) object;
+        return target.getDescription();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceType target = (SequenceType) object;
+          target.setDescription((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
+    // -- _sequence
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_sequence", "sequence",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceType target = (SequenceType) object;
+        return target.getSequence();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceType target = (SequenceType) object;
+          target.setSequence((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _sequence
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _name
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_name", "name",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        SequenceType target = (SequenceType) object;
+        return target.getName();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.SequenceType.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          SequenceType target = (SequenceType) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.SequenceType.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
index 9c2de5b..4703f46 100644
--- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Setting;
@@ -18,603 +18,736 @@ import jalview.schemabinding.version2.Setting;
  * 
  * @version $Revision$ $Date$
  */
-public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SettingDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "setting";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _type
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Setting target = (Setting) object;
-                return target.getType();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    target.setType( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class SettingDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public SettingDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "setting";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _type
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_type", "type",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        return target.getType();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          target.setType((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Setting target = (Setting) object;
-                if (!target.hasColour()) { return null; }
-                return new java.lang.Integer(target.getColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        if (!target.hasColour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _display
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Setting target = (Setting) object;
-                if (!target.hasDisplay()) { return null; }
-                return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    // ignore null values for non optional primitives
-                    if (value == null) { return; }
-                    
-                    target.setDisplay( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _display
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _order
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_order", "order", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Setting target = (Setting) object;
-                if (!target.hasOrder()) { return null; }
-                return new java.lang.Float(target.getOrder());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteOrder();
-                        return;
-                    }
-                    target.setOrder( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _order
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _display
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_display", "display",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        if (!target.hasDisplay())
+        {
+          return null;
         }
-        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
-            {
-                Setting target = (Setting) 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 {
-                    Setting target = (Setting) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMincolour();
-                        return;
-                    }
-                    target.setMincolour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _mincolour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (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());
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Setting target = (Setting) 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 {
-                    Setting target = (Setting) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteThreshold();
-                        return;
-                    }
-                    target.setThreshold( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _display
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _order
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_order", "order",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        if (!target.hasOrder())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshstate
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_threshstate", "threshstate", 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.hasThreshstate()) { return null; }
-                return new java.lang.Integer(target.getThreshstate());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteThreshstate();
-                        return;
-                    }
-                    target.setThreshstate( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshstate
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Float(target.getOrder());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteOrder();
+            return;
+          }
+          target.setOrder(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _max
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", 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.hasMax()) { return null; }
-                return new java.lang.Float(target.getMax());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMax();
-                        return;
-                    }
-                    target.setMax( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _max
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _order
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _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
+      {
+        Setting target = (Setting) object;
+        if (!target.hasMincolour())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _min
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", 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.hasMin()) { return null; }
-                return new java.lang.Float(target.getMin());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Setting target = (Setting) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMin();
-                        return;
-                    }
-                    target.setMin( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _min
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Integer(target.getMincolour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMincolour();
+            return;
+          }
+          target.setMincolour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _colourByLabel
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", 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.hasColourByLabel()) { return null; }
-                return (target.getColourByLabel() ? 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;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColourByLabel();
-                        return;
-                    }
-                    target.setColourByLabel( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourByLabel
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _mincolour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _threshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_threshold", "threshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        if (!target.hasThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _autoScale
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", 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.hasAutoScale()) { return null; }
-                return (target.getAutoScale() ? 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;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteAutoScale();
-                        return;
-                    }
-                    target.setAutoScale( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _autoScale
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Float(target.getThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteThreshold();
+            return;
+          }
+          target.setThreshold(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
+    // -- validation code for: _threshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _threshstate
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_threshstate", "threshstate",
+            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.hasThreshstate())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getThreshstate());
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteThreshstate();
+            return;
+          }
+          target.setThreshstate(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _threshstate
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _max
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_max", "max",
+            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.hasMax())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getMax());
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Setting.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMax();
+            return;
+          }
+          target.setMax(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _max
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+    // -- _min
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_min", "min",
+            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.hasMin())
+        {
+          return null;
+        }
+        return new java.lang.Float(target.getMin());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteMin();
+            return;
+          }
+          target.setMin(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _min
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
     }
+    desc.setValidator(fieldValidator);
+    // -- _colourByLabel
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel",
+            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.hasColourByLabel())
+        {
+          return null;
+        }
+        return (target.getColourByLabel() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColourByLabel();
+            return;
+          }
+          target.setColourByLabel(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colourByLabel
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _autoScale
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_autoScale", "autoScale",
+            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.hasAutoScale())
+        {
+          return null;
+        }
+        return (target.getAutoScale() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteAutoScale();
+            return;
+          }
+          target.setAutoScale(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _autoScale
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Setting.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
index 8759859..16d091b 100644
--- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.StructureState;
@@ -18,586 +18,710 @@ import jalview.schemabinding.version2.StructureState;
  * 
  * @version $Revision$ $Date$
  */
-public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public StructureStateDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "structureState";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- _content
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                return target.getContent();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    target.setContent( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _content
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize attribute descriptors
-        
-        //-- _visible
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasVisible()) { return null; }
-                return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteVisible();
-                        return;
-                    }
-                    target.setVisible( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _visible
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+public class StructureStateDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public StructureStateDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "structureState";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- _content
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_content", "PCDATA",
+            org.exolab.castor.xml.NodeType.Text);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        return target.getContent();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          target.setContent((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _viewId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewId", "viewId", 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
-            {
-                StructureState target = (StructureState) object;
-                return target.getViewId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    target.setViewId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _viewId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _content
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- initialize attribute descriptors
+
+    // -- _visible
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_visible", "visible",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasVisible())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _alignwithAlignPanel
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasAlignwithAlignPanel()) { return null; }
-                return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteAlignwithAlignPanel();
-                        return;
-                    }
-                    target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _alignwithAlignPanel
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return (target.getVisible() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteVisible();
+            return;
+          }
+          target.setVisible(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _colourwithAlignPanel
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourwithAlignPanel", "colourwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasColourwithAlignPanel()) { return null; }
-                return (target.getColourwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColourwithAlignPanel();
-                        return;
-                    }
-                    target.setColourwithAlignPanel( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourwithAlignPanel
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _visible
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _viewId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_viewId", "viewId",
+            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
+      {
+        StructureState target = (StructureState) object;
+        return target.getViewId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          target.setViewId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _colourByJmol
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByJmol", "colourByJmol", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasColourByJmol()) { return null; }
-                return (target.getColourByJmol() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColourByJmol();
-                        return;
-                    }
-                    target.setColourByJmol( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourByJmol
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _viewId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _alignwithAlignPanel
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_alignwithAlignPanel",
+            "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasAlignwithAlignPanel())
+        {
+          return null;
         }
-        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
-            {
-                StructureState target = (StructureState) object;
-                return target.getType();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    target.setType( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteAlignwithAlignPanel();
+            return;
+          }
+          target.setAlignwithAlignPanel(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _width
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasWidth()) { return null; }
-                return new java.lang.Integer(target.getWidth());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWidth();
-                        return;
-                    }
-                    target.setWidth( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _alignwithAlignPanel
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colourwithAlignPanel
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_colourwithAlignPanel",
+            "colourwithAlignPanel",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasColourwithAlignPanel())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _height
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasHeight()) { return null; }
-                return new java.lang.Integer(target.getHeight());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHeight();
-                        return;
-                    }
-                    target.setHeight( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (target.getColourwithAlignPanel() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColourwithAlignPanel();
+            return;
+          }
+          target.setColourwithAlignPanel(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _xpos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasXpos()) { return null; }
-                return new java.lang.Integer(target.getXpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteXpos();
-                        return;
-                    }
-                    target.setXpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colourwithAlignPanel
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colourByJmol
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_colourByJmol", "colourByJmol",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasColourByJmol())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _ypos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                StructureState target = (StructureState) object;
-                if (!target.hasYpos()) { return null; }
-                return new java.lang.Integer(target.getYpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    StructureState target = (StructureState) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteYpos();
-                        return;
-                    }
-                    target.setYpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (target.getColourByJmol() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColourByJmol();
+            return;
+          }
+          target.setColourByJmol(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _colourByJmol
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _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
+      {
+        StructureState target = (StructureState) object;
+        return target.getType();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          target.setType((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _width
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_width", "width",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasWidth())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getWidth());
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.StructureState.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteWidth();
+            return;
+          }
+          target.setWidth(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _height
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_height", "height",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasHeight())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getHeight());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHeight();
+            return;
+          }
+          target.setHeight(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _xpos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_xpos", "xpos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasXpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getXpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteXpos();
+            return;
+          }
+          target.setXpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+    // -- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _ypos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_ypos", "ypos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        StructureState target = (StructureState) object;
+        if (!target.hasYpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getYpos());
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          StructureState target = (StructureState) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteYpos();
+            return;
+          }
+          target.setYpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.StructureState.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
index 851ccb2..8a863d8 100644
--- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.ThresholdLine;
@@ -18,263 +18,292 @@ import jalview.schemabinding.version2.ThresholdLine;
  * 
  * @version $Revision$ $Date$
  */
-public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ThresholdLineDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "thresholdLine";
-        _elementDefinition = true;
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _label
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                ThresholdLine target = (ThresholdLine) object;
-                return target.getLabel();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    ThresholdLine target = (ThresholdLine) object;
-                    target.setLabel( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _label
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class ThresholdLineDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public ThresholdLineDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "thresholdLine";
+    _elementDefinition = true;
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _label
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_label", "label",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        ThresholdLine target = (ThresholdLine) object;
+        return target.getLabel();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          ThresholdLine target = (ThresholdLine) object;
+          target.setLabel((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                ThresholdLine target = (ThresholdLine) object;
-                if (!target.hasValue()) { return null; }
-                return new java.lang.Float(target.getValue());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    ThresholdLine target = (ThresholdLine) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteValue();
-                        return;
-                    }
-                    target.setValue( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _label
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_value", "value",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        ThresholdLine target = (ThresholdLine) object;
+        if (!target.hasValue())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _colour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                ThresholdLine target = (ThresholdLine) object;
-                if (!target.hasColour()) { return null; }
-                return new java.lang.Integer(target.getColour());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    ThresholdLine target = (ThresholdLine) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteColour();
-                        return;
-                    }
-                    target.setColour( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return new java.lang.Float(target.getValue());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          ThresholdLine target = (ThresholdLine) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteValue();
+            return;
+          }
+          target.setValue(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        ThresholdLine target = (ThresholdLine) object;
+        if (!target.hasColour())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getColour());
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          ThresholdLine target = (ThresholdLine) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColour();
+            return;
+          }
+          target.setColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.ThresholdLine.class;
-    }
+  }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.ThresholdLine.class;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
index 5beffc1..8e675f3 100644
--- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Tree;
@@ -18,798 +18,978 @@ import jalview.schemabinding.version2.Tree;
  * 
  * @version $Revision$ $Date$
  */
-public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public TreeDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "tree";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _fontName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getFontName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setFontName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _fontSize
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasFontSize()) { return null; }
-                return new java.lang.Integer(target.getFontSize());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontSize();
-                        return;
-                    }
-                    target.setFontSize( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontSize
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+public class TreeDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public TreeDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "tree";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _fontName
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_fontName", "fontName",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getFontName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setFontName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _fontStyle
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasFontStyle()) { return null; }
-                return new java.lang.Integer(target.getFontStyle());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontStyle();
-                        return;
-                    }
-                    target.setFontStyle( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontStyle
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontSize
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontSize", "fontSize",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasFontSize())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasThreshold()) { return null; }
-                return new java.lang.Float(target.getThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteThreshold();
-                        return;
-                    }
-                    target.setThreshold( ((java.lang.Float) value).floatValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.FloatValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive((float) -3.4028235E38);
-            typeValidator.setMaxInclusive((float) 3.4028235E38);
+        return new java.lang.Integer(target.getFontSize());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontSize();
+            return;
+          }
+          target.setFontSize(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _showBootstrap
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasShowBootstrap()) { return null; }
-                return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowBootstrap();
-                        return;
-                    }
-                    target.setShowBootstrap( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showBootstrap
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontSize
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontStyle
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontStyle", "fontStyle",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasFontStyle())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _showDistances
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasShowDistances()) { return null; }
-                return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowDistances();
-                        return;
-                    }
-                    target.setShowDistances( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showDistances
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Integer(target.getFontStyle());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontStyle();
+            return;
+          }
+          target.setFontStyle(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _markUnlinked
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasMarkUnlinked()) { return null; }
-                return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteMarkUnlinked();
-                        return;
-                    }
-                    target.setMarkUnlinked( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _markUnlinked
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontStyle
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _threshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Float.TYPE, "_threshold", "threshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasThreshold())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _fitToWindow
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasFitToWindow()) { return null; }
-                return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFitToWindow();
-                        return;
-                    }
-                    target.setFitToWindow( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fitToWindow
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        return new java.lang.Float(target.getThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteThreshold();
+            return;
+          }
+          target.setThreshold(((java.lang.Float) value).floatValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _currentTree
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasCurrentTree()) { return null; }
-                return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteCurrentTree();
-                        return;
-                    }
-                    target.setCurrentTree( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _currentTree
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _threshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.FloatValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive((float) -3.4028235E38);
+      typeValidator.setMaxInclusive((float) 3.4028235E38);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showBootstrap
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasShowBootstrap())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        super.setIdentity(desc);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) 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 new java.lang.String();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IdValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IdValidator();
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        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
-            {
-                Tree target = (Tree) object;
-                if (!target.hasWidth()) { return null; }
-                return new java.lang.Integer(target.getWidth());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWidth();
-                        return;
-                    }
-                    target.setWidth( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showBootstrap
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
         }
-        desc.setValidator(fieldValidator);
-        //-- _height
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasHeight()) { return null; }
-                return new java.lang.Integer(target.getHeight());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHeight();
-                        return;
-                    }
-                    target.setHeight( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (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());
         }
-        desc.setValidator(fieldValidator);
-        //-- _xpos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasXpos()) { return null; }
-                return new java.lang.Integer(target.getXpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteXpos();
-                        return;
-                    }
-                    target.setXpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showDistances
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _markUnlinked
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasMarkUnlinked())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _ypos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                if (!target.hasYpos()) { return null; }
-                return new java.lang.Integer(target.getYpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteYpos();
-                        return;
-                    }
-                    target.setYpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
+        return (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());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _title
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getTitle();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setTitle( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _title
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _markUnlinked
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fitToWindow
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasFitToWindow())
+        {
+          return null;
         }
-        desc.setValidator(fieldValidator);
-        //-- _newick
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Tree target = (Tree) object;
-                return target.getNewick();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Tree target = (Tree) object;
-                    target.setNewick( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _newick
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+        return (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());
         }
-        desc.setValidator(fieldValidator);
-    }
+      }
 
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fitToWindow
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _currentTree
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_currentTree", "currentTree",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasCurrentTree())
+        {
+          return null;
+        }
+        return (target.getCurrentTree() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteCurrentTree();
+            return;
+          }
+          target.setCurrentTree(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _currentTree
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    super.setIdentity(desc);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getId();
+      }
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) 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 new java.lang.String();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IdValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IdValidator();
+      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
+      {
+        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());
+        }
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Tree.class;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _height
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_height", "height",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasHeight())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getHeight());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHeight();
+            return;
+          }
+          target.setHeight(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+    // -- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _xpos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_xpos", "xpos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasXpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getXpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteXpos();
+            return;
+          }
+          target.setXpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _ypos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_ypos", "ypos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        if (!target.hasYpos())
+        {
+          return null;
+        }
+        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());
+        }
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _title
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_title", "title",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getTitle();
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setTitle((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _title
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _newick
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_newick", "newick",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Tree target = (Tree) object;
+        return target.getNewick();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Tree target = (Tree) object;
+          target.setNewick((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _newick
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Tree.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
index 7fcc16f..527b16b 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
@@ -7,145 +7,142 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import jalview.schemabinding.version2.UserColourScheme;
 
 /**
  * Class UserColourSchemeDescriptor.
  * 
  * @version $Revision$ $Date$
  */
-public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColourSchemeDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "UserColourScheme";
-        _elementDefinition = true;
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.UserColourScheme.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+public class UserColourSchemeDescriptor
+        extends
+        jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public UserColourSchemeDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "UserColourScheme";
+    _elementDefinition = true;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.UserColourScheme.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
index e5e799b..53dfde4 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.UserColours;
@@ -18,215 +18,229 @@ import jalview.schemabinding.version2.UserColours;
  * 
  * @version $Revision$ $Date$
  */
-public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColoursDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "UserColours";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                UserColours target = (UserColours) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    UserColours target = (UserColours) object;
-                    target.setId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _userColourScheme
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                UserColours target = (UserColours) object;
-                return target.getUserColourScheme();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    UserColours target = (UserColours) object;
-                    target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.UserColourScheme();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _userColourScheme
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
+public class UserColoursDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public UserColoursDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "UserColours";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        UserColours target = (UserColours) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          UserColours target = (UserColours) object;
+          target.setId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.UserColours.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _userColourScheme
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.UserColourScheme.class,
+            "_userColourScheme", "UserColourScheme",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        UserColours target = (UserColours) object;
+        return target.getUserColourScheme();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          UserColours target = (UserColours) object;
+          target.setUserColourScheme((jalview.schemabinding.version2.UserColourScheme) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.UserColourScheme();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _userColourScheme
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.UserColours.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
index 730fe2e..e3470ee 100644
--- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.VAMSAS;
@@ -18,232 +18,256 @@ import jalview.schemabinding.version2.VAMSAS;
  * 
  * @version $Revision$ $Date$
  */
-public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VAMSASDescriptor() {
-        super();
-        _nsURI = "www.vamsas.ac.uk/jalview/version2";
-        _xmlName = "VAMSAS";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- initialize element descriptors
-        
-        //-- _treeList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                VAMSAS target = (VAMSAS) object;
-                return target.getTree();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    VAMSAS target = (VAMSAS) object;
-                    target.addTree( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    VAMSAS target = (VAMSAS) object;
-                    target.removeAllTree();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _treeList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class VAMSASDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public VAMSASDescriptor()
+  {
+    super();
+    _nsURI = "www.vamsas.ac.uk/jalview/version2";
+    _xmlName = "VAMSAS";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _treeList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_treeList", "Tree",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        VAMSAS target = (VAMSAS) object;
+        return target.getTree();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          VAMSAS target = (VAMSAS) object;
+          target.addTree((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _sequenceSetList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                VAMSAS target = (VAMSAS) object;
-                return target.getSequenceSet();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    VAMSAS target = (VAMSAS) object;
-                    target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    VAMSAS target = (VAMSAS) object;
-                    target.removeAllSequenceSet();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.SequenceSet();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceSetList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          VAMSAS target = (VAMSAS) object;
+          target.removeAllTree();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _treeList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _sequenceSetList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.SequenceSet.class,
+            "_sequenceSetList", "SequenceSet",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        VAMSAS target = (VAMSAS) object;
+        return target.getSequenceSet();
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          VAMSAS target = (VAMSAS) object;
+          target.addSequenceSet((jalview.schemabinding.version2.SequenceSet) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          VAMSAS target = (VAMSAS) object;
+          target.removeAllSequenceSet();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.SequenceSet();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _sequenceSetList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+  }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.VAMSAS.class;
-    }
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.VAMSAS.class;
+  }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
index 584c096..fc7f9ba 100644
--- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
@@ -7,145 +7,141 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import jalview.schemabinding.version2.VamsasModel;
 
 /**
  * Class VamsasModelDescriptor.
  * 
  * @version $Revision$ $Date$
  */
-public class VamsasModelDescriptor extends jalview.schemabinding.version2.descriptors.VAMSASDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VamsasModelDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor());
-        _nsURI = "www.jalview.org";
-        _xmlName = "vamsasModel";
-        _elementDefinition = true;
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
-        return null;
-    }
-
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
-    }
-
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.VamsasModel.class;
-    }
-
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
-
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
-    }
-
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
-
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
-    }
-
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
-    }
+public class VamsasModelDescriptor extends
+        jalview.schemabinding.version2.descriptors.VAMSASDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public VamsasModelDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor());
+    _nsURI = "www.jalview.org";
+    _xmlName = "vamsasModel";
+    _elementDefinition = true;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.VamsasModel.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
index cea458c..1df3988 100644
--- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.Viewport;
@@ -18,2102 +18,2700 @@ import jalview.schemabinding.version2.Viewport;
  * 
  * @version $Revision$ $Date$
  */
-public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ViewportDescriptor() {
-        super();
-        _nsURI = "www.jalview.org";
-        _xmlName = "Viewport";
-        _elementDefinition = true;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _conservationSelected
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasConservationSelected()) { return null; }
-                return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteConservationSelected();
-                        return;
-                    }
-                    target.setConservationSelected( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _conservationSelected
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _pidSelected
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasPidSelected()) { return null; }
-                return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePidSelected();
-                        return;
-                    }
-                    target.setPidSelected( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pidSelected
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _bgColour
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getBgColour();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setBgColour( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _bgColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _consThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasConsThreshold()) { return null; }
-                return new java.lang.Integer(target.getConsThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteConsThreshold();
-                        return;
-                    }
-                    target.setConsThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _consThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _pidThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasPidThreshold()) { return null; }
-                return new java.lang.Integer(target.getPidThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deletePidThreshold();
-                        return;
-                    }
-                    target.setPidThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pidThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _title
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getTitle();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setTitle( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _title
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showFullId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowFullId()) { return null; }
-                return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowFullId();
-                        return;
-                    }
-                    target.setShowFullId( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showFullId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _rightAlignIds
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasRightAlignIds()) { return null; }
-                return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteRightAlignIds();
-                        return;
-                    }
-                    target.setRightAlignIds( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _rightAlignIds
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showText
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowText()) { return null; }
-                return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowText();
-                        return;
-                    }
-                    target.setShowText( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showColourText
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowColourText()) { return null; }
-                return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowColourText();
-                        return;
-                    }
-                    target.setShowColourText( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showColourText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showUnconserved
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", 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.hasShowUnconserved()) { return null; }
-                return (target.getShowUnconserved() ? 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.deleteShowUnconserved();
-                        return;
-                    }
-                    target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showUnconserved
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showBoxes
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowBoxes()) { return null; }
-                return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowBoxes();
-                        return;
-                    }
-                    target.setShowBoxes( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showBoxes
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _wrapAlignment
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasWrapAlignment()) { return null; }
-                return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWrapAlignment();
-                        return;
-                    }
-                    target.setWrapAlignment( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _wrapAlignment
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _renderGaps
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasRenderGaps()) { return null; }
-                return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteRenderGaps();
-                        return;
-                    }
-                    target.setRenderGaps( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _renderGaps
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showSequenceFeatures
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowSequenceFeatures()) { return null; }
-                return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowSequenceFeatures();
-                        return;
-                    }
-                    target.setShowSequenceFeatures( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showSequenceFeatures
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showNPfeatureTooltip
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showNPfeatureTooltip", "showNPfeatureTooltip", 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.hasShowNPfeatureTooltip()) { return null; }
-                return (target.getShowNPfeatureTooltip() ? 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.deleteShowNPfeatureTooltip();
-                        return;
-                    }
-                    target.setShowNPfeatureTooltip( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showNPfeatureTooltip
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showDbRefTooltip
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDbRefTooltip", "showDbRefTooltip", 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.hasShowDbRefTooltip()) { return null; }
-                return (target.getShowDbRefTooltip() ? 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.deleteShowDbRefTooltip();
-                        return;
-                    }
-                    target.setShowDbRefTooltip( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showDbRefTooltip
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _followHighlight
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", 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.hasFollowHighlight()) { return null; }
-                return (target.getFollowHighlight() ? 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.deleteFollowHighlight();
-                        return;
-                    }
-                    target.setFollowHighlight( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _followHighlight
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _followSelection
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followSelection", "followSelection", 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.hasFollowSelection()) { return null; }
-                return (target.getFollowSelection() ? 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.deleteFollowSelection();
-                        return;
-                    }
-                    target.setFollowSelection( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _followSelection
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showAnnotation
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasShowAnnotation()) { return null; }
-                return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteShowAnnotation();
-                        return;
-                    }
-                    target.setShowAnnotation( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showAnnotation
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _centreColumnLabels
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColumnLabels", "centreColumnLabels", 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.hasCentreColumnLabels()) { return null; }
-                return (target.getCentreColumnLabels() ? 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.deleteCentreColumnLabels();
-                        return;
-                    }
-                    target.setCentreColumnLabels( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _centreColumnLabels
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showGroupConservation
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConservation", "showGroupConservation", 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.hasShowGroupConservation()) { return null; }
-                return (target.getShowGroupConservation() ? 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.deleteShowGroupConservation();
-                        return;
-                    }
-                    target.setShowGroupConservation( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showGroupConservation
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showGroupConsensus
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConsensus", "showGroupConsensus", 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.hasShowGroupConsensus()) { return null; }
-                return (target.getShowGroupConsensus() ? 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.deleteShowGroupConsensus();
-                        return;
-                    }
-                    target.setShowGroupConsensus( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showGroupConsensus
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showConsensusHistogram
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", 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.hasShowConsensusHistogram()) { return null; }
-                return (target.getShowConsensusHistogram() ? 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.deleteShowConsensusHistogram();
-                        return;
-                    }
-                    target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showConsensusHistogram
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _showSequenceLogo
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", 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.hasShowSequenceLogo()) { return null; }
-                return (target.getShowSequenceLogo() ? 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.deleteShowSequenceLogo();
-                        return;
-                    }
-                    target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showSequenceLogo
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _normaliseSequenceLogo
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_normaliseSequenceLogo", "normaliseSequenceLogo", 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.hasNormaliseSequenceLogo()) { return null; }
-                return (target.getNormaliseSequenceLogo() ? 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.deleteNormaliseSequenceLogo();
-                        return;
-                    }
-                    target.setNormaliseSequenceLogo( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _normaliseSequenceLogo
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _ignoreGapsinConsensus
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", 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.hasIgnoreGapsinConsensus()) { return null; }
-                return (target.getIgnoreGapsinConsensus() ? 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.deleteIgnoreGapsinConsensus();
-                        return;
-                    }
-                    target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ignoreGapsinConsensus
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _startRes
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasStartRes()) { return null; }
-                return new java.lang.Integer(target.getStartRes());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteStartRes();
-                        return;
-                    }
-                    target.setStartRes( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _startRes
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _startSeq
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasStartSeq()) { return null; }
-                return new java.lang.Integer(target.getStartSeq());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteStartSeq();
-                        return;
-                    }
-                    target.setStartSeq( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _startSeq
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _fontName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getFontName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setFontName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _fontSize
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasFontSize()) { return null; }
-                return new java.lang.Integer(target.getFontSize());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontSize();
-                        return;
-                    }
-                    target.setFontSize( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontSize
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _fontStyle
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasFontStyle()) { return null; }
-                return new java.lang.Integer(target.getFontStyle());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteFontStyle();
-                        return;
-                    }
-                    target.setFontStyle( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontStyle
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _scaleProteinAsCdna
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleProteinAsCdna", "scaleProteinAsCdna", 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.hasScaleProteinAsCdna()) { return null; }
-                return (target.getScaleProteinAsCdna() ? 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.deleteScaleProteinAsCdna();
-                        return;
-                    }
-                    target.setScaleProteinAsCdna( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _scaleProteinAsCdna
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _viewName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getViewName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setViewName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _viewName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _sequenceSetId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getSequenceSetId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setSequenceSetId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceSetId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _gatheredViews
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasGatheredViews()) { return null; }
-                return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteGatheredViews();
-                        return;
-                    }
-                    target.setGatheredViews( ((java.lang.Boolean) value).booleanValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _gatheredViews
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _textCol1
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasTextCol1()) { return null; }
-                return new java.lang.Integer(target.getTextCol1());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextCol1();
-                        return;
-                    }
-                    target.setTextCol1( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol1
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _textCol2
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasTextCol2()) { return null; }
-                return new java.lang.Integer(target.getTextCol2());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextCol2();
-                        return;
-                    }
-                    target.setTextCol2( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol2
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _textColThreshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasTextColThreshold()) { return null; }
-                return new java.lang.Integer(target.getTextColThreshold());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteTextColThreshold();
-                        return;
-                    }
-                    target.setTextColThreshold( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textColThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
-        super.setIdentity(desc);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) 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 new java.lang.String();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IdValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IdValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _complementId
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_complementId", "complementId", 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.getComplementId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.setComplementId( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _complementId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _width
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasWidth()) { return null; }
-                return new java.lang.Integer(target.getWidth());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteWidth();
-                        return;
-                    }
-                    target.setWidth( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _height
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasHeight()) { return null; }
-                return new java.lang.Integer(target.getHeight());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteHeight();
-                        return;
-                    }
-                    target.setHeight( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _xpos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasXpos()) { return null; }
-                return new java.lang.Integer(target.getXpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteXpos();
-                        return;
-                    }
-                    target.setXpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _ypos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                Viewport target = (Viewport) object;
-                if (!target.hasYpos()) { return null; }
-                return new java.lang.Integer(target.getYpos());
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteYpos();
-                        return;
-                    }
-                    target.setYpos( ((java.lang.Integer) value).intValue());
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.IntValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setMinInclusive(-2147483648);
-            typeValidator.setMaxInclusive(2147483647);
-        }
-        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 void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.removeAllHiddenColumns();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.HiddenColumns();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _hiddenColumnsList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-        //-- _calcIdParamList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.CalcIdParam.class, "_calcIdParamList", "calcIdParam", 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.getCalcIdParam();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.addCalcIdParam( (jalview.schemabinding.version2.CalcIdParam) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    Viewport target = (Viewport) object;
-                    target.removeAllCalcIdParam();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new jalview.schemabinding.version2.CalcIdParam();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setNameSpaceURI("www.jalview.org");
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _calcIdParamList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
+public class ViewportDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public ViewportDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "Viewport";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _conservationSelected
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_conservationSelected",
+            "conservationSelected",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasConservationSelected())
+        {
+          return null;
+        }
+        return (target.getConservationSelected() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteConservationSelected();
+            return;
+          }
+          target.setConservationSelected(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _conservationSelected
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pidSelected
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_pidSelected", "pidSelected",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasPidSelected())
+        {
+          return null;
+        }
+        return (target.getPidSelected() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePidSelected();
+            return;
+          }
+          target.setPidSelected(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _pidSelected
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _bgColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_bgColour", "bgColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getBgColour();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setBgColour((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _bgColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _consThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_consThreshold", "consThreshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasConsThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getConsThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteConsThreshold();
+            return;
+          }
+          target.setConsThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _consThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pidThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasPidThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getPidThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deletePidThreshold();
+            return;
+          }
+          target.setPidThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _pidThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _title
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_title", "title",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getTitle();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setTitle((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _title
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showFullId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showFullId", "showFullId",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowFullId())
+        {
+          return null;
+        }
+        return (target.getShowFullId() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowFullId();
+            return;
+          }
+          target.setShowFullId(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showFullId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _rightAlignIds
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasRightAlignIds())
+        {
+          return null;
+        }
+        return (target.getRightAlignIds() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteRightAlignIds();
+            return;
+          }
+          target.setRightAlignIds(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _rightAlignIds
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showText
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showText", "showText",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowText())
+        {
+          return null;
+        }
+        return (target.getShowText() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowText();
+            return;
+          }
+          target.setShowText(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showColourText
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showColourText", "showColourText",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowColourText())
+        {
+          return null;
+        }
+        return (target.getShowColourText() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowColourText();
+            return;
+          }
+          target.setShowColourText(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showColourText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showUnconserved
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved",
+            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.hasShowUnconserved())
+        {
+          return null;
+        }
+        return (target.getShowUnconserved() ? 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.deleteShowUnconserved();
+            return;
+          }
+          target.setShowUnconserved(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showUnconserved
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showBoxes
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showBoxes", "showBoxes",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowBoxes())
+        {
+          return null;
+        }
+        return (target.getShowBoxes() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowBoxes();
+            return;
+          }
+          target.setShowBoxes(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showBoxes
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _wrapAlignment
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasWrapAlignment())
+        {
+          return null;
+        }
+        return (target.getWrapAlignment() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteWrapAlignment();
+            return;
+          }
+          target.setWrapAlignment(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _wrapAlignment
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _renderGaps
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_renderGaps", "renderGaps",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasRenderGaps())
+        {
+          return null;
+        }
+        return (target.getRenderGaps() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteRenderGaps();
+            return;
+          }
+          target.setRenderGaps(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _renderGaps
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showSequenceFeatures
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showSequenceFeatures",
+            "showSequenceFeatures",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowSequenceFeatures())
+        {
+          return null;
+        }
+        return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowSequenceFeatures();
+            return;
+          }
+          target.setShowSequenceFeatures(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showSequenceFeatures
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showNPfeatureTooltip
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showNPfeatureTooltip",
+            "showNPfeatureTooltip",
+            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.hasShowNPfeatureTooltip())
+        {
+          return null;
+        }
+        return (target.getShowNPfeatureTooltip() ? 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.deleteShowNPfeatureTooltip();
+            return;
+          }
+          target.setShowNPfeatureTooltip(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showNPfeatureTooltip
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showDbRefTooltip
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showDbRefTooltip",
+            "showDbRefTooltip", 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.hasShowDbRefTooltip())
+        {
+          return null;
+        }
+        return (target.getShowDbRefTooltip() ? 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.deleteShowDbRefTooltip();
+            return;
+          }
+          target.setShowDbRefTooltip(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showDbRefTooltip
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _followHighlight
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_followHighlight", "followHighlight",
+            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.hasFollowHighlight())
+        {
+          return null;
+        }
+        return (target.getFollowHighlight() ? 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.deleteFollowHighlight();
+            return;
+          }
+          target.setFollowHighlight(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _followHighlight
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _followSelection
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_followSelection", "followSelection",
+            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.hasFollowSelection())
+        {
+          return null;
+        }
+        return (target.getFollowSelection() ? 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.deleteFollowSelection();
+            return;
+          }
+          target.setFollowSelection(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _followSelection
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showAnnotation
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasShowAnnotation())
+        {
+          return null;
+        }
+        return (target.getShowAnnotation() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteShowAnnotation();
+            return;
+          }
+          target.setShowAnnotation(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showAnnotation
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _centreColumnLabels
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_centreColumnLabels",
+            "centreColumnLabels", 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.hasCentreColumnLabels())
+        {
+          return null;
+        }
+        return (target.getCentreColumnLabels() ? 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.deleteCentreColumnLabels();
+            return;
+          }
+          target.setCentreColumnLabels(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _centreColumnLabels
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showGroupConservation
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showGroupConservation",
+            "showGroupConservation",
+            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.hasShowGroupConservation())
+        {
+          return null;
+        }
+        return (target.getShowGroupConservation() ? 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.deleteShowGroupConservation();
+            return;
+          }
+          target.setShowGroupConservation(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showGroupConservation
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showGroupConsensus
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showGroupConsensus",
+            "showGroupConsensus", 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.hasShowGroupConsensus())
+        {
+          return null;
+        }
+        return (target.getShowGroupConsensus() ? 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.deleteShowGroupConsensus();
+            return;
+          }
+          target.setShowGroupConsensus(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showGroupConsensus
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _showConsensusHistogram
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showConsensusHistogram",
+            "showConsensusHistogram",
+            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.hasShowConsensusHistogram())
+        {
+          return null;
+        }
+        return (target.getShowConsensusHistogram() ? 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.deleteShowConsensusHistogram();
+            return;
+          }
+          target.setShowConsensusHistogram(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showConsensusHistogram
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _showSequenceLogo
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_showSequenceLogo",
+            "showSequenceLogo", 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.hasShowSequenceLogo())
+        {
+          return null;
+        }
+        return (target.getShowSequenceLogo() ? 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.deleteShowSequenceLogo();
+            return;
+          }
+          target.setShowSequenceLogo(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _showSequenceLogo
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _normaliseSequenceLogo
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_normaliseSequenceLogo",
+            "normaliseSequenceLogo",
+            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.hasNormaliseSequenceLogo())
+        {
+          return null;
+        }
+        return (target.getNormaliseSequenceLogo() ? 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.deleteNormaliseSequenceLogo();
+            return;
+          }
+          target.setNormaliseSequenceLogo(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _normaliseSequenceLogo
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _ignoreGapsinConsensus
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_ignoreGapsinConsensus",
+            "ignoreGapsinConsensus",
+            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.hasIgnoreGapsinConsensus())
+        {
+          return null;
+        }
+        return (target.getIgnoreGapsinConsensus() ? 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.deleteIgnoreGapsinConsensus();
+            return;
+          }
+          target.setIgnoreGapsinConsensus(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _ignoreGapsinConsensus
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _startRes
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_startRes", "startRes",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasStartRes())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getStartRes());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteStartRes();
+            return;
+          }
+          target.setStartRes(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _startRes
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _startSeq
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_startSeq", "startSeq",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasStartSeq())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getStartSeq());
+      }
 
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteStartSeq();
+            return;
+          }
+          target.setStartSeq(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    // -- validation code for: _startSeq
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _fontName
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_fontName", "fontName",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getFontName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setFontName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _fontSize
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontSize", "fontSize",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasFontSize())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getFontSize());
+      }
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontSize();
+            return;
+          }
+          target.setFontSize(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _fontSize
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _fontStyle
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_fontStyle", "fontStyle",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasFontStyle())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getFontStyle());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteFontStyle();
+            return;
+          }
+          target.setFontStyle(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.Viewport.class;
+    // -- validation code for: _fontStyle
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _scaleProteinAsCdna
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_scaleProteinAsCdna",
+            "scaleProteinAsCdna", 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.hasScaleProteinAsCdna())
+        {
+          return null;
+        }
+        return (target.getScaleProteinAsCdna() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteScaleProteinAsCdna();
+            return;
+          }
+          target.setScaleProteinAsCdna(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _scaleProteinAsCdna
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    desc.setValidator(fieldValidator);
+    // -- _viewName
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_viewName", "viewName",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getViewName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setViewName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _viewName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _sequenceSetId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_sequenceSetId", "sequenceSetId",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getSequenceSetId();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setSequenceSetId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _sequenceSetId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    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);
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteGatheredViews();
+            return;
+          }
+          target.setGatheredViews(((java.lang.Boolean) value)
+                  .booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _gatheredViews
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
     }
+    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());
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextCol1();
+            return;
+          }
+          target.setTextCol1(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _textCol1
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
     }
+    desc.setValidator(fieldValidator);
+    // -- _textCol2
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textCol2", "textCol2",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasTextCol2())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getTextCol2());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextCol2();
+            return;
+          }
+          target.setTextCol2(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _textCol2
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _textColThreshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_textColThreshold",
+            "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasTextColThreshold())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getTextColThreshold());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteTextColThreshold();
+            return;
+          }
+          target.setTextColThreshold(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _textColThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            org.exolab.castor.xml.NodeType.Attribute);
+    super.setIdentity(desc);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) 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 new java.lang.String();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IdValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IdValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _complementId
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_complementId", "complementId",
+            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.getComplementId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.setComplementId((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _complementId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _width
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_width", "width",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasWidth())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getWidth());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteWidth();
+            return;
+          }
+          target.setWidth(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _height
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_height", "height",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasHeight())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getHeight());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHeight();
+            return;
+          }
+          target.setHeight(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _xpos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_xpos", "xpos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasXpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getXpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteXpos();
+            return;
+          }
+          target.setXpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _ypos
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_ypos", "ypos",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Viewport target = (Viewport) object;
+        if (!target.hasYpos())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getYpos());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteYpos();
+            return;
+          }
+          target.setYpos(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    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 void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.removeAllHiddenColumns();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.HiddenColumns();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _hiddenColumnsList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _calcIdParamList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.CalcIdParam.class,
+            "_calcIdParamList", "calcIdParam",
+            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.getCalcIdParam();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.addCalcIdParam((jalview.schemabinding.version2.CalcIdParam) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          Viewport target = (Viewport) object;
+          target.removeAllCalcIdParam();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.CalcIdParam();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _calcIdParamList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Viewport.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java
index 8c61a2d..beb5b50 100644
--- a/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.WebServiceParameterSet;
@@ -18,337 +18,379 @@ import jalview.schemabinding.version2.WebServiceParameterSet;
  * 
  * @version $Revision$ $Date$
  */
-public class WebServiceParameterSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _elementDefinition.
-     */
-    private boolean _elementDefinition;
-
-    /**
-     * Field _nsPrefix.
-     */
-    private java.lang.String _nsPrefix;
-
-    /**
-     * Field _nsURI.
-     */
-    private java.lang.String _nsURI;
-
-    /**
-     * Field _xmlName.
-     */
-    private java.lang.String _xmlName;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public WebServiceParameterSetDescriptor() {
-        super();
-        _nsURI = "www.jalview.org/xml/wsparamset";
-        _xmlName = "WebServiceParameterSet";
-        _elementDefinition = false;
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.mapping.FieldHandler             handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- _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
-            {
-                WebServiceParameterSet target = (WebServiceParameterSet) object;
-                return target.getName();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    WebServiceParameterSet target = (WebServiceParameterSet) object;
-                    target.setName( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _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
-            {
-                WebServiceParameterSet target = (WebServiceParameterSet) object;
-                return target.getVersion();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    WebServiceParameterSet target = (WebServiceParameterSet) object;
-                    target.setVersion( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _version
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _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
-            {
-                WebServiceParameterSet target = (WebServiceParameterSet) object;
-                return target.getDescription();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    WebServiceParameterSet target = (WebServiceParameterSet) object;
-                    target.setDescription( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
-        }
-        desc.setValidator(fieldValidator);
-        //-- _serviceURLList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_serviceURLList", "serviceURL", org.exolab.castor.xml.NodeType.Element);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                WebServiceParameterSet target = (WebServiceParameterSet) object;
-                return target.getServiceURL();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    WebServiceParameterSet target = (WebServiceParameterSet) object;
-                    target.addServiceURL( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
-                try {
-                    WebServiceParameterSet target = (WebServiceParameterSet) object;
-                    target.removeAllServiceURL();
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return new java.lang.String();
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _serviceURLList
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
-        //-- _parameters
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_parameters", "parameters", 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
-            {
-                WebServiceParameterSet target = (WebServiceParameterSet) object;
-                return target.getParameters();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    WebServiceParameterSet target = (WebServiceParameterSet) object;
-                    target.setParameters( (java.lang.String) value);
-                } catch (java.lang.Exception ex) {
-                    throw new IllegalStateException(ex.toString());
-                }
-            }
-            public java.lang.Object newInstance(java.lang.Object parent) {
-                return null;
-            }
-        };
-        desc.setHandler(handler);
-        desc.setRequired(true);
-        desc.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _parameters
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            org.exolab.castor.xml.validators.StringValidator typeValidator;
-            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-            fieldValidator.setValidator(typeValidator);
-            typeValidator.setWhiteSpace("preserve");
+public class WebServiceParameterSetDescriptor extends
+        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public WebServiceParameterSetDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org/xml/wsparamset";
+    _xmlName = "WebServiceParameterSet";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _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
+      {
+        WebServiceParameterSet target = (WebServiceParameterSet) object;
+        return target.getName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          WebServiceParameterSet target = (WebServiceParameterSet) object;
+          target.setName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
 
+    // -- _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
+      {
+        WebServiceParameterSet target = (WebServiceParameterSet) object;
+        return target.getVersion();
+      }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          WebServiceParameterSet target = (WebServiceParameterSet) object;
+          target.setVersion((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getAccessMode.
-     * 
-     * @return the access mode specified for this class.
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode(
-    ) {
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    }
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getIdentity.
-     * 
-     * @return the identity field, null if this class has no
-     * identity.
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
-    ) {
-        return super.getIdentity();
+    // -- validation code for: _version
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _description
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_description", "description",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        WebServiceParameterSet target = (WebServiceParameterSet) object;
+        return target.getDescription();
+      }
 
-    /**
-     * Method getJavaClass.
-     * 
-     * @return the Java class represented by this descriptor.
-     */
-    public java.lang.Class getJavaClass(
-    ) {
-        return jalview.schemabinding.version2.WebServiceParameterSet.class;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          WebServiceParameterSet target = (WebServiceParameterSet) object;
+          target.setDescription((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getNameSpacePrefix.
-     * 
-     * @return the namespace prefix to use when marshaling as XML.
-     */
-    public java.lang.String getNameSpacePrefix(
-    ) {
-        return _nsPrefix;
-    }
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
 
-    /**
-     * Method getNameSpaceURI.
-     * 
-     * @return the namespace URI used when marshaling and
-     * unmarshaling as XML.
-     */
-    public java.lang.String getNameSpaceURI(
-    ) {
-        return _nsURI;
+    // -- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+    // -- _serviceURLList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_serviceURLList", "serviceURL",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        WebServiceParameterSet target = (WebServiceParameterSet) object;
+        return target.getServiceURL();
+      }
 
-    /**
-     * Method getValidator.
-     * 
-     * @return a specific validator for the class described by this
-     * ClassDescriptor.
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator(
-    ) {
-        return this;
-    }
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          WebServiceParameterSet target = (WebServiceParameterSet) object;
+          target.addServiceURL((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
 
-    /**
-     * Method getXMLName.
-     * 
-     * @return the XML Name for the Class being described.
-     */
-    public java.lang.String getXMLName(
-    ) {
-        return _xmlName;
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          WebServiceParameterSet target = (WebServiceParameterSet) object;
+          target.removeAllServiceURL();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new java.lang.String();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _serviceURLList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
     }
+    desc.setValidator(fieldValidator);
+    // -- _parameters
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_parameters", "parameters",
+            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
+      {
+        WebServiceParameterSet target = (WebServiceParameterSet) object;
+        return target.getParameters();
+      }
 
-    /**
-     * Method isElementDefinition.
-     * 
-     * @return true if XML schema definition of this Class is that
-     * of a global
-     * element or element with anonymous type definition.
-     */
-    public boolean isElementDefinition(
-    ) {
-        return _elementDefinition;
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          WebServiceParameterSet target = (WebServiceParameterSet) object;
+          target.setParameters((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _parameters
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
     }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.WebServiceParameterSet.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
 
 }
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 133dd36..89b8f07 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -53,12 +53,14 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private boolean predefinedColours = false;
 
   private boolean seqAssociated = false;
+
   /**
    * false if the scheme was constructed without a minColour and maxColour used
    * to decide if existing colours should be taken from annotation elements when
    * they exist
    */
   private boolean noGradient = false;
+
   IdentityHashMap seqannot = null;
 
   @Override
@@ -175,7 +177,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
       // resolve the context containing all the annotation for the sequence
       AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
               : alignment.getContext();
-      boolean f = true,rna=false;
+      boolean f = true, rna = false;
       for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
               .getCalcId()))
       {
@@ -207,6 +209,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
   }
 
   float aamin = 0f, aamax = 0f;
+
   public String getAnnotation()
   {
     return annotation.label;
@@ -266,8 +269,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
   public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour = Color.white;
-    AlignmentAnnotation annotation = (seqAssociated && seqannot!=null ? seqannot.get(seq)
-            : this.annotation);
+    AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
+            .get(seq) : this.annotation);
     if (annotation == null)
     {
       return currentColour;
@@ -396,6 +399,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
     return new Color(dr, dg, db);
 
   }
+
   public boolean isPredefinedColours()
   {
     return predefinedColours;
diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index e85c51d..3c68da0 100755
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -20,7 +20,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 1604da7..effdf59 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -20,15 +20,13 @@
  */
 package jalview.schemes;
 
-import java.awt.Color;
-import java.util.Map;
-
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
+import java.awt.Color;
+import java.util.Map;
+
 public interface ColourSchemeI
 {
   /**
diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index 582faeb..49d5dee 100644
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -20,11 +20,11 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
-import java.util.Hashtable;
-
 import jalview.datamodel.AlignmentAnnotation;
 
+import java.awt.Color;
+import java.util.Hashtable;
+
 /**
  * Became RNAHelicesColour.java. Placeholder for true covariation color scheme
  * 
diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index 143d0f4..1242cd3 100755
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -20,7 +20,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 public class HelixColourScheme extends ScoreColourScheme
 {
diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java
index 1c776a9..055000f 100755
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -20,7 +20,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index 9c43ed1..d2b878d 100644
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -20,7 +20,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * Class is based off of NucleotideColourScheme
diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index ffc013d..d17f510 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -40,7 +40,6 @@ import java.util.Map;
 public class RNAHelicesColour extends ResidueColourScheme
 {
 
-
   /**
    * Maps sequence positions to the RNA helix they belong to. Key: position,
    * Value: helix TODO: Revise or drop in favour of annotation position numbers
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index e3118ad..bca98cf 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -324,7 +324,9 @@ public class ResidueColourScheme implements ColourSchemeI
       return getClass().newInstance();
     } catch (Exception q)
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_duplicate_colour_scheme", new String[]{getClass().getName()}), q);
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_cannot_duplicate_colour_scheme",
+              new String[] { getClass().getName() }), q);
     }
   }
 }
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index ce83875..de99987 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -298,9 +298,9 @@ public class ResidueProperties
     aa2Triplet.put("v", "VAL");
   }
 
-  public static final String[] aa =
-  { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
-      "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " " };
+  public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E",
+      "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B",
+      "Z", "X", "_", "*", ".", " " };
 
   public static final Color midBlue = new Color(100, 100, 255);
 
@@ -320,8 +320,8 @@ public class ResidueProperties
     scaleColours.addElement(Color.white);
   }
 
-  public static final Color[] taylor =
-  { new Color(204, 255, 0), // A Greenish-yellowy-yellow
+  public static final Color[] taylor = { new Color(204, 255, 0), // A
+                                                                 // Greenish-yellowy-yellow
       new Color(0, 0, 255), // R Blueish-bluey-blue
       new Color(204, 0, 255), // N Blueish-reddy-blue
       new Color(255, 0, 0), // D Reddish-reddy-red
@@ -349,8 +349,7 @@ public class ResidueProperties
       Color.white // .
   };
 
-  public static final Color[] nucleotide =
-  { new Color(100, 247, 63), // A
+  public static final Color[] nucleotide = { new Color(100, 247, 63), // A
       new Color(255, 179, 64), // C
       new Color(235, 65, 60), // G
       new Color(60, 136, 238), // T
@@ -364,16 +363,15 @@ public class ResidueProperties
   };
 
   // Added for PurinePyrimidineColourScheme
-  public static final Color[] purinepyrimidine =
-  { new Color(255, 131, 250), // A, G, R purines purplish/orchid
+  public static final Color[] purinepyrimidine = {
+      new Color(255, 131, 250), // A, G, R purines purplish/orchid
       new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise
       Color.white, // all other nucleotides
       Color.white // Gap
   };
 
   // Zappo
-  public static final Color[] zappo =
-  { Color.pink, // A
+  public static final Color[] zappo = { Color.pink, // A
       midBlue, // R
       Color.green, // N
       Color.red, // D
@@ -403,8 +401,7 @@ public class ResidueProperties
   };
 
   // Dunno where I got these numbers from
-  public static final double[] hyd2 =
-  { 0.62, // A
+  public static final double[] hyd2 = { 0.62, // A
       0.29, // R
       -0.90, // N
       -0.74, // D
@@ -429,34 +426,33 @@ public class ResidueProperties
       0.0 // X
   };
 
-  public static final double[] helix =
-  { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
-      1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
+  public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70,
+      1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77,
+      0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
 
   public static final double helixmin = 0.57;
 
   public static final double helixmax = 1.51;
 
-  public static final double[] strand =
-  { 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
-      1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
+  public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19,
+      1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75,
+      1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
 
   public static final double strandmin = 0.37;
 
   public static final double strandmax = 1.7;
 
-  public static final double[] turn =
-  { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
-      0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0,
-      0 };
+  public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98,
+      0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96,
+      0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 };
 
   public static final double turnmin = 0.47;
 
   public static final double turnmax = 1.56;
 
-  public static final double[] buried =
-  { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,
-      0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00 };
+  public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3,
+      0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5,
+      2.9, 0.4, 0.3, 1.358, 0.00 };
 
   public static final double buriedmin = 0.05;
 
@@ -465,9 +461,9 @@ public class ResidueProperties
   // This is hydropathy index
   // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
   // 1157, 105-132, 1982
-  public static final double[] hyd =
-  { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9,
-      1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
+  public static final double[] hyd = { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5,
+      -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9,
+      -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
 
   public static final double hydmax = 4.5;
 
@@ -475,8 +471,7 @@ public class ResidueProperties
 
   // public static final double hydmax = 1.38;
   // public static final double hydmin = -2.53;
-  private static final int[][] BLOSUM62 =
-  {
+  private static final int[][] BLOSUM62 = {
       { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
           -2, 0, -2, -1, 0, -4 },
       { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3,
@@ -526,8 +521,7 @@ public class ResidueProperties
       { -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
           -4, -4, -4, -4, -4, -4, 1 }, };
 
-  static final int[][] PAM250 =
-  {
+  static final int[][] PAM250 = {
       { 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3,
           0, 0, 0, 0, -8 },
       { -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
@@ -603,9 +597,7 @@ public class ResidueProperties
   // treats T and U identically. R and Y weak equivalence with AG and CTU.
   // N matches any other base weakly
   //
-  static final int[][] DNA =
-  {
-  { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A
+  static final int[][] DNA = { { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A
       { -8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1 }, // C
       { -8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1 }, // G
       { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // T
@@ -628,13 +620,12 @@ public class ResidueProperties
 
   }
 
-  public static final Color[] pidColours =
-  { midBlue, new Color(153, 153, 255),
+  public static final Color[] pidColours = { midBlue,
+      new Color(153, 153, 255),
       // Color.lightGray,
       new Color(204, 204, 255), };
 
-  public static final float[] pidThresholds =
-  { 80, 60, 40, };
+  public static final float[] pidThresholds = { 80, 60, 40, };
 
   public static Map> codonHash = new HashMap>();
 
@@ -728,28 +719,17 @@ public class ResidueProperties
     /*
      * Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
      */
-    ambiguityCodes.put("R", new String[]
-    { "A", "G" });
-    ambiguityCodes.put("Y", new String[]
-    { "T", "C" });
-    ambiguityCodes.put("W", new String[]
-    { "A", "T" });
-    ambiguityCodes.put("S", new String[]
-    { "G", "C" });
-    ambiguityCodes.put("M", new String[]
-    { "A", "C" });
-    ambiguityCodes.put("K", new String[]
-    { "G", "T" });
-    ambiguityCodes.put("H", new String[]
-    { "A", "T", "C" });
-    ambiguityCodes.put("B", new String[]
-    { "G", "T", "C" });
-    ambiguityCodes.put("V", new String[]
-    { "G", "A", "C" });
-    ambiguityCodes.put("D", new String[]
-    { "G", "A", "T" });
-    ambiguityCodes.put("N", new String[]
-    { "G", "A", "T", "C" });
+    ambiguityCodes.put("R", new String[] { "A", "G" });
+    ambiguityCodes.put("Y", new String[] { "T", "C" });
+    ambiguityCodes.put("W", new String[] { "A", "T" });
+    ambiguityCodes.put("S", new String[] { "G", "C" });
+    ambiguityCodes.put("M", new String[] { "A", "C" });
+    ambiguityCodes.put("K", new String[] { "G", "T" });
+    ambiguityCodes.put("H", new String[] { "A", "T", "C" });
+    ambiguityCodes.put("B", new String[] { "G", "T", "C" });
+    ambiguityCodes.put("V", new String[] { "G", "A", "C" });
+    ambiguityCodes.put("D", new String[] { "G", "A", "T" });
+    ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" });
 
     // Now build codon translation table
     codonHash2.put("AAA", "K");
@@ -888,8 +868,7 @@ public class ResidueProperties
         }
         else
         {
-          acodon[i] = new String[]
-          {};
+          acodon[i] = new String[] {};
         }
       }
       // enumerate all combinations and test for veracity of translation
@@ -911,8 +890,7 @@ public class ResidueProperties
           if (acodon[ipos].length == 0 || tpos[ipos] < 0)
           {
             _acodon += codon.charAt(ipos);
-            allres[ipos] = new char[]
-            { codon.charAt(ipos) };
+            allres[ipos] = new char[] { codon.charAt(ipos) };
           }
           else
           {
@@ -1389,8 +1367,7 @@ public class ResidueProperties
         propMatrixF[i][j] = 0;
         propMatrixPos[i][j] = 0;
         propMatrixEpos[i][j] = 0;
-        for (Enumeration en = propHash.keys(); en
-                .hasMoreElements();)
+        for (Enumeration en = propHash.keys(); en.hasMoreElements();)
         {
           String ph = en.nextElement();
           Map pph = (Map) propHash
@@ -1808,6 +1785,7 @@ public class ResidueProperties
     }
     System.out.println("};");
   }
+
   // to here
 
   /**
@@ -1836,7 +1814,9 @@ public class ResidueProperties
           result.add(nuc);
         }
       }
-    } else {
+    }
+    else
+    {
       /*
        * Peptide
        */
diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index fe56ff5..1340de3 100755
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -20,7 +20,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 48c52f1..62f3a2e 100644
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -20,7 +20,6 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -33,7 +32,6 @@ import java.awt.Color;
 import java.util.ArrayList;
 import java.util.IdentityHashMap;
 import java.util.Map;
-import java.util.TreeMap;
 
 /**
  * Defines the color score for T-Coffee MSA
@@ -47,8 +45,7 @@ import java.util.TreeMap;
 public class TCoffeeColourScheme extends ResidueColourScheme
 {
 
-  static final Color[] colors =
-  { new Color(102, 102, 255), // #6666FF
+  static final Color[] colors = { new Color(102, 102, 255), // #6666FF
       new Color(0, 255, 0), // #00FF00
       new Color(102, 255, 0), // #66FF00
       new Color(204, 255, 0), // #CCFF00
diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index 428bfc9..22422ff 100755
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -20,7 +20,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 80efaca..92989fb 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -20,14 +20,14 @@
  */
 package jalview.schemes;
 
-import java.awt.Color;
-import java.util.Map;
-import java.util.StringTokenizer;
-
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
+import java.awt.Color;
+import java.util.Map;
+import java.util.StringTokenizer;
+
 public class UserColourScheme extends ResidueColourScheme
 {
   Color[] lowerCaseColours;
diff --git a/src/jalview/structure/SequenceListener.java b/src/jalview/structure/SequenceListener.java
index cb65032..771b8a0 100644
--- a/src/jalview/structure/SequenceListener.java
+++ b/src/jalview/structure/SequenceListener.java
@@ -22,7 +22,6 @@ package jalview.structure;
 
 import jalview.datamodel.SequenceI;
 
-
 public interface SequenceListener
 {
   // TODO remove this? never called on SequenceListener type
diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
index 2364549..e5c5d04 100644
--- a/src/jalview/structure/StructureListener.java
+++ b/src/jalview/structure/StructureListener.java
@@ -20,10 +20,10 @@
  */
 package jalview.structure;
 
-import java.util.List;
-
 import jalview.datamodel.SequenceI;
 
+import java.util.List;
+
 public interface StructureListener
 {
   /**
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 4359877..26b7d48 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -514,7 +514,8 @@ public class StructureSelectionManager
           resNum = tmp.resNumber;
           if (tmp.alignmentMapping >= -1)
           {
-            // TODO (JAL-1836) address root cause: negative residue no in PDB file
+            // TODO (JAL-1836) address root cause: negative residue no in PDB
+            // file
             mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
             mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
           }
@@ -719,7 +720,7 @@ public class StructureSelectionManager
               {
                 results = MappingUtils.buildSearchResults(seq, index,
                         seqmappings);
-               }
+              }
               if (handlingVamsasMo)
               {
                 results.addResult(seq, index, index);
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index b844b52..3c40414 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -1,9 +1,5 @@
 package jalview.structures.models;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
@@ -15,6 +11,10 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * 
  * A base class to hold common function for protein structure model binding.
@@ -202,7 +202,9 @@ public abstract class AAStructureBindingModel extends
   /**
    * Construct a title string for the viewer window based on the data Jalview
    * knows about
-   * @param viewerName TODO
+   * 
+   * @param viewerName
+   *          TODO
    * @param verbose
    * 
    * @return
@@ -210,8 +212,7 @@ public abstract class AAStructureBindingModel extends
   public String getViewerTitle(String viewerName, boolean verbose)
   {
     if (getSequence() == null || getSequence().length < 1
-            || getPdbCount() < 1
-            || getSequence()[0].length < 1)
+            || getPdbCount() < 1 || getSequence()[0].length < 1)
     {
       return ("Jalview " + viewerName + " Window");
     }
@@ -220,9 +221,8 @@ public abstract class AAStructureBindingModel extends
     StringBuilder title = new StringBuilder(64);
     final PDBEntry pdbEntry = getPdbEntry(0);
     title.append(viewerName + " view for " + getSequence()[0][0].getName()
-            + ":"
-            + pdbEntry.getId());
-  
+            + ":" + pdbEntry.getId());
+
     if (verbose)
     {
       if (pdbEntry.getProperty() != null)
@@ -268,8 +268,7 @@ public abstract class AAStructureBindingModel extends
     {
       throw new Error(MessageManager.formatMessage(
               "error.implementation_error_no_pdbentry_from_index",
-              new Object[]
-              { Integer.valueOf(pe).toString() }));
+              new Object[] { Integer.valueOf(pe).toString() }));
     }
     final String nullChain = "TheNullChain";
     List s = new ArrayList();
@@ -339,8 +338,8 @@ public abstract class AAStructureBindingModel extends
    * 
    * @returns the pdb entries added to the current set.
    */
-  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq,
-          String[][] chns)
+  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+          SequenceI[][] seq, String[][] chns)
   {
     List v = new ArrayList();
     List rtn = new ArrayList();
@@ -353,8 +352,7 @@ public abstract class AAStructureBindingModel extends
       int r = v.indexOf(pdbe[i]);
       if (r == -1 || r >= getPdbCount())
       {
-        rtn.add(new int[]
-        { v.size(), i });
+        rtn.add(new int[] { v.size(), i });
         v.add(pdbe[i]);
       }
       else
diff --git a/src/jalview/util/AWTConsole.java b/src/jalview/util/AWTConsole.java
index 3b95f8a..7a585be 100644
--- a/src/jalview/util/AWTConsole.java
+++ b/src/jalview/util/AWTConsole.java
@@ -30,9 +30,23 @@ package jalview.util;
 //
 // RJHM van den Bergh , rvdb@comweb.nl
 
-import java.io.*;
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.GraphicsEnvironment;
+import java.awt.Panel;
+import java.awt.TextArea;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.io.IOException;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
+import java.io.PrintStream;
 
 public class AWTConsole extends WindowAdapter implements WindowListener,
         ActionListener, Runnable
@@ -223,7 +237,8 @@ public class AWTConsole extends WindowAdapter implements WindowListener,
       } catch (InterruptedException ie)
       {
       }
-      throw new NullPointerException(MessageManager.getString("exception.application_test_npe"));
+      throw new NullPointerException(
+              MessageManager.getString("exception.application_test_npe"));
     }
 
   }
diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index cd9c969..4a0b80a 100755
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -20,8 +20,12 @@
  */
 package jalview.util;
 
-import java.io.*;
-import java.lang.reflect.*;
+import java.io.File;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
 
 /**
  * BrowserLauncher is a class that provides one static method, openURL, which
@@ -334,23 +338,19 @@ public class BrowserLauncher
         aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
 
         aeTargetConstructor = aeTargetClass
-                .getDeclaredConstructor(new Class[]
-                { int.class });
+                .getDeclaredConstructor(new Class[] { int.class });
         appleEventConstructor = appleEventClass
-                .getDeclaredConstructor(new Class[]
-                { int.class, int.class, aeTargetClass, int.class, int.class });
-        aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[]
-        { String.class });
+                .getDeclaredConstructor(new Class[] { int.class, int.class,
+                    aeTargetClass, int.class, int.class });
+        aeDescConstructor = aeDescClass
+                .getDeclaredConstructor(new Class[] { String.class });
 
         makeOSType = osUtilsClass.getDeclaredMethod("makeOSType",
-                new Class[]
-                { String.class });
+                new Class[] { String.class });
         putParameter = appleEventClass.getDeclaredMethod("putParameter",
-                new Class[]
-                { int.class, aeDescClass });
+                new Class[] { int.class, aeDescClass });
         sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply",
-                new Class[]
-                {});
+                new Class[] {});
 
         Field keyDirectObjectField = aeClass
                 .getDeclaredField("keyDirectObject");
@@ -399,14 +399,11 @@ public class BrowserLauncher
                 .getDeclaredField("kSystemFolderType");
         kSystemFolderType = systemFolderField.get(null);
         findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder",
-                new Class[]
-                { mrjOSTypeClass });
+                new Class[] { mrjOSTypeClass });
         getFileCreator = mrjFileUtilsClass.getDeclaredMethod(
-                "getFileCreator", new Class[]
-                { File.class });
+                "getFileCreator", new Class[] { File.class });
         getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType",
-                new Class[]
-                { File.class });
+                new Class[] { File.class });
       } catch (ClassNotFoundException cnfe)
       {
         errorMessage = cnfe.getMessage();
@@ -441,10 +438,10 @@ public class BrowserLauncher
       try
       {
         Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
-        Constructor constructor = linker.getConstructor(new Class[]
-        { Class.class });
-        linkage = constructor.newInstance(new Object[]
-        { BrowserLauncher.class });
+        Constructor constructor = linker
+                .getConstructor(new Class[] { Class.class });
+        linkage = constructor
+                .newInstance(new Object[] { BrowserLauncher.class });
       } catch (ClassNotFoundException cnfe)
       {
         errorMessage = cnfe.getMessage();
@@ -480,8 +477,7 @@ public class BrowserLauncher
       {
         mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
         openURL = mrjFileUtilsClass.getDeclaredMethod("openURL",
-                new Class[]
-                { String.class });
+                new Class[] { String.class });
       } catch (ClassNotFoundException cnfe)
       {
         errorMessage = cnfe.getMessage();
@@ -528,14 +524,13 @@ public class BrowserLauncher
       try
       {
         Integer finderCreatorCode = (Integer) makeOSType.invoke(null,
-                new Object[]
-                { FINDER_CREATOR });
-        Object aeTarget = aeTargetConstructor.newInstance(new Object[]
-        { finderCreatorCode });
-        Integer gurlType = (Integer) makeOSType.invoke(null, new Object[]
-        { GURL_EVENT });
-        Object appleEvent = appleEventConstructor.newInstance(new Object[]
-        { gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
+                new Object[] { FINDER_CREATOR });
+        Object aeTarget = aeTargetConstructor
+                .newInstance(new Object[] { finderCreatorCode });
+        Integer gurlType = (Integer) makeOSType.invoke(null,
+                new Object[] { GURL_EVENT });
+        Object appleEvent = appleEventConstructor.newInstance(new Object[] {
+            gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
             kAnyTransactionID });
 
         // Don't set browser = appleEvent because then the next time we call
@@ -573,8 +568,8 @@ public class BrowserLauncher
 
       try
       {
-        systemFolder = (File) findFolder.invoke(null, new Object[]
-        { kSystemFolderType });
+        systemFolder = (File) findFolder.invoke(null,
+                new Object[] { kSystemFolderType });
       } catch (IllegalArgumentException iare)
       {
         browser = null;
@@ -615,13 +610,12 @@ public class BrowserLauncher
           // applications being picked up on certain Mac OS 9 systems,
           // especially German ones, and sending a GURL event to those
           // applications results in a logout under Multiple Users.
-          Object fileType = getFileType.invoke(null, new Object[]
-          { file });
+          Object fileType = getFileType.invoke(null, new Object[] { file });
 
           if (FINDER_TYPE.equals(fileType.toString()))
           {
-            Object fileCreator = getFileCreator.invoke(null, new Object[]
-            { file });
+            Object fileCreator = getFileCreator.invoke(null,
+                    new Object[] { file });
 
             if (FINDER_CREATOR.equals(fileCreator.toString()))
             {
@@ -702,14 +696,17 @@ public class BrowserLauncher
   {
     if (!loadedWithoutErrors)
     {
-      throw new IOException(MessageManager.formatMessage("exception.browser_not_found", new String[]{errorMessage}));
+      throw new IOException(MessageManager.formatMessage(
+              "exception.browser_not_found", new String[] { errorMessage }));
     }
 
     Object browser = locateBrowser();
 
     if (browser == null)
     {
-        throw new IOException(MessageManager.formatMessage("exception.browser_unable_to_locate", new String[]{errorMessage}));
+      throw new IOException(MessageManager.formatMessage(
+              "exception.browser_unable_to_locate",
+              new String[] { errorMessage }));
     }
 
     switch (jvm)
@@ -720,21 +717,25 @@ public class BrowserLauncher
 
       try
       {
-        aeDesc = aeDescConstructor.newInstance(new Object[]
-        { url });
-        putParameter.invoke(browser, new Object[]
-        { keyDirectObject, aeDesc });
-        sendNoReply.invoke(browser, new Object[]
-        {});
+        aeDesc = aeDescConstructor.newInstance(new Object[] { url });
+        putParameter.invoke(browser,
+                new Object[] { keyDirectObject, aeDesc });
+        sendNoReply.invoke(browser, new Object[] {});
       } catch (InvocationTargetException ite)
       {
-        throw new IOException(MessageManager.formatMessage("exception.invocation_target_exception_creating_aedesc", new String[]{ite.getMessage()}));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.invocation_target_exception_creating_aedesc",
+                new String[] { ite.getMessage() }));
       } catch (IllegalAccessException iae)
       {
-    	  throw new IOException(MessageManager.formatMessage("exception.illegal_access_building_apple_evt", new String[]{iae.getMessage()}));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.illegal_access_building_apple_evt", new String[]
+                { iae.getMessage() }));
       } catch (InstantiationException ie)
       {
-    	  throw new IOException(MessageManager.formatMessage("exception.illegal_access_building_apple_evt", new String[]{ie.getMessage()}));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.illegal_access_building_apple_evt", new String[]
+                { ie.getMessage() }));
       } finally
       {
         aeDesc = null; // Encourage it to get disposed if it was created
@@ -744,8 +745,7 @@ public class BrowserLauncher
       break;
 
     case MRJ_2_1:
-      Runtime.getRuntime().exec(new String[]
-      { (String) browser, url });
+      Runtime.getRuntime().exec(new String[] { (String) browser, url });
 
       break;
 
@@ -756,13 +756,11 @@ public class BrowserLauncher
 
       if (result == 0)
       {
-        int[] selectionStart = new int[]
-        { 0 };
+        int[] selectionStart = new int[] { 0 };
         byte[] urlBytes = url.getBytes();
-        int[] selectionEnd = new int[]
-        { urlBytes.length };
-        result = ICLaunchURL(instance[0], new byte[]
-        { 0 }, urlBytes, urlBytes.length, selectionStart, selectionEnd);
+        int[] selectionEnd = new int[] { urlBytes.length };
+        result = ICLaunchURL(instance[0], new byte[] { 0 }, urlBytes,
+                urlBytes.length, selectionStart, selectionEnd);
 
         if (result == 0)
         {
@@ -772,12 +770,16 @@ public class BrowserLauncher
         }
         else
         {
-          throw new IOException(MessageManager.formatMessage("exception.unable_to_launch_url", new String[]{Integer.valueOf(result).toString()}));
+          throw new IOException(MessageManager.formatMessage(
+                  "exception.unable_to_launch_url", new String[] { Integer
+                          .valueOf(result).toString() }));
         }
       }
       else
       {
-        throw new IOException(MessageManager.formatMessage("exception.unable_to_create_internet_config", new String[]{Integer.valueOf(result).toString()}));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.unable_to_create_internet_config",
+                new String[] { Integer.valueOf(result).toString() }));
       }
 
       break;
@@ -786,14 +788,17 @@ public class BrowserLauncher
 
       try
       {
-        openURL.invoke(null, new Object[]
-        { url });
+        openURL.invoke(null, new Object[] { url });
       } catch (InvocationTargetException ite)
       {
-        throw new IOException(MessageManager.formatMessage("exception.invocation_target_calling_url", new String[]{ite.getMessage()}));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.invocation_target_calling_url",
+                new String[] { ite.getMessage() }));
       } catch (IllegalAccessException iae)
       {
-          throw new IOException(MessageManager.formatMessage("exception.illegal_access_calling_url", new String[]{iae.getMessage()}));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.illegal_access_calling_url",
+                new String[] { iae.getMessage() }));
       }
 
       break;
@@ -804,8 +809,7 @@ public class BrowserLauncher
       // Add quotes around the URL to allow ampersands and other special
       // characters to work.
       Process process = Runtime.getRuntime().exec(
-              new String[]
-              { (String) browser, FIRST_WINDOWS_PARAMETER,
+              new String[] { (String) browser, FIRST_WINDOWS_PARAMETER,
                   SECOND_WINDOWS_PARAMETER, THIRD_WINDOWS_PARAMETER,
                   '"' + url + '"' });
 
@@ -818,7 +822,9 @@ public class BrowserLauncher
         process.exitValue();
       } catch (InterruptedException ie)
       {
-          throw new IOException(MessageManager.formatMessage("exception.interrupted_launching_browser", new String[]{ie.getMessage()}));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.interrupted_launching_browser",
+                new String[] { ie.getMessage() }));
       }
 
       break;
@@ -837,8 +843,7 @@ public class BrowserLauncher
        * NETSCAPE_OPEN_NEW_WINDOW + NETSCAPE_OPEN_PARAMETER_END);
        */
       process = Runtime.getRuntime().exec(
-              new String[]
-              {
+              new String[] {
                   (String) browser,
                   NETSCAPE_REMOTE_PARAMETER,
 
@@ -852,12 +857,13 @@ public class BrowserLauncher
 
         if (exitCode != 0)
         { // if Netscape was not open
-          Runtime.getRuntime().exec(new String[]
-          { (String) browser, url });
+          Runtime.getRuntime().exec(new String[] { (String) browser, url });
         }
       } catch (InterruptedException ie)
       {
-          throw new IOException(MessageManager.formatMessage("exception.interrupted_launching_browser", new String[]{ie.getMessage()}));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.interrupted_launching_browser",
+                new String[] { ie.getMessage() }));
       }
 
       break;
@@ -866,8 +872,7 @@ public class BrowserLauncher
 
       // This should never occur, but if it does, we'll try the simplest thing
       // possible
-      Runtime.getRuntime().exec(new String[]
-      { (String) browser, url });
+      Runtime.getRuntime().exec(new String[] { (String) browser, url });
 
       break;
     }
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 835a1b4..95f298b 100644
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -20,11 +20,11 @@
  */
 package jalview.util;
 
+import jalview.datamodel.SequenceI;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import jalview.datamodel.SequenceI;
-
 /**
  * Assorted methods for analysing or comparing sequences.
  */
@@ -40,8 +40,8 @@ public class Comparison
 
   private static final char GAP_DASH = '-';
 
-  public static final String GapChars = new String(new char[]
-  { GAP_SPACE, GAP_DOT, GAP_DASH });
+  public static final String GapChars = new String(new char[] { GAP_SPACE,
+      GAP_DOT, GAP_DASH });
 
   /**
    * DOCUMENT ME!
@@ -320,11 +320,13 @@ public class Comparison
     List flattened = new ArrayList();
     for (SequenceI[] ss : seqs)
     {
-      for (SequenceI s : ss) {
-      flattened.add(s);
+      for (SequenceI s : ss)
+      {
+        flattened.add(s);
       }
     }
-    final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened.size()]);
+    final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
+            .size()]);
     return isNucleotide(oneDArray);
   }
 }
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 123a4e1..518c310 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -118,8 +118,7 @@ public class DBRefUtils
     {
       return false;
     }
-    String coordsys = dasCoordinateSystemsLookup.get(string
-            .toLowerCase());
+    String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
     return coordsys == null ? false : coordsys.equals(dBRefEntry
             .getSource());
   }
@@ -139,8 +138,7 @@ public class DBRefUtils
     {
       return null;
     }
-    String canonical = canonicalSourceNameLookup.get(source
-            .toLowerCase());
+    String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
     return canonical == null ? source : canonical;
   }
 
@@ -436,7 +434,7 @@ public class DBRefUtils
         {
           String pdbid = r.stringMatched(1);
           String chaincode = r.stringMatched(2);
-          if (chaincode==null)
+          if (chaincode == null)
           {
             chaincode = " ";
           }
@@ -455,8 +453,10 @@ public class DBRefUtils
           pdbr.setChainCode(chaincode);
           // pdbr.getProperty().put("CHAIN", chaincode);
           seq.addPDBId(pdbr);
-        } else {
-          System.err.println("Malformed PDB DR line:"+acn);
+        }
+        else
+        {
+          System.err.println("Malformed PDB DR line:" + acn);
         }
       }
       else
diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index 4900fc8..e2e83a4 100644
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -24,7 +24,6 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
 import java.util.Hashtable;
-import java.util.Vector;
 
 public class GroupUrlLink
 {
@@ -83,8 +82,7 @@ public class GroupUrlLink
   {
     if (tokens == null)
     {
-      tokens = new String[]
-      { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
+      tokens = new String[] { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
     }
   }
 
@@ -392,11 +390,12 @@ public class GroupUrlLink
     Hashtable rstrings = new Hashtable();
     rstrings.put(tokens[0], idstrings);
     rstrings.put(tokens[1], seqstrings);
-    rstrings.put(tokens[2], new String[]
-    { dsstring });
+    rstrings.put(tokens[2], new String[] { dsstring });
     if (idstrings.length != seqstrings.length)
     {
-      throw new Error(MessageManager.getString("error.idstring_seqstrings_only_one_per_sequence"));
+      throw new Error(
+              MessageManager
+                      .getString("error.idstring_seqstrings_only_one_per_sequence"));
     }
     return rstrings;
   }
@@ -423,9 +422,8 @@ public class GroupUrlLink
     Object[] stubs = makeUrlsIf(false, rstrings, b);
     if (stubs != null)
     {
-      return new Object[]
-      { stubs[0], stubs[1], rstrings, new boolean[]
-      { b } };
+      return new Object[] { stubs[0], stubs[1], rstrings,
+          new boolean[] { b } };
     }
     // TODO Auto-generated method stub
     return null;
@@ -486,14 +484,19 @@ public class GroupUrlLink
         {
           if (maxs != idseq[i].length)
           {
-            throw new Error(MessageManager.formatMessage("error.cannot_have_mixed_length_replacement_vectors",
-            			new String[]{(mtch[i]), Integer.valueOf(idseq[i].length).toString(),Integer.valueOf(maxs).toString()}));
+            throw new Error(MessageManager.formatMessage(
+                    "error.cannot_have_mixed_length_replacement_vectors",
+                    new String[] { (mtch[i]),
+                        Integer.valueOf(idseq[i].length).toString(),
+                        Integer.valueOf(maxs).toString() }));
           }
         }
       }
       else
       {
-        throw new Error(MessageManager.getString("error.cannot_have_zero_length_vector_replacement_strings"));
+        throw new Error(
+                MessageManager
+                        .getString("error.cannot_have_zero_length_vector_replacement_strings"));
       }
     }
     // iterate through input, collating segments to be inserted into url
@@ -689,9 +692,7 @@ public class GroupUrlLink
     {
       // just return the essential info about what the URL would be generated
       // from
-      return new Object[]
-      { new int[]
-      { seqsmatched }, thismatched };
+      return new Object[] { new int[] { seqsmatched }, thismatched };
     }
     // otherwise, create the URL completely.
 
@@ -706,10 +707,8 @@ public class GroupUrlLink
       }
     }
 
-    return new Object[]
-    { new int[]
-    { seqsmatched }, thismatched, matched, new String[]
-    { submiturl.toString() } };
+    return new Object[] { new int[] { seqsmatched }, thismatched, matched,
+        new String[] { submiturl.toString() } };
   }
 
   /**
@@ -817,8 +816,7 @@ public class GroupUrlLink
   public static void main(String argv[])
   {
     // note - JAL-1383 - these services are all dead
-    String[] links = new String[]
-    {
+    String[] links = new String[] {
         "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
         "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCES$&inputType=1|,",
         "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,",
@@ -834,8 +832,8 @@ public class GroupUrlLink
      */
     };
 
-    SequenceI[] seqs = new SequenceI[]
-    { new Sequence("StupidLabel:gi|9234|pdb|102L|A",
+    SequenceI[] seqs = new SequenceI[] { new Sequence(
+            "StupidLabel:gi|9234|pdb|102L|A",
             "asdiasdpasdpadpwpadasdpaspdw"), };
     String[][] seqsandids = formStrings(seqs);
     for (int i = 0; i < links.length; i++)
diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java
index 8abe965..e1543bf 100755
--- a/src/jalview/util/ImageMaker.java
+++ b/src/jalview/util/ImageMaker.java
@@ -89,7 +89,6 @@ public class ImageMaker
 
   }
 
-
   public ImageMaker(Component parent, TYPE type, String title, int width,
           int height, File file, String fileTitle)
   {
@@ -129,11 +128,10 @@ public class ImageMaker
         {
           setupPNG(width, height);
         }
-      
+
       } catch (Exception ex)
       {
-        System.out.println("Error creating "
- + type.getName() + " file.");
+        System.out.println("Error creating " + type.getName() + " file.");
       }
     }
   }
@@ -143,8 +141,6 @@ public class ImageMaker
     return graphics;
   }
 
-
-
   public void writeImage()
   {
     try
@@ -261,13 +257,14 @@ public class ImageMaker
   static JalviewFileChooser getPNGChooser()
   {
     if (Jalview.isHeadlessMode())
-  {
+    {
       return null;
     }
     return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "png" }, new String[]
-            { "Portable network graphics" }, "Portable network graphics");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "png" },
+            new String[] { "Portable network graphics" },
+            "Portable network graphics");
   }
 
   static JalviewFileChooser getEPSChooser()
@@ -277,20 +274,22 @@ public class ImageMaker
       return null;
     }
     return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "eps" }, new String[]
-            { "Encapsulated Postscript" }, "Encapsulated Postscript");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "eps" },
+            new String[] { "Encapsulated Postscript" },
+            "Encapsulated Postscript");
   }
 
   static JalviewFileChooser getSVGChooser()
   {
     if (Jalview.isHeadlessMode())
-  {
+    {
       return null;
     }
     return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "svg" }, new String[]
-            { "Scalable Vector Graphics" }, "Scalable Vector Graphics");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "svg" },
+            new String[] { "Scalable Vector Graphics" },
+            "Scalable Vector Graphics");
   }
 }
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 662240e..e456dab 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -202,8 +202,7 @@ public class MapList
       fromLowest = Math.min(fromLowest, from[i]);
       fromHighest = Math.max(fromHighest, from[i + 1]);
 
-      fromShifts.add(new int[]
-      { from[i], from[i + 1] });
+      fromShifts.add(new int[] { from[i], from[i + 1] });
     }
 
     toLowest = to[0];
@@ -212,8 +211,7 @@ public class MapList
     {
       toLowest = Math.min(toLowest, to[i]);
       toHighest = Math.max(toHighest, to[i + 1]);
-      toShifts.add(new int[]
-      { to[i], to[i + 1] });
+      toShifts.add(new int[] { to[i], to[i + 1] });
     }
   }
 
@@ -236,16 +234,14 @@ public class MapList
     {
       for (int[] r : map.fromShifts)
       {
-        fromShifts.add(new int[]
-        { r[0], r[1] });
+        fromShifts.add(new int[] { r[0], r[1] });
       }
     }
     if (map.toShifts != null)
     {
       for (int[] r : map.toShifts)
       {
-        toShifts.add(new int[]
-        { r[0], r[1] });
+        toShifts.add(new int[] { r[0], r[1] });
       }
     }
   }
@@ -258,8 +254,8 @@ public class MapList
    * @param fromRatio
    * @param toRatio
    */
-  public MapList(List fromRange, List toRange,
-          int fromRatio, int toRatio)
+  public MapList(List fromRange, List toRange, int fromRatio,
+          int toRatio)
   {
     this.fromShifts = fromRange;
     this.toShifts = toRange;
@@ -268,7 +264,8 @@ public class MapList
 
     fromLowest = Integer.MAX_VALUE;
     fromHighest = 0;
-    for (int[] range : fromRange) {
+    for (int[] range : fromRange)
+    {
       fromLowest = Math.min(fromLowest, range[0]);
       fromHighest = Math.max(fromHighest, range[1]);
     }
@@ -313,8 +310,7 @@ public class MapList
    *         returning mapped position
    */
   private int[][] posMap(List shiftTo, int ratio,
-          List shiftFrom,
-          int toRatio)
+          List shiftFrom, int toRatio)
   {
     // TODO not used - remove??
     int iv = 0, ivSize = shiftTo.size();
@@ -374,9 +370,8 @@ public class MapList
       }
       mp[i] = m;
     }
-    int[][] map = new int[][]
-    { new int[]
-    { from, to, tF, tT }, new int[to - from + 2] };
+    int[][] map = new int[][] { new int[] { from, to, tF, tT },
+        new int[to - from + 2] };
 
     map[0][2] = tF;
     map[0][3] = tT;
@@ -461,8 +456,7 @@ public class MapList
       return null; // throw new Error("Bad Mapping!");
     }
     // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
-    return new int[]
-    { toPos[0], fromRemainder, toPos[1] };
+    return new int[] { toPos[0], fromRemainder, toPos[1] };
   }
 
   /**
@@ -482,8 +476,7 @@ public class MapList
       {
         if (pos >= intv[0] && pos <= intv[1])
         {
-          return new int[]
-          { count + pos - intv[0] + 1, +1 };
+          return new int[] { count + pos - intv[0] + 1, +1 };
         }
         else
         {
@@ -494,8 +487,7 @@ public class MapList
       {
         if (pos >= intv[1] && pos <= intv[0])
         {
-          return new int[]
-          { count + intv[0] - pos + 1, -1 };
+          return new int[] { count + intv[0] - pos + 1, -1 };
         }
         else
         {
@@ -516,8 +508,7 @@ public class MapList
   protected static int[] countToPos(List shiftFrom, int pos)
   {
     int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
-    int[] intv =
-    { 0, 0 };
+    int[] intv = { 0, 0 };
     while (iv < ivSize)
     {
       intv = shiftFrom.get(iv++);
@@ -526,8 +517,7 @@ public class MapList
       {
         if (pos <= count + 1 + diff)
         {
-          return new int[]
-          { pos - count - 1 + intv[0], +1 };
+          return new int[] { pos - count - 1 + intv[0], +1 };
         }
         else
         {
@@ -538,8 +528,7 @@ public class MapList
       {
         if (pos <= count + 1 - diff)
         {
-          return new int[]
-          { intv[0] - (pos - count - 1), -1 };
+          return new int[] { intv[0] - (pos - count - 1), -1 };
         }
         else
         {
@@ -597,8 +586,7 @@ public class MapList
    *         region to final position of ending region inclusive
    */
   protected static int[] getIntervals(List shiftFrom,
-          int[] fromStart,
-          int[] fromEnd, int fromRatio2)
+          int[] fromStart, int[] fromEnd, int fromRatio2)
   {
     if (fromStart == null || fromEnd == null)
     {
@@ -688,8 +676,7 @@ public class MapList
       i = fs;
       // truncate initial interval
       iv = shiftFrom.get(intv++);
-      iv = new int[]
-      { iv[0], iv[1] };// clone
+      iv = new int[] { iv[0], iv[1] };// clone
       if (i == fs)
       {
         iv[0] = startpos;
@@ -698,8 +685,7 @@ public class MapList
       {
         ranges.add(iv); // add initial range
         iv = shiftFrom.get(intv++); // get next interval
-        iv = new int[]
-        { iv[0], iv[1] };// clone
+        iv = new int[] { iv[0], iv[1] };// clone
         i++;
       }
       if (i == fe)
@@ -717,8 +703,7 @@ public class MapList
         i--;
       }
       iv = shiftFrom.get(i);
-      iv = new int[]
-      { iv[1], iv[0] };// reverse and clone
+      iv = new int[] { iv[1], iv[0] };// reverse and clone
       // truncate initial interval
       if (i == fs)
       {
@@ -728,8 +713,7 @@ public class MapList
       { // fix apparent logic bug when fe==-1
         ranges.add(iv); // add (truncated) reversed interval
         iv = shiftFrom.get(i);
-        iv = new int[]
-        { iv[1], iv[0] }; // reverse and clone
+        iv = new int[] { iv[1], iv[0] }; // reverse and clone
       }
       if (i == fe)
       {
@@ -788,8 +772,7 @@ public class MapList
     int[] mp = shiftTo(mpos);
     if (mp != null)
     {
-      return new int[]
-      { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
+      return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
     }
     return null;
   }
@@ -818,8 +801,7 @@ public class MapList
     int[] mp = shiftFrom(pos);
     if (mp != null)
     {
-      return new int[]
-      { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
+      return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
     }
     return null;
   }
diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index f2213ad..adfd397 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -1,13 +1,5 @@
 package jalview.util;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewportI;
 import jalview.commands.CommandI;
@@ -25,6 +17,14 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
 /**
  * Helper methods for manipulations involving sequence mappings.
  * 
@@ -200,8 +200,8 @@ public final class MappingUtils
              */
             int mappedEditPos = action == Action.DELETE_GAP ? match[0]
                     - mappedCount : match[0];
-            Edit e = result.new Edit(action, new SequenceI[]
-            { targetSeq }, mappedEditPos, mappedCount, gapChar);
+            Edit e = result.new Edit(action, new SequenceI[] { targetSeq },
+                    mappedEditPos, mappedCount, gapChar);
             result.addEdit(e);
 
             /*
@@ -339,7 +339,7 @@ public final class MappingUtils
        */
       int startResiduePos = selected.findPosition(firstUngappedPos);
       int endResiduePos = selected.findPosition(lastUngappedPos);
-      
+
       for (AlignedCodonFrame acf : codonFrames)
       {
         SequenceI mappedSequence = targetIsNucleotide ? acf
@@ -424,7 +424,8 @@ public final class MappingUtils
     {
       for (AlignedCodonFrame acf : mappings)
       {
-        SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq) : acf.getAaForDnaSeq(seq);
+        SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
+                : acf.getAaForDnaSeq(seq);
         if (mappedSeq != null)
         {
           for (SequenceI seq2 : mapTo.getSequences())
@@ -645,8 +646,10 @@ public final class MappingUtils
     {
       return result;
     }
-    for (AlignedCodonFrame mapping : mappings) {
-      if (mapping.involvesSequence(sequence)) {
+    for (AlignedCodonFrame mapping : mappings)
+    {
+      if (mapping.involvesSequence(sequence))
+      {
         result.add(mapping);
       }
     }
diff --git a/src/jalview/util/ParseHtmlBodyAndLinks.java b/src/jalview/util/ParseHtmlBodyAndLinks.java
index 7aec22d..5263454 100644
--- a/src/jalview/util/ParseHtmlBodyAndLinks.java
+++ b/src/jalview/util/ParseHtmlBodyAndLinks.java
@@ -32,7 +32,8 @@ import java.util.regex.Pattern;
  */
 public class ParseHtmlBodyAndLinks
 {
-  private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+  private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+          .compile("<");
 
   String orig = null;
 
diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index 4826bc3..2b58095 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -47,7 +47,7 @@ public class QuickSort
     {
       return Float.compare(values[o1], values[o2]);
     }
-    
+
   }
 
   static class IntComparator implements Comparator
@@ -492,13 +492,13 @@ public class QuickSort
         nextZeroValue++;
       }
     }
-  
+
     /*
      * Copy zero values back to original arrays
      */
     System.arraycopy(f1, 0, arr, 0, nextZeroValue);
     System.arraycopy(s1, 0, s, 0, nextZeroValue);
-  
+
     if (nextZeroValue == arr.length)
     {
       return; // all zero
@@ -506,12 +506,11 @@ public class QuickSort
     /*
      * Sort the non-zero values
      */
-    int[] nonZeroInts = Arrays
-            .copyOfRange(f1, nextZeroValue, f1.length);
+    int[] nonZeroInts = Arrays.copyOfRange(f1, nextZeroValue, f1.length);
     char[] nonZeroChars = Arrays.copyOfRange(s1, nextZeroValue, s1.length);
     externalSort(nonZeroInts, nonZeroChars);
     // sort(nonZeroFloats, 0, nonZeroFloats.length - 1, nonZeroChars);
-  
+
     /*
      * Assemble sorted non-zero results
      */
diff --git a/src/jalview/util/ReverseListIterator.java b/src/jalview/util/ReverseListIterator.java
index 69a7345..204a053 100644
--- a/src/jalview/util/ReverseListIterator.java
+++ b/src/jalview/util/ReverseListIterator.java
@@ -21,6 +21,7 @@ public class ReverseListIterator implements Iterator
   {
     this.iterator = stuff.listIterator(stuff.size());
   }
+
   @Override
   public boolean hasNext()
   {
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 38d6a32..1dd18ec 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -57,8 +57,7 @@ public class ShiftList
       }
       if (sidx == shifts.size())
       {
-        shifts.add(sidx, new int[]
-        { pos, shift });
+        shifts.add(sidx, new int[] { pos, shift });
       }
       else
       {
@@ -115,8 +114,7 @@ public class ShiftList
         {
           if (sh != null)
           {
-            inverse.shifts.add(new int[]
-            { sh[0], -sh[1] });
+            inverse.shifts.add(new int[] { sh[0], -sh[1] });
           }
         }
       }
diff --git a/src/jalview/util/StringUtils.java b/src/jalview/util/StringUtils.java
index c55d467..3e004a6 100644
--- a/src/jalview/util/StringUtils.java
+++ b/src/jalview/util/StringUtils.java
@@ -4,10 +4,10 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.regex.Pattern;
 
-
 public class StringUtils
 {
-  private static final Pattern DELIMITERS_PATTERN = Pattern.compile(".*='[^']*(?!')");
+  private static final Pattern DELIMITERS_PATTERN = Pattern
+          .compile(".*='[^']*(?!')");
 
   private static final boolean DEBUG = false;
 
@@ -25,11 +25,10 @@ public class StringUtils
    *          the character to insert
    */
   public static final char[] insertCharAt(char[] in, int position,
-          int count,
-          char ch)
+          int count, char ch)
   {
     char[] tmp = new char[in.length + count];
-  
+
     if (position >= in.length)
     {
       System.arraycopy(in, 0, tmp, 0, in.length);
@@ -39,20 +38,19 @@ public class StringUtils
     {
       System.arraycopy(in, 0, tmp, 0, position);
     }
-  
+
     int index = position;
     while (count > 0)
     {
       tmp[index++] = ch;
       count--;
     }
-  
+
     if (position < in.length)
     {
-      System.arraycopy(in, position, tmp, index,
-              in.length - position);
+      System.arraycopy(in, position, tmp, index, in.length - position);
     }
-  
+
     return tmp;
   }
 
diff --git a/src/jalview/util/TableSorter.java b/src/jalview/util/TableSorter.java
index b14f6c0..666f945 100755
--- a/src/jalview/util/TableSorter.java
+++ b/src/jalview/util/TableSorter.java
@@ -20,14 +20,30 @@
  */
 package jalview.util;
 
-import java.util.*;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import javax.swing.table.*;
+import java.util.Map;
+
+import javax.swing.Icon;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.event.TableModelEvent;
+import javax.swing.event.TableModelListener;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.JTableHeader;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumnModel;
+import javax.swing.table.TableModel;
 
 /**
  * TableSorter is a decorator for TableModels; adding sorting functionality to a
diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 3f72ab4..4297090 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -208,8 +208,7 @@ public class UrlLink
           if (ns == 0)
           {
             // take whole regex
-            return new String[]
-            { rg.stringMatched(),
+            return new String[] { rg.stringMatched(),
                 url_prefix + rg.stringMatched() + url_suffix };
           } /*
              * else if (ns==1) { // take only subgroup match return new String[]
@@ -288,13 +287,11 @@ public class UrlLink
       }
 
       // just return simple url substitution.
-      return new String[]
-      { idstring, url_prefix + idstring + url_suffix };
+      return new String[] { idstring, url_prefix + idstring + url_suffix };
     }
     else
     {
-      return new String[]
-      { "", url_prefix };
+      return new String[] { "", url_prefix };
     }
   }
 
@@ -329,8 +326,7 @@ public class UrlLink
 
   public static void main(String argv[])
   {
-    String[] links = new String[]
-    {
+    String[] links = new String[] {
     /*
      * "AlinkT|Target|http://foo.foo.soo/",
      * "myUrl1|http://$SEQUENCE_ID=/[0-9]+/=$.someserver.org/foo",
@@ -346,8 +342,7 @@ public class UrlLink
      * , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(? hiddenRepSequences;
 
   protected ColumnSelection colSel = new ColumnSelection();
@@ -553,7 +552,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected ColourSchemeI globalColourScheme = null;
 
-
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
@@ -978,7 +976,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean sortByTree = false;
 
-
   /**
    * 
    * 
@@ -1060,7 +1057,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return alignment.getHiddenSequences().getSize() > 0;
   }
 
-
   protected SequenceGroup selectionGroup;
 
   public void setSequenceSetId(String newid)
@@ -1309,8 +1305,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void showSequence(int index)
   {
     List tmp = alignment.getHiddenSequences().showSequence(
-            index,
-            hiddenRepSequences);
+            index, hiddenRepSequences);
     if (tmp.size() > 0)
     {
       if (selectionGroup == null)
@@ -1411,8 +1406,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return alignment.getSeqrep()==seq || (hiddenRepSequences != null
-            && hiddenRepSequences.containsKey(seq));
+    return alignment.getSeqrep() == seq
+            || (hiddenRepSequences != null && hiddenRepSequences
+                    .containsKey(seq));
   }
 
   public SequenceGroup getRepresentedSequences(SequenceI seq)
@@ -1434,7 +1430,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     colSel.invertColumnSelection(0, alignment.getWidth());
   }
 
-
   @Override
   public SequenceI[] getSelectionAsNewSequence()
   {
@@ -1462,7 +1457,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sequences;
   }
 
-
   @Override
   public SequenceI[] getSequenceSelection()
   {
@@ -1478,16 +1472,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sequences;
   }
 
-
   @Override
-  public CigarArray getViewAsCigars(
-          boolean selectedRegionOnly)
+  public CigarArray getViewAsCigars(boolean selectedRegionOnly)
   {
     return new CigarArray(alignment, colSel,
             (selectedRegionOnly ? selectionGroup : null));
   }
 
-
   @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
@@ -1495,7 +1486,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return getAlignmentView(selectedOnly, false);
   }
 
-
   @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
@@ -1505,7 +1495,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
             markGroups);
   }
 
-
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
@@ -1543,7 +1532,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return selection;
   }
 
-
   @Override
   public List getVisibleRegionBoundaries(int min, int max)
   {
@@ -1571,8 +1559,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         }
       }
 
-      regions.add(new int[]
-      { start, end });
+      regions.add(new int[] { start, end });
 
       if (colSel != null && colSel.hasHiddenColumns())
       {
@@ -1587,19 +1574,23 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public List getVisibleAlignmentAnnotation(boolean selectedOnly)
+  public List getVisibleAlignmentAnnotation(
+          boolean selectedOnly)
   {
     ArrayList ala = new ArrayList();
     AlignmentAnnotation[] aa;
-    if ((aa=alignment.getAlignmentAnnotation())!=null)
+    if ((aa = alignment.getAlignmentAnnotation()) != null)
     {
-      for (AlignmentAnnotation annot:aa)
+      for (AlignmentAnnotation annot : aa)
       {
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
-        if (selectedOnly && selectionGroup!=null)
+        if (selectedOnly && selectionGroup != null)
+        {
+          colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
+                  selectionGroup.getEndRes(), clone);
+        }
+        else
         {
-          colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone);
-        } else {
           colSel.makeVisibleAnnotation(clone);
         }
         ala.add(clone);
@@ -1608,14 +1599,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ala;
   }
 
-
   @Override
   public boolean isPadGaps()
   {
     return padGaps;
   }
 
-
   @Override
   public void setPadGaps(boolean padGaps)
   {
@@ -1943,6 +1932,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     oldrfs.clear();
   }
+
   @Override
   public boolean isDisplayReferenceSeq()
   {
@@ -2051,7 +2041,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public boolean areFeaturesDisplayed()
   {
-    return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+    return featuresDisplayed != null
+            && featuresDisplayed.getRegisterdFeaturesCount() > 0;
   }
 
   /**
@@ -2065,6 +2056,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     viewStyle.setShowSequenceFeatures(b);
   }
+
   @Override
   public boolean isShowSequenceFeatures()
   {
@@ -2083,8 +2075,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return viewStyle.isShowSequenceFeaturesHeight();
   }
 
-
-
   @Override
   public void setShowAnnotation(boolean b)
   {
@@ -2329,7 +2319,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected void broadcastCommand(CommandI command, boolean undo)
   {
-    getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
+    getStructureSelectionManager().commandPerformed(command, undo,
+            getVamsasSource());
   }
 
   /**
@@ -2506,15 +2497,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return 0;
     }
     boolean iAmProtein = !getAlignment().isNucleotide();
-    AlignmentI proteinAlignment = iAmProtein ? getAlignment()
-            : complement.getAlignment();
+    AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
+            .getAlignment();
     if (proteinAlignment == null)
     {
       return 0;
     }
     final Set mappings = proteinAlignment
             .getCodonFrames();
-  
+
     /*
      * Heuristic: find the first mapped sequence (if any) with a non-gapped
      * residue in the middle column of the visible region. Scroll the
@@ -2530,9 +2521,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
     int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
     final HiddenSequences hiddenSequences = getAlignment()
             .getHiddenSequences();
-    
+
     /*
-     * searching to the bottom of the alignment gives smoother scrolling across all gapped visible regions
+     * searching to the bottom of the alignment gives smoother scrolling across
+     * all gapped visible regions
      */
     int lastSeq = alignment.getHeight() - 1;
     for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
@@ -2550,10 +2542,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
               .findMappingsForSequence(sequence, mappings);
       if (!seqMappings.isEmpty())
       {
-          break;
+        break;
       }
     }
-  
+
     if (sequence == null)
     {
       /*
diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index c1175b7..b0af302 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -20,13 +20,13 @@
  */
 package jalview.viewmodel;
 
-import java.util.Vector;
-
 import jalview.analysis.PCA;
+import jalview.api.RotatableCanvasI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequencePoint;
-import jalview.api.RotatableCanvasI;
+
+import java.util.Vector;
 
 public class PCAModel
 {
diff --git a/src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java b/src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java
index 3cd4ef7..74d49e8 100644
--- a/src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java
+++ b/src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java
@@ -14,6 +14,7 @@ public class AnnotationFilterParameter
   {
     DISPLAY_STRING, DESCRIPTION;
   }
+
   private ThresholdType thresholdType;
 
   private float thresholdValue;
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 19c6ca8..bedbaf5 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -119,8 +119,7 @@ public abstract class FeatureRendererModel implements
     }
     if (!fdi.isRegistered(featureType))
     {
-      pushFeatureType(Arrays.asList(new String[]
-      { featureType }));
+      pushFeatureType(Arrays.asList(new String[] { featureType }));
     }
     fdi.setVisible(featureType);
   }
@@ -163,7 +162,7 @@ public abstract class FeatureRendererModel implements
     types.toArray(neworder);
     if (renderOrder != null)
     {
-      System.arraycopy(neworder,0,neworder,renderOrder.length,ts);
+      System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
       System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
     }
     renderOrder = neworder;
@@ -186,8 +185,7 @@ public abstract class FeatureRendererModel implements
   protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
   {
     float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
-    final byte[] r = new byte[]
-    { 0, (byte) 255 };
+    final byte[] r = new byte[] { 0, (byte) 255 };
     if (mm != null)
     {
       if (r[0] != 0 || mm[0] < 0.0)
@@ -375,14 +373,13 @@ public abstract class FeatureRendererModel implements
           float[][] mm = (float[][]) minmax.get(features[index].getType());
           if (mm == null)
           {
-            mm = new float[][]
-            { null, null };
+            mm = new float[][] { null, null };
             minmax.put(features[index].getType(), mm);
           }
           if (mm[nonpos] == null)
           {
-            mm[nonpos] = new float[]
-            { features[index].score, features[index].score };
+            mm[nonpos] = new float[] { features[index].score,
+                features[index].score };
 
           }
           else
@@ -433,8 +430,7 @@ public abstract class FeatureRendererModel implements
         {
           if (initOrders)
           {
-            setOrder(oldRender[j], (1 - (1 + (float) j)
-                    / oldRender.length));
+            setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length));
           }
           if (allfeatures.contains(oldRender[j]))
           {
@@ -770,8 +766,7 @@ public abstract class FeatureRendererModel implements
   {
     if (renderOrder == null)
     {
-      return Arrays.asList(new String[]
-      {});
+      return Arrays.asList(new String[] {});
     }
     return Arrays.asList(renderOrder);
   }
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
index 6e85b83..49dcad7 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
@@ -25,7 +25,7 @@ public class FeatureRendererSettings implements Cloneable
           float transparency, Hashtable featureOrder)
   {
     super();
-    this.renderOrder = Arrays.copyOf(renderOrder,renderOrder.length);
+    this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
     this.featureGroups = new ConcurrentHashMap(featureGroups);
     this.featureColours = new ConcurrentHashMap(featureColours);
     this.transparency = transparency;
diff --git a/src/jalview/viewmodel/styles/ViewStyle.java b/src/jalview/viewmodel/styles/ViewStyle.java
index 3ed5634..649d07e 100644
--- a/src/jalview/viewmodel/styles/ViewStyle.java
+++ b/src/jalview/viewmodel/styles/ViewStyle.java
@@ -1,9 +1,9 @@
 package jalview.viewmodel.styles;
 
-import java.awt.Color;
-
 import jalview.api.ViewStyleI;
 
+import java.awt.Color;
+
 /**
  * A container for holding alignment view properties. View properties are
  * data-independent, which means they can be safely copied between views
@@ -255,7 +255,8 @@ public class ViewStyle implements ViewStyleI
             && getWrapAlignment() == vs.getWrapAlignment() && getWrappedWidth() == vs
             .getWrappedWidth());
     /*
-     * and compare non-primitive types; syntax below will match null with null values
+     * and compare non-primitive types; syntax below will match null with null
+     * values
      */
     match = match
             && String.valueOf(getFontName()).equals(
@@ -642,7 +643,6 @@ public class ViewStyle implements ViewStyleI
     abovePIDThreshold = b;
   }
 
-  
   /**
    * DOCUMENT ME!
    * 
@@ -667,7 +667,6 @@ public class ViewStyle implements ViewStyleI
     this.charWidth = w;
   }
 
-
   /**
    * @param value
    *          indicating if subsequent colourscheme changes will be propagated
diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index 566891f..bca3145 100644
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -20,8 +20,6 @@
  */
 package jalview.workers;
 
-import java.util.List;
-
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
@@ -29,6 +27,8 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 
+import java.util.List;
+
 /**
  * Base class for alignment calculation workers
  * 
diff --git a/src/jalview/workers/ComplementConsensusThread.java b/src/jalview/workers/ComplementConsensusThread.java
index 71bfb40..a521314 100644
--- a/src/jalview/workers/ComplementConsensusThread.java
+++ b/src/jalview/workers/ComplementConsensusThread.java
@@ -1,8 +1,5 @@
 package jalview.workers;
 
-import java.util.ConcurrentModificationException;
-import java.util.Hashtable;
-
 import jalview.analysis.AAFrequency;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -10,6 +7,9 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
+import java.util.ConcurrentModificationException;
+import java.util.Hashtable;
+
 /**
  * A thread to recompute the consensus of the cDNA complement for a linked
  * protein alignment.
diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index f244242..a8698e6 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -20,8 +20,6 @@
  */
 package jalview.workers;
 
-import java.util.Hashtable;
-
 import jalview.analysis.AAFrequency;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
@@ -32,6 +30,8 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
+import java.util.Hashtable;
+
 public class ConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
 {
@@ -130,8 +130,7 @@ public class ConsensusThread extends AlignCalcWorker implements
     Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
 
     SequenceI[] aseqs = getSequences();
-    AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus,
-            true);
+    AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
 
     alignViewport.setSequenceConsensusHash(hconsensus);
     setColourSchemeConsensus(hconsensus);
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index e557614..fe28d6c 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -133,8 +133,8 @@ public abstract class AWSThread extends Thread
           {
             // Deal with Transaction exceptions
             wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
-                    .formatMessage("info.server_exception", new Object[]
-                    { WebServiceName, ex.getMessage() }));
+                    .formatMessage("info.server_exception", new Object[] {
+                        WebServiceName, ex.getMessage() }));
             // always output the exception's stack trace to the log
             Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
                     + ") Server exception.");
@@ -199,7 +199,8 @@ public abstract class AWSThread extends Thread
       Cache.log
               .debug("WebServiceJob poll loop finished with no jobs created.");
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-      wsInfo.appendProgressText(MessageManager.getString("info.no_jobs_ran"));
+      wsInfo.appendProgressText(MessageManager
+              .getString("info.no_jobs_ran"));
       wsInfo.setFinishedNoResults();
     }
   }
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index d71c653..5f03ec7 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -283,11 +283,14 @@ public class DBRefFetcher implements Runnable
   {
     if (dbSources == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_must_init_dbsources"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_must_init_dbsources"));
     }
     running = true;
     long startTime = System.currentTimeMillis();
-    af.setProgressBar(MessageManager.getString("status.fetching_db_refs"), startTime);
+    af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+            startTime);
     try
     {
       if (Cache.getDefault("DBREFFETCH_USEPICR", false))
@@ -393,8 +396,8 @@ public class DBRefFetcher implements Runnable
             {
               SequenceI sequence = dataset[seqIndex];
               DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-                      sequence.getDBRef(), new String[]
-                      { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+                      sequence.getDBRef(),
+                      new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
               // });
               // check for existing dbrefs to use
               if (uprefs != null && uprefs.length > 0)
@@ -517,8 +520,7 @@ public class DBRefFetcher implements Runnable
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
-              entry.getDBRef(), new String[]
-              { dbSource });
+              entry.getDBRef(), new String[] { dbSource });
       if (entryRefs == null)
       {
         System.err
@@ -616,11 +618,10 @@ public class DBRefFetcher implements Runnable
           // absStart = 0;
           // create valid mapping between matching region of local sequence and
           // the mapped sequence
-          mp = new Mapping(null, new int[]
-          { sequence.getStart() + absStart,
+          mp = new Mapping(null, new int[] {
+              sequence.getStart() + absStart,
               sequence.getStart() + absStart + entrySeq.length() - 1 },
-                  new int[]
-                  { entry.getStart(),
+                  new int[] { entry.getStart(),
                       entry.getStart() + entrySeq.length() - 1 }, 1, 1);
           updateRefFrame = false; // mapping is based on current start/end so
           // don't modify start and end
diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 3db663d..808d9a0 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -205,8 +205,10 @@ public class DasSequenceFeatureFetcher
         reply = JOptionPane
                 .showInternalConfirmDialog(
                         Desktop.desktop,
-                        MessageManager.getString("info.you_want_jalview_to_find_uniprot_accessions"),
-                        MessageManager.getString("label.find_uniprot_accession_ids"),
+                        MessageManager
+                                .getString("info.you_want_jalview_to_find_uniprot_accessions"),
+                        MessageManager
+                                .getString("label.find_uniprot_accession_ids"),
                         JOptionPane.YES_NO_OPTION,
                         JOptionPane.QUESTION_MESSAGE);
       }
@@ -264,7 +266,9 @@ public class DasSequenceFeatureFetcher
     startTime = System.currentTimeMillis();
     if (af != null)
     {
-      af.setProgressBar(MessageManager.getString("status.fetching_das_sequence_features"), startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.fetching_das_sequence_features"),
+              startTime);
     }
     if (sourceRegistry == null)
     {
@@ -378,8 +382,7 @@ public class DasSequenceFeatureFetcher
                         source));
         for (String id : idl)
         {
-          List qid = Arrays.asList(new String[]
-          { id });
+          List qid = Arrays.asList(new String[] { id });
           try
           {
             DasGFFAdapter dga = featuresc.fetchData(source, qid);
@@ -537,7 +540,9 @@ public class DasSequenceFeatureFetcher
 
     if (af != null)
     {
-      af.setProgressBar(MessageManager.getString("status.no_das_sources_active"), startTime);
+      af.setProgressBar(
+              MessageManager.getString("status.no_das_sources_active"),
+              startTime);
     }
     if (getFeatSettings() != null)
     {
@@ -567,7 +572,9 @@ public class DasSequenceFeatureFetcher
   {
     if (af != null)
     {
-      af.setProgressBar(MessageManager.getString("status.das_feature_fetching_cancelled"), startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.das_feature_fetching_cancelled"),
+              startTime);
     }
     cancelled = true;
   }
@@ -582,7 +589,8 @@ public class DasSequenceFeatureFetcher
     if (!cancelled && af != null)
     {
       // only update the progress bar if we've completed the fetch normally
-      af.setProgressBar(MessageManager.getString("status.das_feature_fetching_complete"), startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.das_feature_fetching_complete"), startTime);
     }
 
     if (af != null && af.featureSettings != null)
@@ -630,8 +638,7 @@ public class DasSequenceFeatureFetcher
       return null;
     }
     DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-            seq.getDBRef(), new String[]
-            {
+            seq.getDBRef(), new String[] {
             // jalview.datamodel.DBRefSource.PDB,
             jalview.datamodel.DBRefSource.UNIPROT,
             // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
@@ -710,8 +717,7 @@ public class DasSequenceFeatureFetcher
       }
     }
 
-    return new Object[]
-    { ids, qstring };
+    return new Object[] { ids, qstring };
   }
 
   /**
diff --git a/src/jalview/ws/HttpClientUtils.java b/src/jalview/ws/HttpClientUtils.java
index c6d6629..2cc3d8d 100644
--- a/src/jalview/ws/HttpClientUtils.java
+++ b/src/jalview/ws/HttpClientUtils.java
@@ -67,8 +67,7 @@ public class HttpClientUtils
    */
   public static BufferedReader doHttpUrlPost(String postUrl,
           List vals, int connectionTimeoutMs,
-          int readTimeoutMs) throws ClientProtocolException,
-          IOException
+          int readTimeoutMs) throws ClientProtocolException, IOException
   {
     // todo use HttpClient 4.3 or later and class RequestConfig
     HttpParams params = new BasicHttpParams();
diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 9c42f0a..6a612a0 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,11 +20,6 @@
  */
 package jalview.ws;
 
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
@@ -33,6 +28,11 @@ import jalview.ws.dbsources.das.api.jalviewSourceI;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
 /**
  * This is the the concrete implementation of the sequence retrieval interface
  * and abstract class in jalview.ws.seqfetcher. This implements the run-time
@@ -167,13 +167,11 @@ public class SequenceFetcher extends ASequenceFetcher
           {
             nm = nm.substring(4);
           }
-          dassrc.add(new String[]
-          { srcs[i], nm.toUpperCase() });
+          dassrc.add(new String[] { srcs[i], nm.toUpperCase() });
         }
         else
         {
-          nondas.add(new String[]
-          { srcs[i], nm.toUpperCase() });
+          nondas.add(new String[] { srcs[i], nm.toUpperCase() });
         }
       }
     }
@@ -331,9 +329,8 @@ public class SequenceFetcher extends ASequenceFetcher
             }
             else
             {
-              noProds.addElement((dna ? new Object[]
-              { al, al } : new Object[]
-              { al }));
+              noProds.addElement((dna ? new Object[] { al, al }
+                      : new Object[] { al }));
             }
 
           }
@@ -369,8 +366,7 @@ public class SequenceFetcher extends ASequenceFetcher
             }
             if (ds == null)
             {
-              ds = new Alignment(new SequenceI[]
-              { sq });
+              ds = new Alignment(new SequenceI[] { sq });
 
             }
             else
diff --git a/src/jalview/ws/WSClient.java b/src/jalview/ws/WSClient.java
index 0761f19..0f5cee8 100755
--- a/src/jalview/ws/WSClient.java
+++ b/src/jalview/ws/WSClient.java
@@ -20,7 +20,7 @@
  */
 package jalview.ws;
 
-import jalview.gui.*;
+import jalview.gui.WebserviceInfo;
 
 public abstract class WSClient // implements WSMenuEntryProviderI
 {
diff --git a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
index 40e2193..7ac6936 100644
--- a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
+++ b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
@@ -20,12 +20,12 @@
  */
 package jalview.ws.dbsources;
 
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
 
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-
 public abstract class EbiFileRetrievedProxy extends DbSourceProxyImpl
 {
 
diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 3a9ebe9..e5fbd6c 100644
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -20,12 +20,12 @@
  */
 package jalview.ws.dbsources;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import com.stevesoft.pat.Regex;
+
 public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
 {
 
diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 5b06c81..893ab41 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -20,12 +20,12 @@
  */
 package jalview.ws.dbsources;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import com.stevesoft.pat.Regex;
+
 /**
  * @author JimP
  * 
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 92e863a..20da45c 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -20,8 +20,6 @@
  */
 package jalview.ws.dbsources;
 
-import java.io.File;
-
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -30,6 +28,8 @@ import jalview.datamodel.xdb.embl.EmblFile;
 import jalview.util.MessageManager;
 import jalview.ws.ebi.EBIFetchClient;
 
+import java.io.File;
+
 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
 {
 
@@ -66,7 +66,9 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     } catch (Exception e)
     {
       stopQuery();
-      throw new Exception(MessageManager.formatMessage("exception.ebiembl_retrieval_failed_on", new String[]{emprefx.toLowerCase(),query.trim()}), e);
+      throw new Exception(MessageManager.formatMessage(
+              "exception.ebiembl_retrieval_failed_on", new String[] {
+                  emprefx.toLowerCase(), query.trim() }), e);
     }
     return getEmblSequenceRecords(emprefx, query, reply);
   }
@@ -98,7 +100,9 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       }
       else
       {
-        result.append(MessageManager.formatMessage("label.no_embl_record_found", new String[]{emprefx.toLowerCase(),query.trim()}));
+        result.append(MessageManager.formatMessage(
+                "label.no_embl_record_found",
+                new String[] { emprefx.toLowerCase(), query.trim() }));
       }
     }
     if (efile != null)
@@ -143,7 +147,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     if (seqs != null && seqs.length > 0)
     {
       al = new Alignment(seqs);
-      result.append(MessageManager.formatMessage("label.embl_successfully_parsed", new String[]{emprefx}));
+      result.append(MessageManager.formatMessage(
+              "label.embl_successfully_parsed", new String[] { emprefx }));
       results = result;
     }
     stopQuery();
diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index e791842..116962b 100644
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -20,12 +20,12 @@
  */
 package jalview.ws.dbsources;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import com.stevesoft.pat.Regex;
+
 /**
  * Test class for accessing GeneDB - not yet finished.
  * 
diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index 04c00ec..320b1c5 100644
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -23,7 +23,6 @@ import com.sun.jersey.api.client.WebResource;
 import com.sun.jersey.api.client.config.ClientConfig;
 import com.sun.jersey.api.client.config.DefaultClientConfig;
 
-
 /**
  * A rest client for querying the Search endpoing of the PDB REST API
  * 
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 836e211..4a50196 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -189,9 +189,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         for (SequenceI pdbcs : toremove)
         {
           pdbfile.deleteSequence(pdbcs);
-          if (pdbcs.getAnnotation()!=null)
+          if (pdbcs.getAnnotation() != null)
           {
-            for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+            for (AlignmentAnnotation aa : pdbcs.getAnnotation())
             {
               pdbfile.deleteAnnotation(aa);
             }
@@ -201,7 +201,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
 
       if (pdbfile == null || pdbfile.getHeight() < 1)
       {
-        throw new Exception(MessageManager.formatMessage("exception.no_pdb_records_for_chain", new String[]{id, ((chain == null) ? "' '" : chain)}));
+        throw new Exception(MessageManager.formatMessage(
+                "exception.no_pdb_records_for_chain", new String[] { id,
+                    ((chain == null) ? "' '" : chain) }));
       }
 
     } catch (Exception ex) // Problem parsing PDB file
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index c8f7ee7..0211bb1 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -20,12 +20,12 @@
  */
 package jalview.ws.dbsources;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import com.stevesoft.pat.Regex;
+
 /**
  * TODO: later PFAM is a complex datasource - it could return a tree in addition
  * to an alignment TODO: create interface to pass alignment properties and tree
diff --git a/src/jalview/ws/dbsources/Rfam.java b/src/jalview/ws/dbsources/Rfam.java
index 62f2b28..b07b8ea 100644
--- a/src/jalview/ws/dbsources/Rfam.java
+++ b/src/jalview/ws/dbsources/Rfam.java
@@ -20,10 +20,10 @@
  */
 package jalview.ws.dbsources;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import com.stevesoft.pat.Regex;
+
 /**
  * Contains methods for fetching sequences from Rfam database
  * 
diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 4c8f3ce..1e8eadb 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -225,8 +225,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
       name.append(n);
     }
 
-    if (entry.getProtein() != null
-            && entry.getProtein().getName() != null)
+    if (entry.getProtein() != null && entry.getProtein().getName() != null)
     {
       for (String nm : entry.getProtein().getName())
       {
diff --git a/src/jalview/ws/dbsources/das/api/jalviewSourceI.java b/src/jalview/ws/dbsources/das/api/jalviewSourceI.java
index 359840a..bc3c8ea 100644
--- a/src/jalview/ws/dbsources/das/api/jalviewSourceI.java
+++ b/src/jalview/ws/dbsources/das/api/jalviewSourceI.java
@@ -20,10 +20,10 @@
  */
 package jalview.ws.dbsources.das.api;
 
-import java.util.List;
-
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.List;
+
 import org.biodas.jdas.schema.sources.MAINTAINER;
 import org.biodas.jdas.schema.sources.VERSION;
 
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index dd3d901..32e4f3e 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -20,6 +20,17 @@
  */
 package jalview.ws.dbsources.das.datamodel;
 
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -39,16 +50,6 @@ import org.biodas.jdas.schema.sources.VERSION;
 
 import com.stevesoft.pat.Regex;
 
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.*;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
 /**
  * an instance of this class is created for each unique DAS Sequence source (ie
  * one capable of handling the 'sequence' for a particular MapMaster)
@@ -101,7 +102,9 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     if (!(jsrc = new JalviewSource(source, connprops, false))
             .isSequenceSource())
     {
-      throw new Exception(MessageManager.formatMessage("exception.das_source_doesnt_support_sequence_command", new String[]{source.getTitle()}));
+      throw new Exception(MessageManager.formatMessage(
+              "exception.das_source_doesnt_support_sequence_command",
+              new String[] { source.getTitle() }));
     }
     this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
     this.source = source;
@@ -172,8 +175,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
                   connprops.getConnectionPropertyProviderFor(sr));
           for (String q : toks)
           {
-            List qset = Arrays.asList(new String[]
-            { q });
+            List qset = Arrays.asList(new String[] { q });
             try
             {
               DasSequenceAdapter s = sq.fetchData(sr, qset);
diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index b3bb342..9cc4239 100644
--- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@ -20,6 +20,10 @@
  */
 package jalview.ws.dbsources.das.datamodel;
 
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.Date;
@@ -37,10 +41,6 @@ import org.biodas.jdas.schema.sources.PROP;
 import org.biodas.jdas.schema.sources.SOURCE;
 import org.biodas.jdas.schema.sources.VERSION;
 
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
 public class JalviewSource implements jalviewSourceI
 {
   SOURCE source;
@@ -347,7 +347,9 @@ public class JalviewSource implements jalviewSourceI
         int p = cap.getQueryUri().lastIndexOf(capname);
         if (p < -1)
         {
-          throw new Exception(MessageManager.formatMessage("exception.invalid_das_source", new String[]{source.getUri()}));
+          throw new Exception(MessageManager.formatMessage(
+                  "exception.invalid_das_source",
+                  new String[] { source.getUri() }));
         }
         if (cap.getQueryUri().charAt(p) == '/')
         {
diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index a785899..c33871d 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.ebi;
 
+import jalview.util.MessageManager;
+
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
@@ -31,8 +33,6 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
 
-import jalview.util.MessageManager;
-
 /**
  * DOCUMENT ME!
  * 
diff --git a/src/jalview/ws/io/mime/MimeTypes.java b/src/jalview/ws/io/mime/MimeTypes.java
index fb13cf1..83252d8 100644
--- a/src/jalview/ws/io/mime/MimeTypes.java
+++ b/src/jalview/ws/io/mime/MimeTypes.java
@@ -34,8 +34,8 @@ public class MimeTypes
    * pair list {String,JvDataType} giving a mime-type followed by its associated
    * JvDataType enumeration.
    */
-  final public static Object[] typemap = new Object[]
-  { "application/x-align", JvDataType.ALIGNMENT,
+  final public static Object[] typemap = new Object[] {
+      "application/x-align", JvDataType.ALIGNMENT,
       "application/x-jalview-annotation", JvDataType.ANNOTATION,
       "application/x-newick", JvDataType.TREE,
       "application/x-new-hampshire", JvDataType.TREE,
diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index 3e9c73a..8c30c69 100644
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -20,7 +20,6 @@
  */
 package jalview.ws.jws1;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
@@ -106,7 +105,9 @@ public class Annotate3D
       }
       else
       {
-        throw new IOException(MessageManager.getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
+        throw new IOException(
+                MessageManager
+                        .getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
                 x);
       }
     }
diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index d544bea..4643119 100644
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -193,28 +193,30 @@ public class Discoverer implements Runnable
         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",
-                    MessageManager.getString("label.muscle_multiple_protein_sequence_alignment")),
+                    MessageManager
+                            .getString("label.muscle_multiple_protein_sequence_alignment")),
             new ServiceHandle(
                     "MsaWS",
                     "Katoh, K., K. Kuma, K., Toh, H.,  and Miyata, T. (2005) "
                             + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
                             + " Nucleic Acids Research, 33 511-518",
                     "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
-                    MessageManager.getString("label.mafft_multiple_sequence_alignment")),
+                    MessageManager
+                            .getString("label.mafft_multiple_sequence_alignment")),
             new ServiceHandle(
                     "MsaWS",
                     "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
                             + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
                             + " Nucleic Acids Research, 22 4673-4680",
                     "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
-                    MessageManager.getString("label.clustalw_multiple_sequence_alignment")),
+                    MessageManager
+                            .getString("label.clustalw_multiple_sequence_alignment")),
             new ServiceHandle(
                     "SecStrPred",
                     "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
@@ -253,12 +255,11 @@ public class Discoverer implements Runnable
       {
         if (jalview.gui.Desktop.desktop != null)
         {
-          JOptionPane
-                  .showMessageDialog(
-                          jalview.gui.Desktop.desktop,
-                          MessageManager.getString("label.set_proxy_settings"),
-                          MessageManager.getString("label.proxy_authorization_failed"),
-                          JOptionPane.WARNING_MESSAGE);
+          JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
+                  MessageManager.getString("label.set_proxy_settings"),
+                  MessageManager
+                          .getString("label.proxy_authorization_failed"),
+                  JOptionPane.WARNING_MESSAGE);
         }
       }
       else
diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index 2e000f8..f13672b 100644
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -154,7 +154,9 @@ public class JPredClient extends WS1Client
     {
       if (!msa && msf.length > 1)
       {
-        throw new Error(MessageManager.getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
       }
 
       String altitle = getPredictionName(WebServiceName) + " for "
@@ -294,7 +296,8 @@ public class JPredClient extends WS1Client
   private WebserviceInfo setWebService()
   {
     WebServiceName = "JNetWS";
-    WebServiceJobTitle = MessageManager.getString("label.jnet_secondary_structure_prediction");
+    WebServiceJobTitle = MessageManager
+            .getString("label.jnet_secondary_structure_prediction");
     WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
             + "multiple sequence alignment profiles to improve protein secondary structure prediction, "
             + "Proteins 40:502-511\".";
@@ -320,13 +323,21 @@ public class JPredClient extends WS1Client
 
     } catch (Exception ex)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-    		  MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL}),
-    		  MessageManager.getString("label.internal_jalview_error"),
-              JOptionPane.WARNING_MESSAGE);
-      wsInfo.setProgressText(MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL})
-    		  + "\n"
-              + ex.getMessage());
+      JOptionPane
+              .showMessageDialog(
+                      Desktop.desktop,
+                      MessageManager
+                              .formatMessage(
+                                      "label.secondary_structure_prediction_service_couldnt_be_located",
+                                      new String[] { WebServiceName, WsURL }),
+                      MessageManager
+                              .getString("label.internal_jalview_error"),
+                      JOptionPane.WARNING_MESSAGE);
+      wsInfo.setProgressText(MessageManager
+              .formatMessage(
+                      "label.secondary_structure_prediction_service_couldnt_be_located",
+                      new String[] { WebServiceName, WsURL })
+              + "\n" + ex.getMessage());
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 
     }
diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index a8a49d0..8c7768d 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -147,10 +147,11 @@ class JPredThread extends JWS1Thread implements WSClientI
             {
               sqs[i] = al.getSequenceAt(i);
             }
-            if (!jalview.analysis.SeqsetUtils.deuniquify(
-                    SequenceInfo, sqs))
+            if (!jalview.analysis.SeqsetUtils.deuniquify(SequenceInfo, sqs))
             {
-              throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment")));
+              throw (new Exception(
+                      MessageManager
+                              .getString("exception.couldnt_recover_sequence_properties_for_alignment")));
             }
           }
           FirstSeq = 0;
@@ -169,7 +170,9 @@ class JPredThread extends JWS1Thread implements WSClientI
         }
         else
         {
-          throw (new Exception(MessageManager.formatMessage("exception.unknown_format_for_file", new String[]{format,result.getAligfile()})));
+          throw (new Exception(MessageManager.formatMessage(
+                  "exception.unknown_format_for_file", new String[] {
+                      format, result.getAligfile() })));
         }
       }
       else
@@ -183,15 +186,17 @@ class JPredThread extends JWS1Thread implements WSClientI
                   .getAlignmentAndColumnSelection(gc)[0];
           if (this.msaIndex >= sqs.length)
           {
-            throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job"));
+            throw new Error(
+                    MessageManager
+                            .getString("error.implementation_error_invalid_msa_index_for_job"));
           }
 
           // ///
           // Uses RemoveGapsCommand
           // ///
-          new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"),
-                  new SequenceI[]
-                  { sqs[msaIndex] }, currentView);
+          new jalview.commands.RemoveGapsCommand(
+                  MessageManager.getString("label.remove_gaps"),
+                  new SequenceI[] { sqs[msaIndex] }, currentView);
 
           SequenceI profileseq = al.getSequenceAt(FirstSeq);
           profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
@@ -200,7 +205,9 @@ class JPredThread extends JWS1Thread implements WSClientI
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
                 al.getSequenceAt(FirstSeq), SequenceInfo))
         {
-          throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
+          throw (new Exception(
+                  MessageManager
+                          .getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
         }
         else
         {
@@ -236,8 +243,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                   alant.sequenceRef);
         }
       }
-      return new Object[]
-      { al, alcsel }; // , FirstSeq, noMsa};
+      return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
     }
 
     /**
@@ -386,8 +392,7 @@ class JPredThread extends JWS1Thread implements WSClientI
     if (job.hasValidInput())
     {
       OutputHeader = wsInfo.getProgressText();
-      jobs = new WSJob[]
-      { job };
+      jobs = new WSJob[] { job };
       job.setJobnum(0);
     }
     else
@@ -405,8 +410,7 @@ class JPredThread extends JWS1Thread implements WSClientI
     JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
     if (job.hasValidInput())
     {
-      jobs = new WSJob[]
-      { job };
+      jobs = new WSJob[] { job };
       OutputHeader = wsInfo.getProgressText();
       job.setJobnum(0);
     }
@@ -420,7 +424,9 @@ class JPredThread extends JWS1Thread implements WSClientI
   {
     if (!(j instanceof JPredJob))
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_startjob_called", new String[]{j.getClass().toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_startjob_called",
+              new String[] { j.getClass().toString() }));
     }
     try
     {
@@ -441,7 +447,9 @@ class JPredThread extends JWS1Thread implements WSClientI
         {
           job.result = new JpredResult();
           job.result.setInvalid(true);
-          job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()}));
+          job.result.setStatus(MessageManager.formatMessage(
+                  "label.submission_params", new String[] { job.getJobId()
+                          .toString() }));
           throw new Exception(job.getJobId());
         }
         else
@@ -453,7 +461,9 @@ class JPredThread extends JWS1Thread implements WSClientI
       }
       else
       {
-        throw new Exception(MessageManager.getString("exception.server_timeout_try_later"));
+        throw new Exception(
+                MessageManager
+                        .getString("exception.server_timeout_try_later"));
       }
     } catch (Exception e)
     {
@@ -477,7 +487,11 @@ class JPredThread extends JWS1Thread implements WSClientI
       {
         wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
         // JBPNote - this could be a popup informing the user of the problem.
-        wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.failed_to_submit_prediction", new String[]{e.getMessage(),wsInfo.getProgressText()}));
+        wsInfo.appendProgressText(j.getJobnum(), MessageManager
+                .formatMessage(
+                        "info.failed_to_submit_prediction",
+                        new String[] { e.getMessage(),
+                            wsInfo.getProgressText() }));
 
         jalview.bin.Cache.log.debug(
                 "Failed Submission of job " + j.getJobnum(), e);
@@ -567,7 +581,9 @@ class JPredThread extends JWS1Thread implements WSClientI
             else
             {
               // do merge with other job results
-              throw new Error(MessageManager.getString("error.multiple_jnet_subjob_merge_not_implemented"));
+              throw new Error(
+                      MessageManager
+                              .getString("error.multiple_jnet_subjob_merge_not_implemented"));
             }
           } catch (Exception e)
           {
@@ -575,7 +591,10 @@ class JPredThread extends JWS1Thread implements WSClientI
                     "JNet Client: JPred Annotation Parse Error", e);
             wsInfo.setStatus(j.getJobnum(),
                     WebserviceInfo.STATE_STOPPED_ERROR);
-            wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.invalid_jnet_job_result_data", new String[]{OutputHeader.toString(),j.result.getStatus(), e.getMessage() }));
+            wsInfo.appendProgressText(j.getJobnum(), MessageManager
+                    .formatMessage("info.invalid_jnet_job_result_data",
+                            new String[] { OutputHeader.toString(),
+                                j.result.getStatus(), e.getMessage() }));
             j.result.setBroken(true);
           }
         }
diff --git a/src/jalview/ws/jws1/JWS1Thread.java b/src/jalview/ws/jws1/JWS1Thread.java
index b2d6868..7ff4e5b 100644
--- a/src/jalview/ws/jws1/JWS1Thread.java
+++ b/src/jalview/ws/jws1/JWS1Thread.java
@@ -20,8 +20,9 @@
  */
 package jalview.ws.jws1;
 
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.WebserviceInfo;
 import jalview.ws.AWSThread;
 
 /**
diff --git a/src/jalview/ws/jws1/MsaWSClient.java b/src/jalview/ws/jws1/MsaWSClient.java
index ef2d78d..95f5527 100644
--- a/src/jalview/ws/jws1/MsaWSClient.java
+++ b/src/jalview/ws/jws1/MsaWSClient.java
@@ -20,15 +20,24 @@
  */
 package jalview.ws.jws1;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
+import ext.vamsas.MuscleWS;
+import ext.vamsas.MuscleWSServiceLocator;
+import ext.vamsas.MuscleWSSoapBindingStub;
+import ext.vamsas.ServiceHandle;
 
 /**
  * DOCUMENT ME!
@@ -70,21 +79,22 @@ public class MsaWSClient extends WS1Client
     alignFrame = _alignFrame;
     if (!sh.getAbstractName().equals("MsaWS"))
     {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager.formatMessage("label.service_called_is_not_msa_service", new String[]{sh.getName()}),
-                      MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.service_called_is_not_msa_service",
+                      new String[] { sh.getName() }), MessageManager
+              .getString("label.internal_jalview_error"),
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
     if ((wsInfo = setWebService(sh)) == null)
     {
-      JOptionPane.showMessageDialog(
-              Desktop.desktop,
-              MessageManager.formatMessage("label.msa_service_is_unknown", new String[]{sh.getName()}),
-              MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.msa_service_is_unknown",
+                      new String[] { sh.getName() }), MessageManager
+              .getString("label.internal_jalview_error"),
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index af3db9c..be21de7 100644
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.java
@@ -20,16 +20,24 @@
  */
 package jalview.ws.jws1;
 
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
 import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
 import vamsas.objects.simple.MsaResult;
 
 class MsaWSThread extends JWS1Thread implements WSClientI
@@ -87,7 +95,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       int nseqs = 0;
       if (minlen < 0)
       {
-        throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_minlen_must_be_greater_zero"));
       }
       for (int i = 0; i < seqs.length; i++)
       {
@@ -125,8 +135,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
                     .extractGaps(jalview.util.Comparison.GapChars,
                             seqs[i].getSequenceAsString());
           }
-          emptySeqs.add(new String[]
-          { newname, empty });
+          emptySeqs.add(new String[] { newname, empty });
         }
       }
       this.seqs = new vamsas.objects.simple.SequenceSet();
@@ -245,8 +254,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
         jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
         // account for any missing sequences
         jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
-        return new Object[]
-        { alseqs, msaorder };
+        return new Object[] { alseqs, msaorder };
       }
       return null;
     }
@@ -431,7 +439,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI
   {
     if (!(job instanceof MsaWSJob))
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_msawbjob_called",
+              new String[] { job.getClass().toString() }));
     }
     MsaWSJob j = (MsaWSJob) job;
     if (j.isSubmitted())
@@ -449,7 +459,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       j.setSubmitted(true);
       j.result = new MsaResult();
       j.result.setFinished(true);
-      j.result.setStatus(MessageManager.getString("label.empty_alignment_job"));
+      j.result.setStatus(MessageManager
+              .getString("label.empty_alignment_job"));
       ((MsaResult) j.result).setMsa(null);
     }
     try
@@ -467,7 +478,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       {
         if (jobsubmit == null)
         {
-          throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+          throw new Exception(MessageManager.formatMessage(
+                  "exception.web_service_returned_null_try_later",
+                  new String[] { WsUrl }));
         }
 
         throw new Exception(jobsubmit.getJobId());
@@ -485,9 +498,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo.setStatus(j.getJobnum(),
               WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.appendProgressText(
-              j.getJobnum(),
-              MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+      wsInfo.appendProgressText(j.getJobnum(), MessageManager
+              .getString("info.failed_to_submit_sequences_for_alignment"));
 
       // e.printStackTrace(); // TODO: JBPNote DEBUG
     }
@@ -532,8 +544,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
                   .getMsa();
           if (valign != null)
           {
-            wsInfo.appendProgressText(jobs[j].getJobnum(),
-                    MessageManager.getString("info.alignment_object_method_notes"));
+            wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager
+                    .getString("info.alignment_object_method_notes"));
             String[] lines = valign.getMethod();
             for (int line = 0; line < lines.length; line++)
             {
diff --git a/src/jalview/ws/jws1/SeqSearchWSClient.java b/src/jalview/ws/jws1/SeqSearchWSClient.java
index b688978..d731ced 100644
--- a/src/jalview/ws/jws1/SeqSearchWSClient.java
+++ b/src/jalview/ws/jws1/SeqSearchWSClient.java
@@ -20,6 +20,13 @@
  */
 package jalview.ws.jws1;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+
 import java.awt.Component;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -28,12 +35,14 @@ import java.util.Hashtable;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
+import ext.vamsas.SeqSearchI;
+import ext.vamsas.SeqSearchServiceLocator;
+import ext.vamsas.SeqSearchServiceSoapBindingStub;
+import ext.vamsas.ServiceHandle;
 
 /**
  * DOCUMENT ME!
@@ -76,18 +85,22 @@ public class SeqSearchWSClient extends WS1Client
     // name to service client name
     if (!sh.getAbstractName().equals(this.getServiceActionKey()))
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-    		  MessageManager.formatMessage("label.service_called_is_not_seq_search_service", new String[]{sh.getName()}),
-              MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage(
+                      "label.service_called_is_not_seq_search_service",
+                      new String[] { sh.getName() }), MessageManager
+              .getString("label.internal_jalview_error"),
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
     if ((wsInfo = setWebService(sh)) == null)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-    		  MessageManager.formatMessage("label.seq_search_service_is_unknown", new String[]{sh.getName()}),
-              MessageManager.getString("label.internal_jalview_error"),
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.seq_search_service_is_unknown",
+                      new String[] { sh.getName() }), MessageManager
+              .getString("label.internal_jalview_error"),
               JOptionPane.WARNING_MESSAGE);
 
       return;
@@ -208,13 +221,14 @@ public class SeqSearchWSClient extends WS1Client
     }
     if (!locateWebService())
     {
-      throw new Exception(MessageManager.formatMessage("exception.cannot_contact_service_endpoint_at", new String[]{WsURL}));
+      throw new Exception(MessageManager.formatMessage(
+              "exception.cannot_contact_service_endpoint_at",
+              new String[] { WsURL }));
     }
     String database = server.getDatabase();
     if (database == null)
     {
-      dbParamsForEndpoint.put(WsURL, new String[]
-      {});
+      dbParamsForEndpoint.put(WsURL, new String[] {});
       return null;
     }
     StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index 5d44ddd..a6e3731 100644
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -20,17 +20,23 @@
  */
 package jalview.ws.jws1;
 
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
 import jalview.io.NewickFile;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
 import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
 import vamsas.objects.simple.MsaResult;
 import vamsas.objects.simple.SeqSearchResult;
 
@@ -85,7 +91,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       int nseqs = 0;
       if (minlen < 0)
       {
-          throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_minlen_must_be_greater_zero"));
       }
       for (int i = 0; i < seqs.length; i++)
       {
@@ -126,8 +134,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
                     .extractGaps(jalview.util.Comparison.GapChars,
                             seqs[i].getSequenceAsString());
           }
-          emptySeqs.add(new String[]
-          { newname, empty });
+          emptySeqs.add(new String[] { newname, empty });
         }
       }
       if (submitGaps)
@@ -259,8 +266,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
          * trigger a 'fetchDBids' to annotate sequences with database ids...
          */
 
-        return new Object[]
-        { al, nf };
+        return new Object[] { al, nf };
       }
       return null;
     }
@@ -446,7 +452,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
   {
     if (!(job instanceof SeqSearchWSJob))
     {
-        throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_msawbjob_called",
+              new String[] { job.getClass().toString() }));
     }
     SeqSearchWSJob j = (SeqSearchWSJob) job;
     if (j.isSubmitted())
@@ -464,7 +472,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       j.setSubmitted(true);
       j.result = new MsaResult();
       j.result.setFinished(true);
-      j.result.setStatus(MessageManager.getString("label.empty_alignment_job"));
+      j.result.setStatus(MessageManager
+              .getString("label.empty_alignment_job"));
       ((MsaResult) j.result).setMsa(null);
     }
     try
@@ -483,7 +492,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       {
         if (jobsubmit == null)
         {
-          throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+          throw new Exception(MessageManager.formatMessage(
+                  "exception.web_service_returned_null_try_later",
+                  new String[] { WsUrl }));
         }
 
         throw new Exception(jobsubmit.getJobId());
@@ -501,9 +512,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo.setStatus(j.getJobnum(),
               WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.appendProgressText(
-              j.getJobnum(),
-              MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+      wsInfo.appendProgressText(j.getJobnum(), MessageManager
+              .getString("info.failed_to_submit_sequences_for_alignment"));
 
       // e.printStackTrace(); // TODO: JBPNote DEBUG
     }
@@ -541,8 +551,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
                   .getAlignment();
           if (valign != null)
           {
-            wsInfo.appendProgressText(jobs[j].getJobnum(),
-                    MessageManager.getString("info.alignment_object_method_notes"));
+            wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager
+                    .getString("info.alignment_object_method_notes"));
             String[] lines = valign.getMethod();
             for (int line = 0; line < lines.length; line++)
             {
@@ -642,7 +652,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       if (nf != null)
       {
-        af.ShowNewickTree(nf, MessageManager.formatMessage("label.tree_from", new String[]{this.alTitle}));
+        af.ShowNewickTree(nf, MessageManager.formatMessage(
+                "label.tree_from", new String[] { this.alTitle }));
       }
       // initialise with same renderer settings as in parent alignframe.
       af.getFeatureRenderer().transferSettings(this.featureSettings);
diff --git a/src/jalview/ws/jws1/WS1Client.java b/src/jalview/ws/jws1/WS1Client.java
index 07b9980..f111760 100644
--- a/src/jalview/ws/jws1/WS1Client.java
+++ b/src/jalview/ws/jws1/WS1Client.java
@@ -111,7 +111,9 @@ public abstract class WS1Client extends WSClient implements
   {
     if (serviceHandle == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_cannot_attach_ws_menu_entry"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_cannot_attach_ws_menu_entry"));
     }
     attachWSMenuEntry(wsmenu, serviceHandle, alignFrame);
   }
diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index 91be2e6..f929b1e 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -104,34 +104,29 @@ public class AADisorderClient extends JabawsCalcWorker implements
     Map fmap;
     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
             fmap = new HashMap());
-    fmap.put("Glob", new String[]
-    { "Globular Domain", "Predicted globular domain" });
+    fmap.put("Glob", new String[] { "Globular Domain",
+        "Predicted globular domain" });
     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
             fmap = new HashMap());
     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
             fmap = new HashMap());
-    fmap.put("REM465", new String[]
-    { "REM465", "Missing density" });
-    fmap.put("HOTLOOPS", new String[]
-    { "HOTLOOPS", "Flexible loops" });
-    fmap.put("COILS", new String[]
-    { "COILS", "Random coil" });
+    fmap.put("REM465", new String[] { "REM465", "Missing density" });
+    fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
+    fmap.put("COILS", new String[] { "COILS", "Random coil" });
     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
             fmap = new HashMap());
-    fmap.put("GlobDoms", new String[]
-    { "Globular Domain", "Predicted globular domain" });
-    fmap.put("Disorder", new String[]
-    { "Protein Disorder", "Probable unstructured peptide region" });
+    fmap.put("GlobDoms", new String[] { "Globular Domain",
+        "Predicted globular domain" });
+    fmap.put("Disorder", new String[] { "Protein Disorder",
+        "Probable unstructured peptide region" });
     Map> amap;
     annotMap = new HashMap>>();
     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
             amap = new HashMap>());
     amap.put("Dydx", new HashMap());
     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
-    amap.get("Dydx").put(THRESHOLD, new double[]
-    { 1, 0 });
-    amap.get("Dydx").put(RANGE, new float[]
-    { -1, +1 });
+    amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
+    amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
 
     amap.put("SmoothedScore", new HashMap());
     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
@@ -142,39 +137,27 @@ public class AADisorderClient extends JabawsCalcWorker implements
     amap.put("COILS", new HashMap());
     amap.put("HOTLOOPS", new HashMap());
     amap.put("REM465", new HashMap());
-    amap.get("COILS").put(THRESHOLD, new double[]
-    { 1, 0.516 });
-    amap.get("COILS").put(RANGE, new float[]
-    { 0, 1 });
-
-    amap.get("HOTLOOPS").put(THRESHOLD, new double[]
-    { 1, 0.6 });
-    amap.get("HOTLOOPS").put(RANGE, new float[]
-    { 0, 1 });
-    amap.get("REM465").put(THRESHOLD, new double[]
-    { 1, 0.1204 });
-    amap.get("REM465").put(RANGE, new float[]
-    { 0, 1 });
+    amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
+    amap.get("COILS").put(RANGE, new float[] { 0, 1 });
+
+    amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
+    amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
+    amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
+    amap.get("REM465").put(RANGE, new float[] { 0, 1 });
 
     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
             amap = new HashMap>());
     amap.put("Long", new HashMap());
     amap.put("Short", new HashMap());
-    amap.get("Long").put(THRESHOLD, new double[]
-    { 1, 0.5 });
-    amap.get("Long").put(RANGE, new float[]
-    { 0, 1 });
-    amap.get("Short").put(THRESHOLD, new double[]
-    { 1, 0.5 });
-    amap.get("Short").put(RANGE, new float[]
-    { 0, 1 });
+    amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
+    amap.get("Long").put(RANGE, new float[] { 0, 1 });
+    amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
+    amap.get("Short").put(RANGE, new float[] { 0, 1 });
     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
             amap = new HashMap>());
     amap.put("JRonn", new HashMap());
-    amap.get("JRonn").put(THRESHOLD, new double[]
-    { 1, 0.5 });
-    amap.get("JRonn").put(RANGE, new float[]
-    { 0, 1 });
+    amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
+    amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
   }
 
   @Override
@@ -249,8 +232,8 @@ public class AADisorderClient extends JabawsCalcWorker implements
                 if (type == null)
                 {
                   // create a default type for this feature
-                  type = new String[]
-                  { typeName + " (" + scr.getMethod() + ")",
+                  type = new String[] {
+                      typeName + " (" + scr.getMethod() + ")",
                       service.getActionText() };
                 }
                 if (vals.hasNext())
@@ -285,8 +268,7 @@ public class AADisorderClient extends JabawsCalcWorker implements
                       typename = service.serviceType + " ("
                               + scr.getMethod() + ")",
                       calcName = service.getServiceTypeURI() + "/"
-                              + scr.getMethod(),
-                      aseq, base + 1, scr);
+                              + scr.getMethod(), aseq, base + 1, scr);
               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 
               Map styleMap = (annotTypeMap == null) ? null
diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index a7cc5b6..43d6202 100644
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -364,11 +364,13 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
 
   /**
    * validate input for dynamic/non-dynamic update context
+   * 
    * @param dynamic
    * @param seqs
    * @return true if input is valid
    */
-  abstract boolean checkValidInputSeqs(boolean dynamic, List seqs);
+  abstract boolean checkValidInputSeqs(boolean dynamic,
+          List seqs);
 
   abstract String submitToService(
           List seqs)
@@ -390,11 +392,11 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
       String id = rslt;
       if (cancelJob(rslt))
       {
-        System.err.println("Cancelled job "+id);
+        System.err.println("Cancelled job " + id);
       }
-      else 
+      else
       {
-        System.err.println("Job "+id+" couldn't be cancelled.");
+        System.err.println("Job " + id + " couldn't be cancelled.");
       }
     } catch (Exception q)
     {
diff --git a/src/jalview/ws/jws2/JPred301Client.java b/src/jalview/ws/jws2/JPred301Client.java
index db70fa0..e4d6329 100644
--- a/src/jalview/ws/jws2/JPred301Client.java
+++ b/src/jalview/ws/jws2/JPred301Client.java
@@ -128,8 +128,7 @@ public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
           String[] k = jpredRowLabels.get(fsq.getId());
           if (k == null)
           {
-            k = new String[]
-            { fsq.getId(), "JNet Output" };
+            k = new String[] { fsq.getId(), "JNet Output" };
           }
           if (fsq.getId().startsWith("JNETSOL"))
           {
@@ -142,7 +141,8 @@ public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
               {
                 sol[spos] = '0';
               }
-              if (vseq[spos] == 'B' && (sol[spos]=='0' || sol[spos] < amnt))
+              if (vseq[spos] == 'B'
+                      && (sol[spos] == '0' || sol[spos] < amnt))
               {
                 sol[spos] = amnt;
               }
@@ -252,7 +252,7 @@ public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
         try
         {
           elm[i] = new Annotation("" + annot, "" + annot, annot,
-                  Integer.valueOf(""+annot));
+                  Integer.valueOf("" + annot));
         } catch (Exception x)
         {
           System.err.println("Expected numeric value in character '"
diff --git a/src/jalview/ws/jws2/JWs2Job.java b/src/jalview/ws/jws2/JWs2Job.java
index d820318..9482d1d 100644
--- a/src/jalview/ws/jws2/JWs2Job.java
+++ b/src/jalview/ws/jws2/JWs2Job.java
@@ -20,10 +20,10 @@
  */
 package jalview.ws.jws2;
 
-import compbio.metadata.JobStatus;
-
 import jalview.ws.AWsJob;
 
+import compbio.metadata.JobStatus;
+
 /**
  * job status processing for JWS2 jobs.
  * 
diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java
index baa1d9d..34b8a72 100644
--- a/src/jalview/ws/jws2/JabaParamStore.java
+++ b/src/jalview/ws/jws2/JabaParamStore.java
@@ -20,6 +20,16 @@
  */
 package jalview.ws.jws2;
 
+import jalview.util.MessageManager;
+import jalview.ws.jws2.dm.JabaOption;
+import jalview.ws.jws2.dm.JabaParameter;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.WsParamSetI;
+
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -34,16 +44,6 @@ import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
-import jalview.util.MessageManager;
-import jalview.ws.jws2.dm.JabaOption;
-import jalview.ws.jws2.dm.JabaParameter;
-import jalview.ws.jws2.dm.JabaWsParamSet;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParamManager;
-import jalview.ws.params.WsParamSetI;
-
 public class JabaParamStore implements ParamDatastoreI
 {
 
@@ -166,7 +166,9 @@ public class JabaParamStore implements ParamDatastoreI
       }
       if (narg == null)
       {
-        throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cannot_handle_jaba_param",
+                new String[] { rg.getClass().toString() }));
       }
       else
       {
@@ -201,7 +203,9 @@ public class JabaParamStore implements ParamDatastoreI
               .getOption() : null;
       if (narg == null)
       {
-          throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cannot_handle_jaba_param",
+                new String[] { rg.getClass().toString() }));
       }
       else
       {
@@ -239,7 +243,9 @@ public class JabaParamStore implements ParamDatastoreI
     }
     if (servicePresets.containsKey(name))
     {
-      throw new Error(MessageManager.getString("error.implementation_error_attempt_to_delete_service_preset"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_attempt_to_delete_service_preset"));
     }
   }
 
@@ -248,8 +254,7 @@ public class JabaParamStore implements ParamDatastoreI
           List jobParams)
   {
     JabaWsParamSet jps = new JabaWsParamSet(presetName, text, jobParams);
-    jps.setApplicableUrls(new String[]
-    { service.getUri() });
+    jps.setApplicableUrls(new String[] { service.getUri() });
     editedParams.put(jps.getName(), jps);
     if (manager != null)
     {
@@ -265,13 +270,16 @@ public class JabaParamStore implements ParamDatastoreI
             : getPreset(presetName));
     if (jps == null)
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_locate_oldname_presetname", new String[]{oldName,presetName}));
+      throw new Error(
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_cannot_locate_oldname_presetname",
+                              new String[] { oldName, presetName }));
     }
     jps.setName(presetName);
     jps.setDescription(text);
     jps.setArguments(jobParams);
-    jps.setApplicableUrls(new String[]
-    { service.getUri() });
+    jps.setApplicableUrls(new String[] { service.getUri() });
     if (oldName != null && !oldName.equals(jps.getName()))
     {
       editedParams.remove(oldName);
@@ -315,7 +323,9 @@ public class JabaParamStore implements ParamDatastoreI
   {
     if (!involves(urls))
     {
-      throw new IOException(MessageManager.getString("error.implementation_error_cannot_find_service_url_in_given_set"));
+      throw new IOException(
+              MessageManager
+                      .getString("error.implementation_error_cannot_find_service_url_in_given_set"));
 
     }
     JabaWsParamSet wsp = new JabaWsParamSet();
@@ -340,11 +350,17 @@ public class JabaParamStore implements ParamDatastoreI
   {
     if (!involves(pset.getApplicableUrls()))
     {
-      throw new IOException(MessageManager.formatMessage("error.implementation_error_cannot_find_service_url_in_given_set_param_store", new String[]{service.getUri()}));
+      throw new IOException(
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_cannot_find_service_url_in_given_set_param_store",
+                              new String[] { service.getUri() }));
     }
     if (!(pset instanceof JabaWsParamSet))
     {
-      throw new Error(MessageManager.getString("error.implementation_error_jabaws_param_set_only_handled_by"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_jabaws_param_set_only_handled_by"));
     }
 
     StringBuffer rslt = new StringBuffer();
diff --git a/src/jalview/ws/jws2/JabaPreset.java b/src/jalview/ws/jws2/JabaPreset.java
index 64298f5..279a4f0 100644
--- a/src/jalview/ws/jws2/JabaPreset.java
+++ b/src/jalview/ws/jws2/JabaPreset.java
@@ -56,8 +56,7 @@ public class JabaPreset implements WsParamSetI
   @Override
   public String[] getApplicableUrls()
   {
-    return new String[]
-    { service.getUri() };
+    return new String[] { service.getUri() };
   }
 
   @Override
@@ -75,7 +74,9 @@ public class JabaPreset implements WsParamSetI
   @Override
   public void setSourceFile(String newfile)
   {
-    throw new Error(MessageManager.formatMessage("error.cannot_set_source_file_for", new String[]{getClass().toString()}));
+    throw new Error(MessageManager.formatMessage(
+            "error.cannot_set_source_file_for", new String[] { getClass()
+                    .toString() }));
   }
 
   @Override
@@ -88,13 +89,17 @@ public class JabaPreset implements WsParamSetI
     } catch (Exception e)
     {
       e.printStackTrace();
-      throw new Error(MessageManager.getString("error.mismatch_service_instance_preset"));
+      throw new Error(
+              MessageManager
+                      .getString("error.mismatch_service_instance_preset"));
     }
   }
 
   @Override
   public void setArguments(List args)
   {
-    throw new Error(MessageManager.getString("error.cannot_set_params_for_ws_preset"));
+    throw new Error(
+            MessageManager
+                    .getString("error.cannot_set_params_for_ws_preset"));
   }
 }
diff --git a/src/jalview/ws/jws2/JabaWsServerQuery.java b/src/jalview/ws/jws2/JabaWsServerQuery.java
index 5b83e11..a3ed47a 100644
--- a/src/jalview/ws/jws2/JabaWsServerQuery.java
+++ b/src/jalview/ws/jws2/JabaWsServerQuery.java
@@ -74,15 +74,15 @@ public class JabaWsServerQuery implements Runnable
     this.jwsserver = server;
   }
 
-  Services[] JABAWS1SERVERS = new Services[]
-  { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
-      Services.ProbconsWS, Services.TcoffeeWS };
+  Services[] JABAWS1SERVERS = new Services[] { Services.ClustalWS,
+      Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
+      Services.TcoffeeWS };
 
-  Services[] JABAWS2SERVERS = new Services[]
-  { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
-      Services.ProbconsWS, Services.TcoffeeWS, Services.AAConWS,
-      Services.DisemblWS, Services.GlobPlotWS, Services.IUPredWS,
-      Services.JronnWS, Services.RNAalifoldWS };
+  Services[] JABAWS2SERVERS = new Services[] { Services.ClustalWS,
+      Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
+      Services.TcoffeeWS, Services.AAConWS, Services.DisemblWS,
+      Services.GlobPlotWS, Services.IUPredWS, Services.JronnWS,
+      Services.RNAalifoldWS };
 
   /*
    * (non-Javadoc)
@@ -169,9 +169,8 @@ public class JabaWsServerQuery implements Runnable
               service = Jws2Client.connect(jwsserver, srv);
             } catch (Exception e)
             {
-              System.err.println("Jws2 Discoverer: Problem on "
-                      + jwsserver + " with service " + srv + ":\n"
-                      + e.getMessage());
+              System.err.println("Jws2 Discoverer: Problem on " + jwsserver
+                      + " with service " + srv + ":\n" + e.getMessage());
               if (!(e instanceof javax.xml.ws.WebServiceException))
               {
                 e.printStackTrace();
@@ -237,8 +236,10 @@ public class JabaWsServerQuery implements Runnable
   {
     // return Jws2Client.validURL(jwsserver); // checks syntax only
     boolean result = false;
-    if (server != null) {
-      try {
+    if (server != null)
+    {
+      try
+      {
         URL url = new URL(server);
         url.openStream().close();
         result = true;
diff --git a/src/jalview/ws/jws2/JabawsCalcWorker.java b/src/jalview/ws/jws2/JabawsCalcWorker.java
index 551b957..4388f6c 100644
--- a/src/jalview/ws/jws2/JabawsCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsCalcWorker.java
@@ -115,7 +115,10 @@ public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
         rslt = aaservice.customAnalize(seqs, getJabaArguments());
       } catch (WrongParameterException x)
       {
-        throw new JobSubmissionException(MessageManager.getString("exception.jobsubmission_invalid_params_set"), x);
+        throw new JobSubmissionException(
+                MessageManager
+                        .getString("exception.jobsubmission_invalid_params_set"),
+                x);
 
       }
     }
diff --git a/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
index 83bac78..0baa767 100644
--- a/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
@@ -20,32 +20,31 @@
  */
 package jalview.ws.jws2;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
 import java.util.Iterator;
 import java.util.List;
 
 import compbio.data.msa.MsaWS;
-import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.Score;
-import compbio.data.sequence.ScoreManager;
 import compbio.metadata.Argument;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.metadata.WrongParameterException;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.util.MessageManager;
-import jalview.workers.AlignCalcWorker;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
 
-public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalcWorker
+public abstract class JabawsMsaInterfaceAlignCalcWorker extends
+        AbstractJabaCalcWorker
 {
 
   @SuppressWarnings("unchecked")
@@ -59,8 +58,8 @@ public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalc
     super(alignViewport, alignPanel);
   }
 
-  public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
-          WsParamSetI preset, List paramset)
+  public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
+          AlignFrame alignFrame, WsParamSetI preset, List paramset)
   {
     this(alignFrame.getCurrentView(), alignFrame.alignPanel);
     this.guiProgress = alignFrame;
@@ -130,7 +129,10 @@ public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalc
         rslt = msaservice.customAlign(seqs, getJabaArguments());
       } catch (WrongParameterException x)
       {
-          throw new JobSubmissionException(MessageManager.getString("exception.jobsubmission_invalid_params_set"), x);
+        throw new JobSubmissionException(
+                MessageManager
+                        .getString("exception.jobsubmission_invalid_params_set"),
+                x);
       }
     }
     return rslt;
diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java
index 696ddeb..c0b701b 100644
--- a/src/jalview/ws/jws2/Jws2Client.java
+++ b/src/jalview/ws/jws2/Jws2Client.java
@@ -78,7 +78,9 @@ public abstract class Jws2Client extends jalview.ws.WSClient
          * arguments. for (Argument opt : arguments) { newargs.add(opt); } }
          * paramset = newargs; } else {
          */
-        throw new Error(MessageManager.getString("error.implementation_error_can_only_instantiate_jaba_param_sets"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_can_only_instantiate_jaba_param_sets"));
       }
     }
     else
@@ -174,7 +176,6 @@ public abstract class Jws2Client extends jalview.ws.WSClient
    */
   abstract void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
           final AlignFrame alignFrame);
-  
 
   protected boolean registerAAConWSInstance(final JMenu wsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
@@ -231,7 +232,8 @@ public abstract class Jws2Client extends jalview.ws.WSClient
       final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
               aaui.getAAconToggle());
 
-      aaConEnabled.setToolTipText(JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip()));
+      aaConEnabled.setToolTipText(JvSwingUtils.wrapTooltip(true,
+              aaui.getAAconToggleTooltip()));
       aaConEnabled.addActionListener(new ActionListener()
       {
         @Override
@@ -254,9 +256,11 @@ public abstract class Jws2Client extends jalview.ws.WSClient
       });
       wsmenu.add(aaConEnabled);
       final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
-      modifyParams.setToolTipText("
"
-              + JvSwingUtils.wrapTooltip(false, aaui.getAAeditSettingsTooltip()
-                      + "
") + "");
+      modifyParams
+              .setToolTipText("
"
+                      + JvSwingUtils.wrapTooltip(false,
+                              aaui.getAAeditSettingsTooltip() + "
")
+                      + "");
       modifyParams.addActionListener(new ActionListener()
       {
 
@@ -408,7 +412,8 @@ public abstract class Jws2Client extends jalview.ws.WSClient
     {
       // TODO raise dialog box explaining error, and/or open the JABA
       // preferences menu.
-      throw new Error(MessageManager.getString("error.no_aacon_service_found"));
+      throw new Error(
+              MessageManager.getString("error.no_aacon_service_found"));
     }
     return new AAConSettings(true, service, null, null);
   }
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 792e93f..1b2c708 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -145,6 +145,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     this.aborted = aborted;
 
   }
+
   public void run()
   {
 
@@ -172,9 +173,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
     // first set up exclusion list if needed
     final Set ignoredServices = new HashSet();
-    for (String ignored : Cache.getDefault(
-            "IGNORED_JABAWS_SERVICETYPES", "")
-            .split("\\|"))
+    for (String ignored : Cache.getDefault("IGNORED_JABAWS_SERVICETYPES",
+            "").split("\\|"))
     {
       ignoredServices.add(ignored);
     }
@@ -425,9 +425,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       service.attachWSMenuEntry(atpoint, alignFrame);
       if (alternates.containsKey(service.serviceType))
       {
-        atpoint.add(hitm = new JMenu(MessageManager.getString("label.switch_server")));
-        hitm.setToolTipText(JvSwingUtils
-                .wrapTooltip(false, MessageManager.getString("label.choose_jabaws_server")));
+        atpoint.add(hitm = new JMenu(MessageManager
+                .getString("label.switch_server")));
+        hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
+                MessageManager.getString("label.choose_jabaws_server")));
         for (final Jws2Instance sv : alternates.get(service.serviceType))
         {
           JMenuItem itm;
@@ -516,7 +517,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
           atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
           if (atpoint.getToolTipText() == null)
           {
-            atpoint.setToolTipText(MessageManager.formatMessage("label.services_at", new String[]{host}));
+            atpoint.setToolTipText(MessageManager.formatMessage(
+                    "label.services_at", new String[] { host }));
           }
         }
         if (bytype)
@@ -560,8 +562,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                 Desktop.showUrl(service.getHost());
               }
             });
-            hitm.setToolTipText(JvSwingUtils
-                    .wrapTooltip(true, MessageManager.getString("label.open_jabaws_web_page")));
+            hitm.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                    MessageManager.getString("label.open_jabaws_web_page")));
             lasthostFor.put(service.action, host);
           }
           hostLabels.add(host + service.serviceType
@@ -710,9 +712,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
           }
         } catch (MalformedURLException ex)
         {
-          Cache.log
-                  .warn("Problem whilst trying to make a URL from '"
-                          + ((url != null) ? url : "") + "'");
+          Cache.log.warn("Problem whilst trying to make a URL from '"
+                  + ((url != null) ? url : "") + "'");
           Cache.log
                   .warn("This was probably due to a malformed comma separated list"
                           + " in the "
@@ -723,9 +724,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       }
     } catch (Exception ex)
     {
-      Cache.log.warn(
-              "Error parsing comma separated list of urls in "
-                      + JWS2HOSTURLS + " preference.", ex);
+      Cache.log.warn("Error parsing comma separated list of urls in "
+              + JWS2HOSTURLS + " preference.", ex);
     }
     return urls;
   }
@@ -746,8 +746,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     try
     {
-      compbio.ws.client.WSTester.main(new String[]
-      { "-h=" + foo.toString() });
+      compbio.ws.client.WSTester
+              .main(new String[] { "-h=" + foo.toString() });
     } catch (Exception e)
     {
       e.printStackTrace();
diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 5fe3e74..47130a3 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -109,8 +109,7 @@ public class MsaWSClient extends Jws2Client
       // redundant at mo - but may change
       JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.service_called_is_not_msa_service",
-                      new String[]
-                      { sh.serviceType }), MessageManager
+                      new String[] { sh.serviceType }), MessageManager
               .getString("label.internal_jalview_error"),
               JOptionPane.WARNING_MESSAGE);
 
@@ -120,8 +119,8 @@ public class MsaWSClient extends Jws2Client
     if ((wsInfo = setWebService(sh, false)) == null)
     {
       JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
-              .formatMessage("label.msa_service_is_unknown", new String[]
-              { sh.serviceType }), MessageManager
+              .formatMessage("label.msa_service_is_unknown",
+                      new String[] { sh.serviceType }), MessageManager
               .getString("label.internal_jalview_error"),
               JOptionPane.WARNING_MESSAGE);
 
@@ -130,7 +129,6 @@ public class MsaWSClient extends Jws2Client
 
     startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
 
-
   }
 
   public MsaWSClient()
@@ -195,8 +193,6 @@ public class MsaWSClient extends Jws2Client
     System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"));
   }
 
-
-
   protected String getServiceActionKey()
   {
     return "MsaWS";
@@ -251,8 +247,7 @@ public class MsaWSClient extends Jws2Client
       {
         action = "Realign ";
         msawsmenu = new JMenu(MessageManager.formatMessage(
-                "label.realign_with_params", new String[]
-                { svcname }));
+                "label.realign_with_params", new String[] { svcname }));
         msawsmenu.setToolTipText(MessageManager
                 .getString("label.align_sequences_to_existing_alignment"));
         rmsawsmenu.add(msawsmenu);
@@ -260,11 +255,11 @@ public class MsaWSClient extends Jws2Client
       final boolean withGaps = submitGaps;
 
       JMenuItem method = new JMenuItem(MessageManager.formatMessage(
-              "label.calcname_with_default_settings", new String[]
-              { calcName }));
-      method.setToolTipText(MessageManager.formatMessage(
-              "label.action_with_default_settings", new String[]
-              { action }));
+              "label.calcname_with_default_settings",
+              new String[] { calcName }));
+      method.setToolTipText(MessageManager
+              .formatMessage("label.action_with_default_settings",
+                      new String[] { action }));
 
       method.addActionListener(new ActionListener()
       {
@@ -274,9 +269,9 @@ public class MsaWSClient extends Jws2Client
 
           if (msa != null)
           {
-          new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
-                  true, alignFrame.getViewport().getAlignment()
-                          .getDataset(), alignFrame);
+            new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+                    true, alignFrame.getViewport().getAlignment()
+                            .getDataset(), alignFrame);
           }
 
         }
@@ -299,8 +294,9 @@ public class MsaWSClient extends Jws2Client
             if (msa != null)
             {
               new MsaWSClient(service, null, null, true, alignFrame
-                    .getTitle(), msa, withGaps, true, alignFrame
-                    .getViewport().getAlignment().getDataset(), alignFrame);
+                      .getTitle(), msa, withGaps, true, alignFrame
+                      .getViewport().getAlignment().getDataset(),
+                      alignFrame);
             }
 
           }
@@ -309,9 +305,10 @@ public class MsaWSClient extends Jws2Client
         List presets = service.getParamStore().getPresets();
         if (presets != null && presets.size() > 0)
         {
-          JMenu presetlist = new JMenu(MessageManager.formatMessage(
-                  "label.run_with_preset_params", new String[]
-                  { calcName }));
+          JMenu presetlist = new JMenu(
+                  MessageManager.formatMessage(
+                          "label.run_with_preset_params",
+                          new String[] { calcName }));
 
           final int showToolTipFor = ToolTipManager.sharedInstance()
                   .getDismissDelay();
@@ -333,7 +330,8 @@ public class MsaWSClient extends Jws2Client
               @Override
               public void mouseExited(MouseEvent e)
               {
-                ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
+                ToolTipManager.sharedInstance().setDismissDelay(
+                        showToolTipFor);
               }
 
             });
@@ -356,9 +354,9 @@ public class MsaWSClient extends Jws2Client
                 if (msa != null)
                 {
                   MsaWSClient msac = new MsaWSClient(service, preset,
-                          alignFrame.getTitle(),
-                        msa, false, true, alignFrame.getViewport()
-                                .getAlignment().getDataset(), alignFrame);
+                          alignFrame.getTitle(), msa, false, true,
+                          alignFrame.getViewport().getAlignment()
+                                  .getDataset(), alignFrame);
                 }
 
               }
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index d2c1b38..e2f3a7c 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -125,7 +125,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       int nseqs = 0;
       if (minlen < 0)
       {
-        throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_minlen_must_be_greater_zero"));
       }
       for (int i = 0; i < seqs.length; i++)
       {
@@ -164,8 +166,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
                     .extractGaps(jalview.util.Comparison.GapChars,
                             seqs[i].getSequenceAsString());
           }
-          emptySeqs.add(new String[]
-          { newname, empty });
+          emptySeqs.add(new String[] { newname, empty });
         }
       }
       return valid;
@@ -296,8 +297,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
         // account for any missing sequences
         jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
-        return new Object[]
-        { alseqs, msaorder };
+        return new Object[] { alseqs, msaorder };
       }
       return null;
     }
@@ -529,6 +529,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   {
     return validInput;
   }
+
   public boolean isCancellable()
   {
     return true;
@@ -655,7 +656,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     // boiler plate template
     if (!(job instanceof MsaWSJob))
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_msawbjob_called",
+              new String[] { job.getClass().toString() }));
     }
     MsaWSJob j = (MsaWSJob) job;
     if (j.isSubmitted())
@@ -701,28 +704,39 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       }
       else
       {
-        throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+        throw new Exception(MessageManager.formatMessage(
+                "exception.web_service_returned_null_try_later",
+                new String[] { WsUrl }));
       }
     } catch (compbio.metadata.UnsupportedRuntimeException _lex)
     {
       lex = _lex;
-      wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_server_doesnt_support_program", new String[]{_lex.getMessage()}));
-      wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.service_not_supported"));
+      wsInfo.appendProgressText(MessageManager.formatMessage(
+              "info.job_couldnt_be_run_server_doesnt_support_program",
+              new String[] { _lex.getMessage() }));
+      wsInfo.warnUser(_lex.getMessage(),
+              MessageManager.getString("warn.service_not_supported"));
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo.setStatus(j.getJobnum(),
               WebserviceInfo.STATE_STOPPED_SERVERERROR);
     } catch (compbio.metadata.LimitExceededException _lex)
     {
       lex = _lex;
-      wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_exceeded_hard_limit", new String[]{_lex.getMessage()}));
-      wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.input_is_too_big"));
+      wsInfo.appendProgressText(MessageManager.formatMessage(
+              "info.job_couldnt_be_run_exceeded_hard_limit",
+              new String[] { _lex.getMessage() }));
+      wsInfo.warnUser(_lex.getMessage(),
+              MessageManager.getString("warn.input_is_too_big"));
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
       wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
     } catch (compbio.metadata.WrongParameterException _lex)
     {
       lex = _lex;
-      wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.invalid_job_param_set"));
-      wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_incorrect_param_setting", new String[]{_lex.getMessage()}));
+      wsInfo.warnUser(_lex.getMessage(),
+              MessageManager.getString("warn.invalid_job_param_set"));
+      wsInfo.appendProgressText(MessageManager.formatMessage(
+              "info.job_couldnt_be_run_incorrect_param_setting",
+              new String[] { _lex.getMessage() }));
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
       wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
     } catch (Error e)
@@ -755,8 +769,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         // TODO: JBPNote catch timeout or other fault types explicitly
 
         j.setAllowedServerExceptions(0);
-        wsInfo.appendProgressText(j.getJobnum(),
-                MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+        wsInfo.appendProgressText(j.getJobnum(), MessageManager
+                .getString("info.failed_to_submit_sequences_for_alignment"));
       }
     }
   }
@@ -764,7 +778,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   public void parseResult()
   {
     long progbar = System.currentTimeMillis();
-    wsInfo.setProgressBar(MessageManager.getString("status.collecting_job_results"), progbar);
+    wsInfo.setProgressBar(
+            MessageManager.getString("status.collecting_job_results"),
+            progbar);
     int results = 0; // number of result sets received
     JobStateSummary finalState = new JobStateSummary();
     try
@@ -995,8 +1011,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI
      * SplitFrame with the other pane similarly aligned.
      */
     AlignFrame requestedBy = getRequestingAlignFrame();
-    if (requestedBy != null && requestedBy.getSplitViewContainer() != null
-    		&& requestedBy.getSplitViewContainer().getComplement(requestedBy)!=null)
+    if (requestedBy != null
+            && requestedBy.getSplitViewContainer() != null
+            && requestedBy.getSplitViewContainer().getComplement(
+                    requestedBy) != null)
     {
       AlignmentI complement = requestedBy.getSplitViewContainer()
               .getComplement(requestedBy);
diff --git a/src/jalview/ws/jws2/ParameterUtils.java b/src/jalview/ws/jws2/ParameterUtils.java
index 855f4d9..62ddd0a 100644
--- a/src/jalview/ws/jws2/ParameterUtils.java
+++ b/src/jalview/ws/jws2/ParameterUtils.java
@@ -22,12 +22,15 @@ package jalview.ws.jws2;
 
 import jalview.util.MessageManager;
 
-import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 
-import compbio.metadata.*;
+import compbio.metadata.Option;
+import compbio.metadata.Parameter;
+import compbio.metadata.RunnerConfig;
+import compbio.metadata.ValueConstrain;
+import compbio.metadata.WrongParameterException;
 
 public class ParameterUtils
 {
@@ -146,8 +149,7 @@ public class ParameterUtils
       }
       else
       {
-        copy.addOptionNames(names.toArray(new String[]
-        {}));
+        copy.addOptionNames(names.toArray(new String[] {}));
       }
     }
     try
@@ -183,7 +185,9 @@ public class ParameterUtils
     } catch (Exception e)
     {
       e.printStackTrace();
-      throw new Error(MessageManager.getString("error.implementation_error_couldnt_copy_value_constraint"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_couldnt_copy_value_constraint"));
     }
   }
 
@@ -198,8 +202,7 @@ public class ParameterUtils
     List pv = parameter.getPossibleValues();
     if (pv != null)
     {
-      copy.addPossibleValues(pv.toArray(new String[]
-      {}));
+      copy.addPossibleValues(pv.toArray(new String[] {}));
     }
     setOptionFrom(copy, parameter);
     return copy;
diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index ca1fd50..41aa223 100644
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -372,8 +372,7 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
       description = typename;
     }
 
-    return new String[]
-    { typename, description };
+    return new String[] { typename, description };
   }
 
   // Check whether, at position i there is a base contact and return all the
diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index 1ddc02d..187540c 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -21,7 +21,6 @@
 package jalview.ws.jws2;
 
 import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
@@ -35,12 +34,8 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.List;
 
-import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
 
 /**
  * @author jprocter
@@ -98,15 +93,15 @@ public class SequenceAnnotationWSClient extends Jws2Client
         try
         {
           worker = (AbstractJabaCalcWorker) (clientClass
-                  .getConstructor(new Class[]
-                  { Jws2Instance.class, AlignFrame.class,
-                      WsParamSetI.class, List.class })
-                  .newInstance(new Object[]
-                  { sh, alignFrame, this.preset, paramset }));
+                  .getConstructor(new Class[] { Jws2Instance.class,
+                      AlignFrame.class, WsParamSetI.class, List.class })
+                  .newInstance(new Object[] { sh, alignFrame, this.preset,
+                      paramset }));
         } catch (Exception x)
         {
           x.printStackTrace();
-          throw new Error(MessageManager.getString("error.implementation_error"), x);
+          throw new Error(
+                  MessageManager.getString("error.implementation_error"), x);
         }
         alignFrame.getViewport().getCalcManager().registerWorker(worker);
         alignFrame.getViewport().getCalcManager().startWorker(worker);
@@ -176,8 +171,8 @@ public class SequenceAnnotationWSClient extends Jws2Client
             service.serviceType.length() - 2);
 
     JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
-            "label.calcname_with_default_settings", new String[]
-            { calcName }));
+            "label.calcname_with_default_settings",
+            new String[] { calcName }));
     annotservice.addActionListener(new ActionListener()
     {
 
@@ -209,15 +204,20 @@ public class SequenceAnnotationWSClient extends Jws2Client
       List presets = service.getParamStore().getPresets();
       if (presets != null && presets.size() > 0)
       {
-        JMenu presetlist = new JMenu(MessageManager.formatMessage("label.run_with_preset", new String[]{calcName}));
+        JMenu presetlist = new JMenu(MessageManager.formatMessage(
+                "label.run_with_preset", new String[] { calcName }));
 
         for (final WsParamSetI preset : presets)
         {
           final JMenuItem methodR = new JMenuItem(preset.getName());
-          methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, ""
-                          + (preset.isModifiable() ? MessageManager.getString("label.user_preset")
-                                  : MessageManager.getString("label.service_preset")) + "
"
-                          + preset.getDescription()));
+          methodR.setToolTipText(JvSwingUtils.wrapTooltip(
+                  true,
+                  ""
+                          + (preset.isModifiable() ? MessageManager
+                                  .getString("label.user_preset")
+                                  : MessageManager
+                                          .getString("label.service_preset"))
+                          + "
" + preset.getDescription()));
           methodR.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -248,7 +248,9 @@ public class SequenceAnnotationWSClient extends Jws2Client
             Desktop.instance.showUrl(service.docUrl);
           }
         });
-        annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.view_service_doc_url", new String[]{service.docUrl,service.docUrl})));
+        annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                MessageManager.formatMessage("label.view_service_doc_url",
+                        new String[] { service.docUrl, service.docUrl })));
         wsmenu.add(annotservice);
       }
     }
diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java
index ea04709..5f068b0 100644
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -20,12 +20,6 @@
  */
 package jalview.ws.jws2.dm;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import compbio.metadata.Argument;
-import compbio.metadata.Option;
-
 import jalview.util.MessageManager;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.JabaPreset;
@@ -34,6 +28,12 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import compbio.metadata.Argument;
+import compbio.metadata.Option;
+
 /**
  * preferences for running AACon service
  * 
@@ -93,7 +93,9 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
         return;
       }
       // Try even harder to migrate arguments.
-      throw new Error(MessageManager.getString("error.parameter_migration_not_implemented_yet"));
+      throw new Error(
+              MessageManager
+                      .getString("error.parameter_migration_not_implemented_yet"));
     }
   }
 
@@ -146,7 +148,6 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
   @Override
   public String[] getServiceURLs()
   {
-    return new String[]
-    { service.getUri() };
+    return new String[] { service.getUri() };
   }
 }
diff --git a/src/jalview/ws/jws2/dm/JabaOption.java b/src/jalview/ws/jws2/dm/JabaOption.java
index 69d6170..d9f8f46 100644
--- a/src/jalview/ws/jws2/dm/JabaOption.java
+++ b/src/jalview/ws/jws2/dm/JabaOption.java
@@ -95,7 +95,9 @@ public class JabaOption implements jalview.ws.params.OptionI
     } catch (Exception e)
     {
       e.printStackTrace();
-      throw new Error(MessageManager.getString("error.implementation_error_cannot_set_jaba_option"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_cannot_set_jaba_option"));
     }
   }
 
diff --git a/src/jalview/ws/jws2/dm/JabaParameter.java b/src/jalview/ws/jws2/dm/JabaParameter.java
index 293d2e3..5da71ab 100644
--- a/src/jalview/ws/jws2/dm/JabaParameter.java
+++ b/src/jalview/ws/jws2/dm/JabaParameter.java
@@ -23,6 +23,7 @@ package jalview.ws.jws2.dm;
 import jalview.ws.jws2.ParameterUtils;
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.ValueConstrainI;
+
 import compbio.metadata.Parameter;
 import compbio.metadata.ValueConstrain;
 
diff --git a/src/jalview/ws/jws2/dm/JabaValueConstrain.java b/src/jalview/ws/jws2/dm/JabaValueConstrain.java
index 59dce92..b99c381 100644
--- a/src/jalview/ws/jws2/dm/JabaValueConstrain.java
+++ b/src/jalview/ws/jws2/dm/JabaValueConstrain.java
@@ -20,11 +20,11 @@
  */
 package jalview.ws.jws2.dm;
 
-import compbio.metadata.ValueConstrain;
-
 import jalview.util.MessageManager;
 import jalview.ws.params.ValueConstrainI;
 
+import compbio.metadata.ValueConstrain;
+
 public class JabaValueConstrain implements ValueConstrainI
 {
 
@@ -46,7 +46,11 @@ public class JabaValueConstrain implements ValueConstrainI
     {
       return ValueType.Integer;
     }
-    throw new Error(MessageManager.formatMessage("error.implementation_error_valuetype_doesnt_support_jabaws_type", new String[]{vc.toString()}));
+    throw new Error(
+            MessageManager
+                    .formatMessage(
+                            "error.implementation_error_valuetype_doesnt_support_jabaws_type",
+                            new String[] { vc.toString() }));
   }
 
   @Override
diff --git a/src/jalview/ws/jws2/dm/JabaWsParamSet.java b/src/jalview/ws/jws2/dm/JabaWsParamSet.java
index d7ca7ef..6d2b057 100644
--- a/src/jalview/ws/jws2/dm/JabaWsParamSet.java
+++ b/src/jalview/ws/jws2/dm/JabaWsParamSet.java
@@ -20,16 +20,16 @@
  */
 package jalview.ws.jws2.dm;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import compbio.metadata.Option;
-
 import jalview.util.MessageManager;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import compbio.metadata.Option;
+
 public class JabaWsParamSet implements WsParamSetI
 {
   /**
@@ -54,7 +54,9 @@ public class JabaWsParamSet implements WsParamSetI
       {
         if (!allJaba(jobParams))
         {
-          throw new Error(MessageManager.getString("error.cannot_create_jabaws_param_set"));
+          throw new Error(
+                  MessageManager
+                          .getString("error.cannot_create_jabaws_param_set"));
         }
         else
         {
@@ -177,7 +179,9 @@ public class JabaWsParamSet implements WsParamSetI
   {
     if (!allJaba(args))
     {
-      throw new Error(MessageManager.getString("error.cannot_set_arguments_to_jabaws_param_set"));
+      throw new Error(
+              MessageManager
+                      .getString("error.cannot_set_arguments_to_jabaws_param_set"));
     }
     jabaArguments = new ArrayList