JAL-1894 update year/version in copyright
authorJim Procter <jprocter@issues.jalview.org>
Thu, 8 Oct 2015 11:21:30 +0000 (12:21 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Thu, 8 Oct 2015 11:21:30 +0000 (12:21 +0100)
commit838e4f91d4a53dd315640dbc9ff6ef7a815ee576
treecab7e82097679ce3c318526f6abcfa8262116b01
parent2860a1bcd936fe7bcd89fbeee6ccbcfc0f71c0b5
JAL-1894 update year/version in copyright
901 files changed:
build.xml
doc/AddingGroovySupport.html
doc/AnnotationPostAnalysis.txt
doc/JalviewRNASupport.html
doc/UnitTesting.html
doc/biojsmsa-templates.html
doc/building.html
doc/developing.html
doc/i18n.html
doc/index.html
doc/newdmobj.html
examples/appletParameters.html
examples/applets.html
examples/css/ie6.css
examples/css/ie7.css
examples/css/reset.css
examples/css/style.css
examples/embedded.html
examples/exampleFeatures.txt
examples/formComplete.html
examples/groovy/JvLoadTestHarness.groovy
examples/groovy/JvLoadTester.groovy
examples/groovy/alignLoadedFile.groovy
examples/groovy/annotationForSelectedSequence.groovy
examples/groovy/annotationsascsv.groovy
examples/groovy/closures.groovy
examples/groovy/iterateOverAlignments.groovy
examples/groovy/parseproperties.groovy
examples/groovy/printtitle.groovy
examples/groovy/removeFeaturesByGroup.groovy
examples/groovy/selectColumnsByFeatureAndGroup.groovy
examples/groovy/sitesForSelectedColumns.groovy
examples/groovy/stripUniprotPrefixes.groovy
examples/includes/footer_jv.html
examples/includes/header_jv.html
examples/includes/nav_jv.html
examples/jalviewLiteJs.html
examples/javascript/jalview.js
examples/javascript/jvcontroller.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/referenceseq.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/bioJsonFormat.html
help/html/features/biojsmsa.html
help/html/features/chimera.html
help/html/features/clarguments.html
help/html/features/codingfeatures.html
help/html/features/columnFilterByAnnotation.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/pdbsequencefetcher.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/splitView.html
help/html/features/structurechooser.html
help/html/features/varna.html
help/html/features/viewingpdbs.html
help/html/features/wrap.html
help/html/features/xsspannotation.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/keys.html
help/html/memory.html
help/html/menus/alignmentMenu.html
help/html/menus/alwannotation.html
help/html/menus/alwannotationpanel.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/RNAalifold.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
jalview-jalopy.xml
nbbuild.xml
nbproject/project.xml
resources/embl_mapping.xml
resources/uniprot_mapping.xml
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/castor.properties
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/AlignmentAnnotationUtils.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/AnnotationSorter.java
src/jalview/analysis/CodingUtils.java
src/jalview/analysis/CodonComparator.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/SecStrConsensus.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/analysis/SequenceIdMatcher.java
src/jalview/analysis/StructureFrequency.java
src/jalview/analysis/WUSSParseException.java
src/jalview/analysis/scoremodels/FeatureScoreModel.java
src/jalview/analysis/scoremodels/PIDScoreModel.java
src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
src/jalview/analysis/scoremodels/SWScoreModel.java
src/jalview/api/AlignCalcManagerI.java
src/jalview/api/AlignCalcWorkerI.java
src/jalview/api/AlignExportSettingI.java
src/jalview/api/AlignViewControllerGuiI.java
src/jalview/api/AlignViewControllerI.java
src/jalview/api/AlignViewportI.java
src/jalview/api/AlignmentViewPanel.java
src/jalview/api/BuildDetailsI.java
src/jalview/api/ComplexAlignFile.java
src/jalview/api/FeatureRenderer.java
src/jalview/api/FeatureSettingsControllerI.java
src/jalview/api/FeatureSettingsModelI.java
src/jalview/api/FeaturesDisplayedI.java
src/jalview/api/OOMHandlerI.java
src/jalview/api/RotatableCanvasI.java
src/jalview/api/SequenceRenderer.java
src/jalview/api/SequenceStructureBinding.java
src/jalview/api/SplitContainerI.java
src/jalview/api/StructureSelectionManagerProvider.java
src/jalview/api/ViewStyleI.java
src/jalview/api/analysis/ScoreModelI.java
src/jalview/api/analysis/ViewBasedAnalysisI.java
src/jalview/api/structures/JalviewStructureDisplayI.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/AnnotationColumnChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/AnnotationRowFilter.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/SplitFrame.java
src/jalview/appletgui/TitledPanel.java
src/jalview/appletgui/Tooltip.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/TreePanel.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/BuildDetails.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/bin/JalviewLiteURLRetrieve.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/controller/AlignViewController.java
src/jalview/controller/FeatureSettingsController.java
src/jalview/controller/FeatureSettingsControllerGuiI.java
src/jalview/datamodel/ASequence.java
src/jalview/datamodel/ASequenceI.java
src/jalview/datamodel/AlignedCodon.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentExportData.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/IncompleteCodonException.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/RnaViewerModel.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/SecondaryStructureAnnotation.java
src/jalview/datamodel/SeqCigar.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceCollectionI.java
src/jalview/datamodel/SequenceDummy.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/StructureViewerModel.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/exceptions/JalviewException.java
src/jalview/exceptions/NoFileSelectedException.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolCommands.java
src/jalview/ext/jmol/PDBFileWithJmol.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
src/jalview/ext/rbvi/chimera/ChimeraListener.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/ext/varna/JalviewVarnaBinding.java
src/jalview/ext/varna/RnaModel.java
src/jalview/ext/varna/VarnaCommands.java
src/jalview/gui/AlignExportSettings.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationChooser.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationColumnChooser.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/AnnotationRowFilter.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/ChimeraViewFrame.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/HTMLOptions.java
src/jalview/gui/Help.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/JalviewChimeraBindingModel.java
src/jalview/gui/JalviewDialog.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/MenuChooser.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/PDBSearchPanel.java
src/jalview/gui/PaintRefresher.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/ProgressBar.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/SVGOptions.java
src/jalview/gui/ScalePanel.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/SplitFrame.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/StructureViewer.java
src/jalview/gui/StructureViewerBase.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/httpserver/AbstractRequestHandler.java
src/jalview/httpserver/HttpServer.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/BioJsHTMLOutput.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/Gff3File.java
src/jalview/io/HTMLOutput.java
src/jalview/io/HtmlFile.java
src/jalview/io/HtmlSvgOutput.java
src/jalview/io/IdentifyFile.java
src/jalview/io/InputStreamParser.java
src/jalview/io/JPredFile.java
src/jalview/io/JSONFile.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/PhylipFile.java
src/jalview/io/PileUpfile.java
src/jalview/io/RnamlFile.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/GAlignExportSettings.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/GSplitFrame.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/jbgui/PDBDocFieldPreferences.java
src/jalview/json/binding/biojs/BioJSReleasePojo.java
src/jalview/json/binding/biojs/BioJSRepositoryPojo.java
src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
src/jalview/json/binding/biojson/v1/AlignmentPojo.java
src/jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.java
src/jalview/json/binding/biojson/v1/AnnotationPojo.java
src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
src/jalview/json/binding/biojson/v1/SequencePojo.java
src/jalview/math/AlignmentDimension.java
src/jalview/math/Matrix.java
src/jalview/math/RotatableMatrix.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/AwtRenderPanelI.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/rest/RestHandler.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/FollowerColourScheme.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/RNAInteractionColourScheme.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/AtomSpec.java
src/jalview/structure/CommandListener.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/structures/models/AAStructureBindingModel.java
src/jalview/structures/models/SequenceStructureBindingModel.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/HttpUtils.java
src/jalview/util/ImageMaker.java
src/jalview/util/MapList.java
src/jalview/util/MappingUtils.java
src/jalview/util/MessageManager.java
src/jalview/util/ParseHtmlBodyAndLinks.java
src/jalview/util/Platform.java
src/jalview/util/QuickSort.java
src/jalview/util/ReverseListIterator.java
src/jalview/util/ShiftList.java
src/jalview/util/StringUtils.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/viewmodel/annotationfilter/AnnotationFilterParameter.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java
src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
src/jalview/viewmodel/styles/ViewStyle.java
src/jalview/workers/AlignCalcManager.java
src/jalview/workers/AlignCalcWorker.java
src/jalview/workers/ComplementConsensusThread.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/HttpClientUtils.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/PDBRestClient.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/Annotate3D.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/AbstractJabaCalcWorker.java
src/jalview/ws/jws2/JPred301Client.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/JabawsCalcWorker.java
src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.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/RNAalifoldClient.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/jws2/jabaws2/Jws2InstanceFactory.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/jalview/ws/uimodel/AlignAnalysisUIText.java
src/org/jibble/epsgraphics/EpsDocument.java
src/org/jibble/epsgraphics/EpsException.java
src/org/jibble/epsgraphics/EpsGraphics2D.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/MCview/AtomTest.java
test/MCview/BondTest.java
test/MCview/PDBChainTest.java
test/MCview/PDBfileTest.java
test/MCview/ResidueTest.java
test/jalview/analysis/AAFrequencyTest.java
test/jalview/analysis/AlignSeqTest.java
test/jalview/analysis/AlignmentAnnotationUtilsTest.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/AnnotationSorterTest.java
test/jalview/analysis/CodingUtilsTest.java
test/jalview/analysis/CrossRefTest.java
test/jalview/analysis/DnaAlignmentGenerator.java
test/jalview/analysis/DnaTest.java
test/jalview/analysis/GroupingTest.java
test/jalview/analysis/ParsePropertiesTest.java
test/jalview/analysis/RnaTest.java
test/jalview/analysis/TestAlignSeq.java
test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
test/jalview/bin/CommandLineOperations.java
test/jalview/bin/JalviewLiteTest.java
test/jalview/commands/EditCommandTest.java
test/jalview/datamodel/AlignedCodonFrameTest.java
test/jalview/datamodel/AlignedCodonIteratorTest.java
test/jalview/datamodel/AlignedCodonTest.java
test/jalview/datamodel/AlignmentAnnotationTests.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/datamodel/AlignmentViewTest.java
test/jalview/datamodel/ColumnSelectionTest.java
test/jalview/datamodel/DBRefEntryTest.java
test/jalview/datamodel/MappingTest.java
test/jalview/datamodel/MatchTest.java
test/jalview/datamodel/PDBEntryTest.java
test/jalview/datamodel/SearchResultsTest.java
test/jalview/datamodel/SeqCigarTest.java
test/jalview/datamodel/SequenceDummyTest.java
test/jalview/datamodel/SequenceTest.java
test/jalview/datamodel/xdb/embl/EmblFileTest.java
test/jalview/ext/jmol/JmolViewerTest.java
test/jalview/ext/jmol/PDBFileWithJmolTest.java
test/jalview/ext/paradise/TestAnnotate3D.java
test/jalview/ext/rbvi/chimera/AllTests.java
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
test/jalview/ext/rbvi/chimera/ChimeraConnect.java
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
test/jalview/gui/AlignViewportTest.java
test/jalview/gui/AnnotationChooserTest.java
test/jalview/gui/AppVarnaTest.java
test/jalview/gui/FontChooserTest.java
test/jalview/gui/HelpTest.java
test/jalview/gui/JAL1353bugdemo.java
test/jalview/gui/JvSwingUtilsTest.java
test/jalview/gui/PDBSearchPanelTest.java
test/jalview/gui/PaintRefresherTest.java
test/jalview/gui/PopupMenuTest.java
test/jalview/gui/ProgressBarTest.java
test/jalview/gui/SequenceRendererTest.java
test/jalview/gui/StructureChooserTest.java
test/jalview/io/AnnotatedPDBFileInputTest.java
test/jalview/io/AnnotationFileIOTest.java
test/jalview/io/BioJsHTMLOutputTest.java
test/jalview/io/FeaturesFileTest.java
test/jalview/io/FileIOTester.java
test/jalview/io/Gff3tests.java
test/jalview/io/HtmlFileTest.java
test/jalview/io/IdentifyFileTest.java
test/jalview/io/JSONFileTest.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/JalviewExportPropertiesTests.java
test/jalview/io/NewickFileTests.java
test/jalview/io/PhylipFileTests.java
test/jalview/io/RNAMLfileTest.java
test/jalview/io/StockholmFileTest.java
test/jalview/io/TCoffeeScoreFileTest.java
test/jalview/schemes/DnaCodonTests.java
test/jalview/schemes/ResiduePropertiesTest.java
test/jalview/schemes/ScoreMatrixPrinter.java
test/jalview/structure/Mapping.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/structures/models/AAStructureBindingModelTest.java
test/jalview/util/ColorUtilsTest.java
test/jalview/util/ComparisonTest.java
test/jalview/util/DBRefUtilsTest.java
test/jalview/util/MapListTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/util/ParseHtmlBodyAndLinksTest.java
test/jalview/util/QuickSortTest.java
test/jalview/util/ShiftListTest.java
test/jalview/util/StringUtilsTest.java
test/jalview/viewmodel/styles/ViewStyleTest.java
test/jalview/ws/PDBSequenceFetcherTest.java
test/jalview/ws/dbsources/PDBRestClientTest.java
test/jalview/ws/dbsources/UniprotTest.java
test/jalview/ws/gui/Jws2ParamView.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
test/jalview/ws/jabaws/MinJabawsClientTests.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/jws2/ParameterUtilsTest.java
test/jalview/ws/rest/RestClientTest.java
test/jalview/ws/rest/ShmmrRSBSService.java
test/jalview/ws/seqfetcher/DasSequenceFetcher.java
test/jalview/ws/seqfetcher/DbRefFetcherTest.java
utils/InstallAnywhere/Jalview.iap_xml
utils/InstallAnywhere/jalview_buildinstaller.xml
utils/JettyExamplesDir.java
utils/eclipse/JalviewCodeStyle.xml
utils/getJavaVersion.java
utils/gff2annot.pl
utils/help2Website.java
utils/jarunsigner.pl
utils/patchGt.pl
utils/splitstockholm.pl