Jalview 2.8 Source Header
authorjprocter <jprocter@compbio.dundee.ac.uk>
Thu, 4 Oct 2012 16:43:26 +0000 (17:43 +0100)
committerjprocter <jprocter@compbio.dundee.ac.uk>
Mon, 22 Oct 2012 21:42:07 +0000 (22:42 +0100)
commit59d682209891099d46b960509907c79e3fb276fe
treedccbdb951aba6d4c3de6f48260a13beb17a9ffb5
parentd1b697c33b69a6dfe55df789eec5ac9881013681
Jalview 2.8 Source Header
758 files changed:
doc/AddingGroovySupport.html
doc/JalviewRNASupport.html
doc/building.html
doc/developing.html
doc/index.html
doc/newdmobj.html
examples/appletParameters.html
examples/applets.html
examples/embedded.html
examples/embeddedWJmol.html
examples/exampleFeatures.txt
examples/formComplete.html
examples/jalviewLiteJs.html
examples/javascript/jalview.js
examples/javascriptLaunch.html
examples/linkedapplets_ng.html
help/help.hs
help/help.jhm
help/helpTOC.xml
help/html/calculations/consensus.html
help/html/calculations/conservation.html
help/html/calculations/pairwise.html
help/html/calculations/pca.html
help/html/calculations/quality.html
help/html/calculations/recoverInputdata.html
help/html/calculations/redundancy.html
help/html/calculations/scorematrices.html
help/html/calculations/sorting.html
help/html/calculations/structureconsensus.html
help/html/calculations/tree.html
help/html/calculations/treeviewer.html
help/html/colourSchemes/abovePID.html
help/html/colourSchemes/annotationColouring.html
help/html/colourSchemes/blosum.html
help/html/colourSchemes/buried.html
help/html/colourSchemes/clustal.html
help/html/colourSchemes/conservation.html
help/html/colourSchemes/helix.html
help/html/colourSchemes/hydrophobic.html
help/html/colourSchemes/index.html
help/html/colourSchemes/nucleotide.html
help/html/colourSchemes/pid.html
help/html/colourSchemes/purinepyrimidine.html
help/html/colourSchemes/rnahelicesColouring.html
help/html/colourSchemes/strand.html
help/html/colourSchemes/taylor.html
help/html/colourSchemes/textcolour.html
help/html/colourSchemes/turn.html
help/html/colourSchemes/user.html
help/html/colourSchemes/zappo.html
help/html/editing/index.html
help/html/features/annotation.html
help/html/features/annotationsFormat.html
help/html/features/clarguments.html
help/html/features/codingfeatures.html
help/html/features/commandline.html
help/html/features/creatinFeatures.html
help/html/features/cursorMode.html
help/html/features/dasfeatures.html
help/html/features/dassettings.html
help/html/features/editingFeatures.html
help/html/features/featuresFormat.html
help/html/features/featureschemes.html
help/html/features/featuresettings.html
help/html/features/groovy.html
help/html/features/hiddenRegions.html
help/html/features/jalarchive.html
help/html/features/jmol.html
help/html/features/multipleViews.html
help/html/features/newkeystrokes.html
help/html/features/overview.html
help/html/features/pdbviewer.html
help/html/features/preferences.html
help/html/features/search.html
help/html/features/seqfeatures.html
help/html/features/seqfetch.html
help/html/features/seqmappings.html
help/html/features/varna.html
help/html/features/viewingpdbs.html
help/html/features/wrap.html
help/html/index.html
help/html/io/export.html
help/html/io/exportseqreport.html
help/html/io/fileformats.html
help/html/io/index.html
help/html/io/modellerpir.html
help/html/io/tcoffeescores.html
help/html/jalviewjnlp.html
help/html/keys.html
help/html/memory.html
help/html/menus/alignmentMenu.html
help/html/menus/alwannotations.html
help/html/menus/alwcalculate.html
help/html/menus/alwcolour.html
help/html/menus/alwedit.html
help/html/menus/alwfile.html
help/html/menus/alwformat.html
help/html/menus/alwselect.html
help/html/menus/alwview.html
help/html/menus/desktopMenu.html
help/html/menus/index.html
help/html/menus/popupMenu.html
help/html/menus/wsmenu.html
help/html/misc/aaproperties.html
help/html/misc/aminoAcids.html
help/html/misc/geneticCode.html
help/html/na/index.html
help/html/privacy.html
help/html/releases.html
help/html/vamsas/index.html
help/html/webServices/AACon.html
help/html/webServices/JABAWS.html
help/html/webServices/dbreffetcher.html
help/html/webServices/index.html
help/html/webServices/jnet.html
help/html/webServices/msaclient.html
help/html/webServices/newsreader.html
help/html/webServices/proteinDisorder.html
help/html/webServices/shmr.html
help/html/webServices/urllinks.html
help/html/webServices/webServicesParams.html
help/html/webServices/webServicesPrefs.html
help/html/whatsNew.html
nbproject/genfiles.properties
nbproject/project.properties
nbproject/project.xml
resources/embl_mapping.xml
resources/uniprot_mapping.xml
schemas/JalviewUserColours.xsd
schemas/JalviewWsParamSet.xsd
schemas/castor-mapping.xsd
schemas/jalview.nodesc.properties
schemas/jalview.properties
schemas/jalview.xsd
schemas/jalviewJvV1.xsd
schemas/vamsas.xsd
schemas/vamsasJvV1.xsd
src/MCview/AppletPDBCanvas.java
src/MCview/AppletPDBViewer.java
src/MCview/Atom.java
src/MCview/Bond.java
src/MCview/MCMatrix.java
src/MCview/PDBCanvas.java
src/MCview/PDBChain.java
src/MCview/PDBViewer.java
src/MCview/PDBfile.java
src/MCview/Residue.java
src/MCview/Zsort.java
src/ext/vamsas/IRegistry.java
src/ext/vamsas/IRegistryService.java
src/ext/vamsas/IRegistryServiceLocator.java
src/ext/vamsas/Jpred.java
src/ext/vamsas/JpredService.java
src/ext/vamsas/JpredServiceLocator.java
src/ext/vamsas/JpredSoapBindingStub.java
src/ext/vamsas/MuscleWS.java
src/ext/vamsas/MuscleWSService.java
src/ext/vamsas/MuscleWSServiceLocator.java
src/ext/vamsas/MuscleWSSoapBindingStub.java
src/ext/vamsas/RegistryServiceSoapBindingStub.java
src/ext/vamsas/SeqSearchI.java
src/ext/vamsas/SeqSearchServiceLocator.java
src/ext/vamsas/SeqSearchServiceService.java
src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
src/ext/vamsas/ServiceHandle.java
src/ext/vamsas/ServiceHandles.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/analysis/Finder.java
src/jalview/analysis/Grouping.java
src/jalview/analysis/NJTree.java
src/jalview/analysis/PCA.java
src/jalview/analysis/ParseProperties.java
src/jalview/analysis/Rna.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/analysis/SequenceIdMatcher.java
src/jalview/analysis/StructureFrequency.java
src/jalview/analysis/WUSSParseException.java
src/jalview/api/AlignCalcManagerI.java
src/jalview/api/AlignCalcWorkerI.java
src/jalview/api/AlignViewportI.java
src/jalview/api/AlignmentViewPanel.java
src/jalview/api/FeatureRenderer.java
src/jalview/api/OOMHandlerI.java
src/jalview/api/RotatableCanvasI.java
src/jalview/api/SequenceRenderer.java
src/jalview/api/SequenceStructureBinding.java
src/jalview/api/StructureSelectionManagerProvider.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/EditNameDialog.java
src/jalview/appletgui/EmbmenuFrame.java
src/jalview/appletgui/ExtJmol.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/FontChooser.java
src/jalview/appletgui/IdCanvas.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/IdwidthAdjuster.java
src/jalview/appletgui/JVDialog.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/PCAPanel.java
src/jalview/appletgui/PaintRefresher.java
src/jalview/appletgui/PairwiseAlignPanel.java
src/jalview/appletgui/RedundancyPanel.java
src/jalview/appletgui/RotatableCanvas.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SequenceRenderer.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/Tooltip.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/TreePanel.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/bin/JalviewLiteURLRetrieve.java
src/jalview/binding/Alignment.java
src/jalview/binding/Annotation.java
src/jalview/binding/AnnotationElement.java
src/jalview/binding/Colour.java
src/jalview/binding/Feature.java
src/jalview/binding/FeatureSettings.java
src/jalview/binding/Features.java
src/jalview/binding/JGroup.java
src/jalview/binding/JSeq.java
src/jalview/binding/JalviewModel.java
src/jalview/binding/JalviewModelSequence.java
src/jalview/binding/JalviewUserColours.java
src/jalview/binding/Pdbentry.java
src/jalview/binding/PdbentryItem.java
src/jalview/binding/Pdbids.java
src/jalview/binding/Property.java
src/jalview/binding/Sequence.java
src/jalview/binding/SequenceSet.java
src/jalview/binding/SequenceType.java
src/jalview/binding/Setting.java
src/jalview/binding/Tree.java
src/jalview/binding/UserColourScheme.java
src/jalview/binding/UserColours.java
src/jalview/binding/VAMSAS.java
src/jalview/binding/VamsasModel.java
src/jalview/binding/Viewport.java
src/jalview/commands/ChangeCaseCommand.java
src/jalview/commands/CommandI.java
src/jalview/commands/EditCommand.java
src/jalview/commands/OrderCommand.java
src/jalview/commands/RemoveGapColCommand.java
src/jalview/commands/RemoveGapsCommand.java
src/jalview/commands/SlideSequencesCommand.java
src/jalview/commands/TrimRegionCommand.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentOrder.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/AnnotatedCollectionI.java
src/jalview/datamodel/Annotation.java
src/jalview/datamodel/BinaryNode.java
src/jalview/datamodel/BinarySequence.java
src/jalview/datamodel/CigarArray.java
src/jalview/datamodel/CigarBase.java
src/jalview/datamodel/CigarCigar.java
src/jalview/datamodel/CigarSimple.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/DBRefSource.java
src/jalview/datamodel/FeatureProperties.java
src/jalview/datamodel/GraphLine.java
src/jalview/datamodel/HiddenSequences.java
src/jalview/datamodel/Mapping.java
src/jalview/datamodel/NodeTransformI.java
src/jalview/datamodel/PDBEntry.java
src/jalview/datamodel/Provenance.java
src/jalview/datamodel/ProvenanceEntry.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/SeqCigar.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceCollectionI.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/SequenceNode.java
src/jalview/datamodel/SequencePoint.java
src/jalview/datamodel/UniprotEntry.java
src/jalview/datamodel/UniprotFile.java
src/jalview/datamodel/UniprotProteinName.java
src/jalview/datamodel/UniprotSequence.java
src/jalview/datamodel/xdb/embl/BasePosition.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/datamodel/xdb/embl/EmblError.java
src/jalview/datamodel/xdb/embl/EmblFeature.java
src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
src/jalview/datamodel/xdb/embl/EmblFile.java
src/jalview/datamodel/xdb/embl/EmblSequence.java
src/jalview/datamodel/xdb/embl/Qualifier.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolCommands.java
src/jalview/ext/varna/JalviewVarnaBinding.java
src/jalview/ext/varna/VarnaCommands.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/AppJmol.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/AppVarna.java
src/jalview/gui/AppVarnaBinding.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/BlogReader.java
src/jalview/gui/Console.java
src/jalview/gui/CutAndPasteHtmlTransfer.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/EPSOptions.java
src/jalview/gui/EditNameDialog.java
src/jalview/gui/FeatureColourChooser.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/FontChooser.java
src/jalview/gui/IProgressIndicator.java
src/jalview/gui/IProgressIndicatorHandler.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/IdPanel.java
src/jalview/gui/IdwidthAdjuster.java
src/jalview/gui/JDatabaseTree.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/JalviewAppender.java
src/jalview/gui/JalviewChangeSupport.java
src/jalview/gui/JalviewDialog.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OOMWarning.java
src/jalview/gui/OptsAndParamsPage.java
src/jalview/gui/OptsParametersContainerI.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PaintRefresher.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/PromptUserConfig.java
src/jalview/gui/RedundancyPanel.java
src/jalview/gui/RestInputParamEditDialog.java
src/jalview/gui/RestServiceEditorPane.java
src/jalview/gui/RotatableCanvas.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/ScriptWindow.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SequenceRenderer.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/TextColourChooser.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/UserQuestionnaireCheck.java
src/jalview/gui/VamsasApplication.java
src/jalview/gui/ViewSelectionMenu.java
src/jalview/gui/WebserviceInfo.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/WsParamSetManager.java
src/jalview/gui/WsPreferences.java
src/jalview/io/AMSAFile.java
src/jalview/io/AlignFile.java
src/jalview/io/AlignmentProperties.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BLCFile.java
src/jalview/io/ClansFile.java
src/jalview/io/ClustalFile.java
src/jalview/io/DBRefFile.java
src/jalview/io/FastaFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileLoader.java
src/jalview/io/FileParse.java
src/jalview/io/FormatAdapter.java
src/jalview/io/HTMLOutput.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JPredFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/JalviewFileFilter.java
src/jalview/io/JalviewFileView.java
src/jalview/io/JnetAnnotationMaker.java
src/jalview/io/MSFfile.java
src/jalview/io/MatrixFile.java
src/jalview/io/ModellerDescription.java
src/jalview/io/NewickFile.java
src/jalview/io/PIRFile.java
src/jalview/io/PfamFile.java
src/jalview/io/PileUpfile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/SimpleBlastFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/WSWUBlastClient.java
src/jalview/io/packed/DataProvider.java
src/jalview/io/packed/JalviewDataset.java
src/jalview/io/packed/ParsePackedSet.java
src/jalview/io/packed/SimpleDataProvider.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/io/vamsas/DatastoreItem.java
src/jalview/io/vamsas/DatastoreRegistry.java
src/jalview/io/vamsas/Dbref.java
src/jalview/io/vamsas/LocalDocSyncObject.java
src/jalview/io/vamsas/Rangetype.java
src/jalview/io/vamsas/Sequencefeature.java
src/jalview/io/vamsas/Sequencemapping.java
src/jalview/io/vamsas/Tree.java
src/jalview/javascript/JSFunctionExec.java
src/jalview/javascript/JalviewLiteJsApi.java
src/jalview/javascript/JsCallBack.java
src/jalview/javascript/JsSelectionSender.java
src/jalview/javascript/MouseOverListener.java
src/jalview/javascript/MouseOverStructureListener.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GAlignmentPanel.java
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
src/jalview/jbgui/GCutAndPasteTransfer.java
src/jalview/jbgui/GDasSourceBrowser.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GFinder.java
src/jalview/jbgui/GFontChooser.java
src/jalview/jbgui/GPCAPanel.java
src/jalview/jbgui/GPairwiseAlignPanel.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GRestInputParamEditDialog.java
src/jalview/jbgui/GRestServiceEditorPane.java
src/jalview/jbgui/GRnaStructureViewer.java
src/jalview/jbgui/GSequenceLink.java
src/jalview/jbgui/GSliderPanel.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/jbgui/GTreePanel.java
src/jalview/jbgui/GUserDefinedColours.java
src/jalview/jbgui/GWebserviceInfo.java
src/jalview/jbgui/GWsPreferences.java
src/jalview/math/Matrix.java
src/jalview/math/RotatableMatrix.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/AwtRenderPanelI.java
src/jalview/schemabinding/version2/AlcodMap.java
src/jalview/schemabinding/version2/Alcodon.java
src/jalview/schemabinding/version2/AlcodonFrame.java
src/jalview/schemabinding/version2/Annotation.java
src/jalview/schemabinding/version2/AnnotationColours.java
src/jalview/schemabinding/version2/AnnotationElement.java
src/jalview/schemabinding/version2/CalcIdParam.java
src/jalview/schemabinding/version2/Colour.java
src/jalview/schemabinding/version2/DBRef.java
src/jalview/schemabinding/version2/Feature.java
src/jalview/schemabinding/version2/FeatureSettings.java
src/jalview/schemabinding/version2/Features.java
src/jalview/schemabinding/version2/Group.java
src/jalview/schemabinding/version2/HiddenColumns.java
src/jalview/schemabinding/version2/JGroup.java
src/jalview/schemabinding/version2/JSeq.java
src/jalview/schemabinding/version2/JalviewModel.java
src/jalview/schemabinding/version2/JalviewModelSequence.java
src/jalview/schemabinding/version2/JalviewUserColours.java
src/jalview/schemabinding/version2/MapListFrom.java
src/jalview/schemabinding/version2/MapListTo.java
src/jalview/schemabinding/version2/MapListType.java
src/jalview/schemabinding/version2/Mapping.java
src/jalview/schemabinding/version2/MappingChoice.java
src/jalview/schemabinding/version2/OtherData.java
src/jalview/schemabinding/version2/Pdbentry.java
src/jalview/schemabinding/version2/PdbentryItem.java
src/jalview/schemabinding/version2/Pdbids.java
src/jalview/schemabinding/version2/Property.java
src/jalview/schemabinding/version2/Sequence.java
src/jalview/schemabinding/version2/SequenceSet.java
src/jalview/schemabinding/version2/SequenceSetProperties.java
src/jalview/schemabinding/version2/SequenceType.java
src/jalview/schemabinding/version2/Setting.java
src/jalview/schemabinding/version2/StructureState.java
src/jalview/schemabinding/version2/ThresholdLine.java
src/jalview/schemabinding/version2/Tree.java
src/jalview/schemabinding/version2/UserColourScheme.java
src/jalview/schemabinding/version2/UserColours.java
src/jalview/schemabinding/version2/VAMSAS.java
src/jalview/schemabinding/version2/VamsasModel.java
src/jalview/schemabinding/version2/Viewport.java
src/jalview/schemabinding/version2/WebServiceParameterSet.java
src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java
src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/Blosum62ColourScheme.java
src/jalview/schemes/BuriedColourScheme.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/schemes/ColourSchemeI.java
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/Consensus.java
src/jalview/schemes/CovariationColourScheme.java
src/jalview/schemes/GraduatedColor.java
src/jalview/schemes/HelixColourScheme.java
src/jalview/schemes/HydrophobicColourScheme.java
src/jalview/schemes/NucleotideColourScheme.java
src/jalview/schemes/PIDColourScheme.java
src/jalview/schemes/PurinePyrimidineColourScheme.java
src/jalview/schemes/RNAHelicesColour.java
src/jalview/schemes/RNAHelicesColourChooser.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/ScoreColourScheme.java
src/jalview/schemes/ScoreMatrix.java
src/jalview/schemes/StrandColourScheme.java
src/jalview/schemes/TCoffeeColourScheme.java
src/jalview/schemes/TaylorColourScheme.java
src/jalview/schemes/TurnColourScheme.java
src/jalview/schemes/UserColourScheme.java
src/jalview/schemes/ZappoColourScheme.java
src/jalview/structure/AlignmentViewPanelListener.java
src/jalview/structure/SecondaryStructureListener.java
src/jalview/structure/SelectionListener.java
src/jalview/structure/SelectionSource.java
src/jalview/structure/SequenceListener.java
src/jalview/structure/StructureListener.java
src/jalview/structure/StructureMapping.java
src/jalview/structure/StructureMappingcommandSet.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structure/VamsasListener.java
src/jalview/structure/VamsasSource.java
src/jalview/util/AWTConsole.java
src/jalview/util/BrowserLauncher.java
src/jalview/util/ColorUtils.java
src/jalview/util/Comparison.java
src/jalview/util/DBRefUtils.java
src/jalview/util/Format.java
src/jalview/util/GroupUrlLink.java
src/jalview/util/ImageMaker.java
src/jalview/util/MapList.java
src/jalview/util/ParseHtmlBodyAndLinks.java
src/jalview/util/Platform.java
src/jalview/util/QuickSort.java
src/jalview/util/ShiftList.java
src/jalview/util/TableSorter.java
src/jalview/util/UrlLink.java
src/jalview/util/jarInputStreamProvider.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/PCAModel.java
src/jalview/workers/AlignCalcManager.java
src/jalview/workers/AlignCalcWorker.java
src/jalview/workers/ConsensusThread.java
src/jalview/workers/ConservationThread.java
src/jalview/workers/StrucConsensusThread.java
src/jalview/ws/AWSThread.java
src/jalview/ws/AWsJob.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/DasSequenceFeatureFetcher.java
src/jalview/ws/EnfinEnvision2OneWay.java
src/jalview/ws/JobStateSummary.java
src/jalview/ws/SequenceFetcher.java
src/jalview/ws/WSClient.java
src/jalview/ws/WSClientI.java
src/jalview/ws/WSMenuEntryProviderI.java
src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
src/jalview/ws/dbsources/EmblCdsSouce.java
src/jalview/ws/dbsources/EmblSource.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/dbsources/GeneDbSource.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/dbsources/Pfam.java
src/jalview/ws/dbsources/PfamFull.java
src/jalview/ws/dbsources/PfamSeed.java
src/jalview/ws/dbsources/Rfam.java
src/jalview/ws/dbsources/RfamFull.java
src/jalview/ws/dbsources/RfamSeed.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/dbsources/UnprotName.java
src/jalview/ws/dbsources/Xfam.java
src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
src/jalview/ws/dbsources/das/api/jalviewSourceI.java
src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
src/jalview/ws/ebi/EBIFetchClient.java
src/jalview/ws/io/mime/HttpContentHandler.java
src/jalview/ws/io/mime/JalviewMimeContentHandler.java
src/jalview/ws/io/mime/MimeTypes.java
src/jalview/ws/jws1/Discoverer.java
src/jalview/ws/jws1/JPredClient.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws1/JWS1Thread.java
src/jalview/ws/jws1/MsaWSClient.java
src/jalview/ws/jws1/MsaWSThread.java
src/jalview/ws/jws1/SeqSearchWSClient.java
src/jalview/ws/jws1/SeqSearchWSThread.java
src/jalview/ws/jws1/WS1Client.java
src/jalview/ws/jws1/WSJob.java
src/jalview/ws/jws2/AAConClient.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/jws2/AWS2Thread.java
src/jalview/ws/jws2/JWs2Job.java
src/jalview/ws/jws2/JabaParamStore.java
src/jalview/ws/jws2/JabaPreset.java
src/jalview/ws/jws2/JabaWsServerQuery.java
src/jalview/ws/jws2/JabawsAlignCalcWorker.java
src/jalview/ws/jws2/Jws2Client.java
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/jws2/MsaWSThread.java
src/jalview/ws/jws2/ParameterUtils.java
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
src/jalview/ws/jws2/dm/AAConSettings.java
src/jalview/ws/jws2/dm/JabaOption.java
src/jalview/ws/jws2/dm/JabaParameter.java
src/jalview/ws/jws2/dm/JabaValueConstrain.java
src/jalview/ws/jws2/dm/JabaWsParamSet.java
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
src/jalview/ws/params/ArgumentI.java
src/jalview/ws/params/AutoCalcSetting.java
src/jalview/ws/params/InvalidArgumentException.java
src/jalview/ws/params/OptionI.java
src/jalview/ws/params/ParamDatastoreI.java
src/jalview/ws/params/ParamManager.java
src/jalview/ws/params/ParameterI.java
src/jalview/ws/params/ValueConstrainI.java
src/jalview/ws/params/WsParamSetI.java
src/jalview/ws/params/simple/BooleanOption.java
src/jalview/ws/params/simple/IntegerParameter.java
src/jalview/ws/params/simple/Option.java
src/jalview/ws/params/simple/Parameter.java
src/jalview/ws/params/simple/StringChoiceParameter.java
src/jalview/ws/rest/AlignmentProcessor.java
src/jalview/ws/rest/HttpResultSet.java
src/jalview/ws/rest/InputType.java
src/jalview/ws/rest/NoValidInputDataException.java
src/jalview/ws/rest/RestClient.java
src/jalview/ws/rest/RestJob.java
src/jalview/ws/rest/RestJobThread.java
src/jalview/ws/rest/RestServiceDescription.java
src/jalview/ws/rest/params/Alignment.java
src/jalview/ws/rest/params/AnnotationFile.java
src/jalview/ws/rest/params/JobConstant.java
src/jalview/ws/rest/params/SeqGroupIndexVector.java
src/jalview/ws/rest/params/SeqIdVector.java
src/jalview/ws/rest/params/SeqVector.java
src/jalview/ws/rest/params/Tree.java
src/jalview/ws/seqfetcher/ASequenceFetcher.java
src/jalview/ws/seqfetcher/DbSourceProxy.java
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
src/uk/ac/ebi/picr/model/CrossReference.java
src/uk/ac/ebi/picr/model/CrossReference_Helper.java
src/uk/ac/ebi/picr/model/UPEntry.java
src/uk/ac/ebi/picr/model/UPEntry_Helper.java
src/uk/ac/ebi/www/Data.java
src/uk/ac/ebi/www/InputParams.java
src/uk/ac/ebi/www/WSFile.java
src/uk/ac/ebi/www/WSWUBlast.java
src/uk/ac/ebi/www/WSWUBlastService.java
src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java
src/vamsas/IMsaWS.java
src/vamsas/objects/simple/Alignment.java
src/vamsas/objects/simple/Alignment_Helper.java
src/vamsas/objects/simple/JpredResult.java
src/vamsas/objects/simple/JpredResult_Helper.java
src/vamsas/objects/simple/MsaResult.java
src/vamsas/objects/simple/MsaResult_Helper.java
src/vamsas/objects/simple/Msfalignment.java
src/vamsas/objects/simple/Msfalignment_Helper.java
src/vamsas/objects/simple/Object.java
src/vamsas/objects/simple/Object_Helper.java
src/vamsas/objects/simple/Result.java
src/vamsas/objects/simple/Result_Helper.java
src/vamsas/objects/simple/Secstructpred.java
src/vamsas/objects/simple/Secstructpred_Helper.java
src/vamsas/objects/simple/SeqSearchResult.java
src/vamsas/objects/simple/SeqSearchResult_Helper.java
src/vamsas/objects/simple/Sequence.java
src/vamsas/objects/simple/SequenceSet.java
src/vamsas/objects/simple/SequenceSet_Helper.java
src/vamsas/objects/simple/Sequence_Helper.java
src/vamsas/objects/simple/WsJobId.java
src/vamsas/objects/simple/WsJobId_Helper.java
test/jalview/io/TCoffeeScoreFileTest.java
test/jalview/schemes/ScoreMatrixPrinter.java
test/jalview/ws/gui/Jws2ParamView.java
utils/InstallAnywhere/jalview_buildinstaller.xml
utils/eclipse/JalviewCodeStyle.xml
utils/getJavaVersion.java
utils/gff2annot.pl
utils/help2Website.java
utils/jalopy/readme.html
utils/jarunsigner.pl
utils/patchGt.pl
utils/splitstockholm.pl