[Git][java-team/jalview][upstream] New upstream version 2.11.4.1+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Java Maintainers / jalview


Commits:
ea14fe6f by Pierre Gruet at 2025-02-16T11:24:29+01:00
New upstream version 2.11.4.1+dfsg
- - - - -


1376 changed files:

- .settings/org.eclipse.jdt.core.prefs
- RELEASE
- build.gradle
- build_properties
- doc/AddingGroovySupport.html
- doc/JalviewRNASupport.html
- doc/UnitTesting.html
- doc/biojsmsa-templates.html
- doc/developing.html
- doc/i18n.html
- doc/index.html
- doc/newdmobj.html
- examples/appletDeployment.html
- examples/appletParameters.html
- examples/applets.html
- examples/embedded.html
- examples/formComplete.html
- examples/groovy/JvLoadTestHarness.groovy
- examples/groovy/JvLoadTester.groovy
- examples/groovy/PIDmatrix.groovy
- examples/groovy/alignLoadedFile.groovy
- examples/groovy/annotationForSelectedSequence.groovy
- examples/groovy/annotationsascsv.groovy
- examples/groovy/closures.groovy
- examples/groovy/colourConserved.groovy
- examples/groovy/colourUnconserved.groovy
- examples/groovy/exportconsensus.groovy
- examples/groovy/featuresCounter.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/groovy/visibleFeaturesCounter.groovy
- examples/includes/footer_jv.html
- examples/includes/header_jv.html
- examples/includes/nav_jv.html
- examples/jalviewLiteJs.html
- examples/javascriptLaunch.html
- examples/linkedapplets_ng.html
- examples/testdata/test.html
- help/help/helpTOC.xml
- help/help/html/calculations/calculations.html
- help/help/html/calculations/consensus.html
- help/help/html/calculations/conservation.html
- help/help/html/calculations/pairwise.html
- help/help/html/calculations/pasimap.html
- help/help/html/calculations/pca.html
- help/help/html/calculations/protssconsensus.html
- help/help/html/calculations/quality.html
- help/help/html/calculations/recoverInputdata.html
- help/help/html/calculations/redundancy.html
- help/help/html/calculations/referenceseq.html
- help/help/html/calculations/scorematrices.html
- help/help/html/calculations/sorting.html
- help/help/html/calculations/structureconsensus.html
- help/help/html/calculations/tree.html
- help/help/html/calculations/treeviewer.html
- help/help/html/colourSchemes/abovePID.html
- help/help/html/colourSchemes/annotationColouring.html
- help/help/html/colourSchemes/blosum.html
- help/help/html/colourSchemes/buried.html
- help/help/html/colourSchemes/clustal.html
- help/help/html/colourSchemes/conservation.html
- help/help/html/colourSchemes/gecos-blossom.html
- help/help/html/colourSchemes/gecos-flower.html
- help/help/html/colourSchemes/gecos-ocean.html
- help/help/html/colourSchemes/gecos-sunset.html
- help/help/html/colourSchemes/helix.html
- help/help/html/colourSchemes/hydrophobic.html
- help/help/html/colourSchemes/index.html
- help/help/html/colourSchemes/nucleotide.html
- help/help/html/colourSchemes/nucleotideambiguity.html
- help/help/html/colourSchemes/pid.html
- help/help/html/colourSchemes/purinepyrimidine.html
- help/help/html/colourSchemes/rnahelicesColouring.html
- help/help/html/colourSchemes/strand.html
- help/help/html/colourSchemes/taylor.html
- help/help/html/colourSchemes/textcolour.html
- help/help/html/colourSchemes/turn.html
- help/help/html/colourSchemes/user.html
- help/help/html/colourSchemes/zappo.html
- help/help/html/editing/index.html
- help/help/html/features/annotation.html
- help/help/html/features/annotationsFormat.html
- help/help/html/features/bioJsonFormat.html
- help/help/html/features/biojsmsa.html
- help/help/html/features/chimera.html
- help/help/html/features/clarguments-advanced.html
- help/help/html/features/clarguments-argfiles.html
- help/help/html/features/clarguments-basic.html
- help/help/html/features/clarguments-old.html
- help/help/html/features/codingfeatures.html
- help/help/html/features/columnFilterByAnnotation.html
- help/help/html/features/commandline.html
- help/help/html/features/creatinFeatures.html
- help/help/html/features/cursorMode.html
- help/help/html/features/editingFeatures.html
- help/help/html/features/ensemblsequencefetcher.html
- help/help/html/features/featuresFormat.html
- help/help/html/features/featureschemes.html
- help/help/html/features/featuresettings.html
- help/help/html/features/groovy.html
- help/help/html/features/hiddenRegions.html
- help/help/html/features/importvcf.html
- help/help/html/features/jalarchive.html
- help/help/html/features/jmol.html
- help/help/html/features/jvlfiles.html
- help/help/html/features/mmcif.html
- help/help/html/features/multipleViews.html
- help/help/html/features/newkeystrokes.html
- help/help/html/features/overview.html
- help/help/html/features/paematrices.html
- help/help/html/features/pdbsequencefetcher.html
- help/help/html/features/pdbviewer.html
- help/help/html/features/preferences.html
- help/help/html/features/pymol.html
- help/help/html/features/search.html
- help/help/html/features/seqfeaturereport.html
- help/help/html/features/seqfeatures.html
- help/help/html/features/seqfetch.html
- help/help/html/features/seqmappings.html
- help/help/html/features/siftsmapping.html
- help/help/html/features/splitView.html
- help/help/html/features/structurechooser.html
- help/help/html/features/uniprotqueryfields.html
- help/help/html/features/uniprotsequencefetcher.html
- help/help/html/features/varna.html
- help/help/html/features/viewingpdbs.html
- help/help/html/features/wrap.html
- help/help/html/features/xsspannotation.html
- help/help/html/groovy/featuresCounter.html
- help/help/html/index.html
- help/help/html/io/export.html
- help/help/html/io/exportseqreport.html
- help/help/html/io/fileformats.html
- help/help/html/io/index.html
- help/help/html/io/modellerpir.html
- help/help/html/io/paematrixformat.html
- help/help/html/io/tcoffeescores.html
- help/help/html/keys.html
- help/help/html/logging.html
- help/help/html/memory.html
- help/help/html/menus/alignmentMenu.html
- help/help/html/menus/alwannotation.html
- help/help/html/menus/alwannotationpanel.html
- help/help/html/menus/alwcalculate.html
- help/help/html/menus/alwcolour.html
- help/help/html/menus/alwedit.html
- help/help/html/menus/alwfile.html
- help/help/html/menus/alwformat.html
- help/help/html/menus/alwselect.html
- help/help/html/menus/alwview.html
- help/help/html/menus/desktopMenu.html
- help/help/html/menus/index.html
- help/help/html/menus/popupMenu.html
- help/help/html/menus/wsmenu.html
- help/help/html/misc/aaproperties.html
- help/help/html/misc/aminoAcids.html
- help/help/html/misc/geneticCode.html
- help/help/html/na/index.html
- help/help/html/privacy.html
- help/help/html/webServices/AACon.html
- help/help/html/webServices/JABAWS.html
- help/help/html/webServices/RNAalifold.html
- help/help/html/webServices/dbreffetcher.html
- help/help/html/webServices/index.html
- help/help/html/webServices/jnet.html
- help/help/html/webServices/msaclient.html
- help/help/html/webServices/newsreader.html
- help/help/html/webServices/proteinDisorder.html
- help/help/html/webServices/shmr.html
- help/help/html/webServices/urllinks.html
- help/help/html/webServices/webServicesParams.html
- help/help/html/webServices/webServicesPrefs.html
- + help/markdown/releases/release-2_11_4_1.md
- + help/markdown/whatsnew/whatsnew-2_11_4_1.md
- help/templates/releases.html
- help/templates/whatsNew.html
- jalview-jalopy.xml
- nbbuild.xml
- nbproject/project.xml
- schemas/jalview.nodesc.properties
- schemas/jalview.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/AverageDistanceEngine.java
- src/jalview/analysis/AverageDistanceTree.java
- src/jalview/analysis/CodingUtils.java
- src/jalview/analysis/CodonComparator.java
- src/jalview/analysis/Connectivity.java
- src/jalview/analysis/ConnectivityException.java
- src/jalview/analysis/Conservation.java
- src/jalview/analysis/CrossRef.java
- src/jalview/analysis/Dna.java
- src/jalview/analysis/Finder.java
- src/jalview/analysis/GeneticCodeI.java
- src/jalview/analysis/GeneticCodes.java
- src/jalview/analysis/Grouping.java
- src/jalview/analysis/NJTree.java
- src/jalview/analysis/PCA.java
- src/jalview/analysis/PaSiMap.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/TreeBuilder.java
- src/jalview/analysis/TreeEngine.java
- src/jalview/analysis/TreeModel.java
- src/jalview/analysis/WUSSParseException.java
- src/jalview/analysis/ccAnalysis.java
- src/jalview/analysis/scoremodels/DistanceScoreModel.java
- src/jalview/analysis/scoremodels/FeatureDistanceModel.java
- src/jalview/analysis/scoremodels/PIDModel.java
- src/jalview/analysis/scoremodels/ScoreMatrix.java
- src/jalview/analysis/scoremodels/ScoreModels.java
- src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
- src/jalview/analysis/scoremodels/SimilarityParams.java
- src/jalview/analysis/scoremodels/SimilarityScoreModel.java
- src/jalview/analysis/scoremodels/SmithWatermanModel.java
- src/jalview/analytics/Plausible.java
- src/jalview/api/AlignCalcManagerI.java
- src/jalview/api/AlignCalcWorkerI.java
- src/jalview/api/AlignExportSettingsI.java
- src/jalview/api/AlignViewControllerGuiI.java
- src/jalview/api/AlignViewControllerI.java
- src/jalview/api/AlignViewportI.java
- src/jalview/api/AlignmentColsCollectionI.java
- src/jalview/api/AlignmentRowsCollectionI.java
- src/jalview/api/AlignmentViewPanel.java
- src/jalview/api/BuildDetailsI.java
- src/jalview/api/ComplexAlignFile.java
- src/jalview/api/DBRefEntryI.java
- src/jalview/api/FeatureColourI.java
- src/jalview/api/FeatureRenderer.java
- src/jalview/api/FeatureSettingsControllerI.java
- src/jalview/api/FeatureSettingsModelI.java
- src/jalview/api/FeaturesDisplayedI.java
- src/jalview/api/FeaturesSourceI.java
- src/jalview/api/FinderI.java
- src/jalview/api/OOMHandlerI.java
- src/jalview/api/RendererListenerI.java
- src/jalview/api/RotatableCanvasI.java
- src/jalview/api/SequenceRenderer.java
- src/jalview/api/SequenceStructureBinding.java
- src/jalview/api/SiftsClientI.java
- src/jalview/api/SplitContainerI.java
- src/jalview/api/StructureSelectionManagerProvider.java
- src/jalview/api/ViewStyleI.java
- src/jalview/api/analysis/PairwiseScoreModelI.java
- src/jalview/api/analysis/ScoreModelI.java
- src/jalview/api/analysis/SimilarityParamsI.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/OverviewCanvas.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/ArgsParser.java
- src/jalview/bin/BuildDetails.java
- src/jalview/bin/Cache.java
- src/jalview/bin/Commands.java
- src/jalview/bin/Console.java
- src/jalview/bin/GetMemory.java
- src/jalview/bin/GetdownLauncherUpdate.java
- src/jalview/bin/HiDPISetting.java
- src/jalview/bin/Jalview.java
- src/jalview/bin/JalviewJS2.java
- src/jalview/bin/JalviewLite.java
- src/jalview/bin/JalviewLiteURLRetrieve.java
- src/jalview/bin/JalviewTaskbar.java
- src/jalview/bin/Launcher.java
- src/jalview/bin/MemorySetting.java
- src/jalview/bin/ScreenInfo.java
- src/jalview/bin/argparser/Arg.java
- src/jalview/bin/argparser/ArgParser.java
- src/jalview/bin/argparser/ArgValue.java
- src/jalview/bin/argparser/ArgValues.java
- src/jalview/bin/argparser/ArgValuesMap.java
- src/jalview/bin/argparser/BootstrapArgs.java
- src/jalview/bin/argparser/SubVals.java
- src/jalview/bin/groovy/JalviewObject.java
- src/jalview/bin/groovy/JalviewObjectI.java
- src/jalview/commands/ChangeCaseCommand.java
- src/jalview/commands/CommandI.java
- src/jalview/commands/EditCommand.java
- src/jalview/commands/JustifyLeftOrRightCommand.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/AlignExportSettingsAdapter.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/AllColsCollection.java
- src/jalview/datamodel/AllColsIterator.java
- src/jalview/datamodel/AllRowsCollection.java
- src/jalview/datamodel/AllRowsIterator.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/ContactListI.java
- src/jalview/datamodel/ContactListImpl.java
- src/jalview/datamodel/ContactListProviderI.java
- src/jalview/datamodel/ContactMapHolder.java
- src/jalview/datamodel/ContactMapHolderI.java
- src/jalview/datamodel/ContactMatrix.java
- src/jalview/datamodel/ContactMatrixI.java
- src/jalview/datamodel/ContactRange.java
- src/jalview/datamodel/ContiguousI.java
- src/jalview/datamodel/DBRefEntry.java
- src/jalview/datamodel/DBRefSource.java
- src/jalview/datamodel/FeatureProperties.java
- src/jalview/datamodel/FloatContactMatrix.java
- src/jalview/datamodel/GeneLociI.java
- src/jalview/datamodel/GeneLocus.java
- src/jalview/datamodel/GraphLine.java
- src/jalview/datamodel/GroupSet.java
- src/jalview/datamodel/GroupSetHolder.java
- src/jalview/datamodel/GroupSetI.java
- src/jalview/datamodel/HiddenColumns.java
- src/jalview/datamodel/HiddenColumnsCursor.java
- src/jalview/datamodel/HiddenCursorPosition.java
- src/jalview/datamodel/HiddenSequences.java
- src/jalview/datamodel/IncompleteCodonException.java
- src/jalview/datamodel/MappedFeatures.java
- src/jalview/datamodel/Mapping.java
- src/jalview/datamodel/MappingType.java
- src/jalview/datamodel/NodeTransformI.java
- src/jalview/datamodel/PDBEntry.java
- src/jalview/datamodel/Point.java
- src/jalview/datamodel/Profile.java
- src/jalview/datamodel/ProfileI.java
- src/jalview/datamodel/Profiles.java
- src/jalview/datamodel/ProfilesI.java
- src/jalview/datamodel/Provenance.java
- src/jalview/datamodel/ProvenanceEntry.java
- src/jalview/datamodel/Range.java
- src/jalview/datamodel/RangeElementsIterator.java
- src/jalview/datamodel/RangeIterator.java
- src/jalview/datamodel/ResidueCount.java
- src/jalview/datamodel/RnaViewerModel.java
- src/jalview/datamodel/SearchResultMatchI.java
- src/jalview/datamodel/SearchResults.java
- src/jalview/datamodel/SearchResultsI.java
- src/jalview/datamodel/SecondaryStructureAnnotation.java
- src/jalview/datamodel/SecondaryStructureCount.java
- src/jalview/datamodel/SeqCigar.java
- src/jalview/datamodel/SeqDistanceContactMatrix.java
- src/jalview/datamodel/Sequence.java
- src/jalview/datamodel/SequenceCollectionI.java
- src/jalview/datamodel/SequenceCursor.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/StartRegionIterator.java
- src/jalview/datamodel/StructureViewerModel.java
- src/jalview/datamodel/VisibleColsCollection.java
- src/jalview/datamodel/VisibleContigsIterator.java
- src/jalview/datamodel/VisibleRowsCollection.java
- src/jalview/datamodel/VisibleRowsIterator.java
- src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java
- src/jalview/datamodel/annotations/AnnotationRowBuilder.java
- src/jalview/datamodel/features/FeatureAttributeType.java
- src/jalview/datamodel/features/FeatureAttributes.java
- src/jalview/datamodel/features/FeatureLocationI.java
- src/jalview/datamodel/features/FeatureMatcher.java
- src/jalview/datamodel/features/FeatureMatcherI.java
- src/jalview/datamodel/features/FeatureMatcherSet.java
- src/jalview/datamodel/features/FeatureMatcherSetI.java
- src/jalview/datamodel/features/FeatureSource.java
- src/jalview/datamodel/features/FeatureSourceI.java
- src/jalview/datamodel/features/FeatureSources.java
- src/jalview/datamodel/features/FeatureStore.java
- src/jalview/datamodel/features/SequenceFeatures.java
- src/jalview/datamodel/features/SequenceFeaturesI.java
- src/jalview/exceptions/JalviewException.java
- src/jalview/ext/android/ContainerHelpers.java
- src/jalview/ext/android/SparseDoubleArray.java
- src/jalview/ext/android/SparseIntArray.java
- src/jalview/ext/android/SparseShortArray.java
- src/jalview/ext/ensembl/EnsemblCdna.java
- src/jalview/ext/ensembl/EnsemblCds.java
- src/jalview/ext/ensembl/EnsemblData.java
- src/jalview/ext/ensembl/EnsemblFeatures.java
- src/jalview/ext/ensembl/EnsemblGene.java
- src/jalview/ext/ensembl/EnsemblGenome.java
- src/jalview/ext/ensembl/EnsemblGenomes.java
- src/jalview/ext/ensembl/EnsemblInfo.java
- src/jalview/ext/ensembl/EnsemblLookup.java
- src/jalview/ext/ensembl/EnsemblMap.java
- src/jalview/ext/ensembl/EnsemblProtein.java
- src/jalview/ext/ensembl/EnsemblRestClient.java
- src/jalview/ext/ensembl/EnsemblSeqProxy.java
- src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
- src/jalview/ext/ensembl/EnsemblSymbol.java
- src/jalview/ext/ensembl/EnsemblXref.java
- src/jalview/ext/ensembl/Species.java
- src/jalview/ext/htsjdk/HtsContigDb.java
- src/jalview/ext/htsjdk/VCFReader.java
- src/jalview/ext/jmol/JalviewJmolBinding.java
- src/jalview/ext/jmol/JmolCommands.java
- src/jalview/ext/jmol/JmolParser.java
- src/jalview/ext/paradise/Annotate3D.java
- src/jalview/ext/pymol/PymolCommands.java
- src/jalview/ext/pymol/PymolManager.java
- src/jalview/ext/rbvi/chimera/ChimeraCommands.java
- src/jalview/ext/rbvi/chimera/ChimeraListener.java
- src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
- src/jalview/ext/rbvi/chimera/ChimeraXManager.java
- src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
- src/jalview/ext/so/SequenceOntology.java
- src/jalview/ext/varna/JalviewVarnaBinding.java
- src/jalview/ext/varna/RnaModel.java
- src/jalview/ext/varna/VarnaCommands.java
- src/jalview/fts/api/FTSData.java
- src/jalview/fts/api/FTSDataColumnI.java
- src/jalview/fts/api/FTSRestClientI.java
- src/jalview/fts/api/GFTSPanelI.java
- src/jalview/fts/api/StructureFTSRestClientI.java
- src/jalview/fts/core/DecimalFormatTableCellRenderer.java
- src/jalview/fts/core/FTSDataColumnPreferences.java
- src/jalview/fts/core/FTSRestClient.java
- src/jalview/fts/core/FTSRestRequest.java
- src/jalview/fts/core/FTSRestResponse.java
- src/jalview/fts/core/GFTSPanel.java
- src/jalview/fts/service/alphafold/AlphafoldRestClient.java
- src/jalview/fts/service/pdb/PDBFTSPanel.java
- src/jalview/fts/service/pdb/PDBFTSRestClient.java
- src/jalview/fts/service/threedbeacons/TDB_FTSData.java
- src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
- src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
- src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
- src/jalview/fts/service/uniprot/UniprotFTSPanel.java
- src/jalview/gui/APQHandlers.java
- src/jalview/gui/AlignExportOptions.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/CalculationChooser.java
- src/jalview/gui/ChimeraViewFrame.java
- src/jalview/gui/ChimeraXViewFrame.java
- src/jalview/gui/ColourMenuHelper.java
- src/jalview/gui/ComboBoxTooltipRenderer.java
- src/jalview/gui/Console.java
- src/jalview/gui/CrossRefAction.java
- src/jalview/gui/CutAndPasteHtmlTransfer.java
- src/jalview/gui/CutAndPasteTransfer.java
- src/jalview/gui/Desktop.java
- src/jalview/gui/EditNameDialog.java
- src/jalview/gui/FeatureEditor.java
- src/jalview/gui/FeatureRenderer.java
- src/jalview/gui/FeatureSettings.java
- src/jalview/gui/FeatureTypeSettings.java
- src/jalview/gui/Finder.java
- src/jalview/gui/FontChooser.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/ImageExporter.java
- src/jalview/gui/JDatabaseTree.java
- src/jalview/gui/JalviewBooleanRadioButtons.java
- src/jalview/gui/JalviewChangeSupport.java
- src/jalview/gui/JalviewChimeraBindingModel.java
- src/jalview/gui/JalviewChimeraXBindingModel.java
- src/jalview/gui/JalviewColourChooser.java
- src/jalview/gui/JalviewDialog.java
- src/jalview/gui/JvOptionPane.java
- src/jalview/gui/JvSwingUtils.java
- src/jalview/gui/LineartOptions.java
- src/jalview/gui/MenuChooser.java
- src/jalview/gui/OOMWarning.java
- src/jalview/gui/OptsAndParamsPage.java
- src/jalview/gui/OptsParametersContainerI.java
- src/jalview/gui/OverviewCanvas.java
- src/jalview/gui/OverviewPanel.java
- src/jalview/gui/PCAPanel.java
- src/jalview/gui/PaSiMapPanel.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/ProgressPanel.java
- src/jalview/gui/PromptUserConfig.java
- src/jalview/gui/PymolBindingModel.java
- src/jalview/gui/PymolViewer.java
- src/jalview/gui/QuitHandler.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/SeqCanvas.java
- src/jalview/gui/SeqPanel.java
- src/jalview/gui/SequenceFetcher.java
- src/jalview/gui/SequenceRenderer.java
- src/jalview/gui/Slider.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/gui/structurechooser/PDBStructureChooserQuerySource.java
- src/jalview/gui/structurechooser/StructureChooserQuerySource.java
- src/jalview/gui/structurechooser/TDBResultAnalyser.java
- src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
- src/jalview/httpserver/AbstractRequestHandler.java
- src/jalview/httpserver/HttpServer.java
- src/jalview/io/AMSAFile.java
- src/jalview/io/AlignFile.java
- src/jalview/io/AlignmentFileReaderI.java
- src/jalview/io/AlignmentFileWriterI.java
- src/jalview/io/AlignmentProperties.java
- src/jalview/io/AnnotationFile.java
- src/jalview/io/AppletFormatAdapter.java
- src/jalview/io/BLCFile.java
- src/jalview/io/BackupFilenameFilter.java
- src/jalview/io/BackupFilenameParts.java
- src/jalview/io/BackupFiles.java
- src/jalview/io/BackupFilesPresetEntry.java
- src/jalview/io/BioJsHTMLOutput.java
- src/jalview/io/ClustalFile.java
- src/jalview/io/DBRefFile.java
- src/jalview/io/DataSourceType.java
- src/jalview/io/EMBLLikeFlatFile.java
- src/jalview/io/EmblFlatFile.java
- src/jalview/io/FastaFile.java
- src/jalview/io/FeaturesFile.java
- src/jalview/io/FileFormat.java
- src/jalview/io/FileFormatException.java
- src/jalview/io/FileFormatI.java
- src/jalview/io/FileFormats.java
- src/jalview/io/FileLoader.java
- src/jalview/io/FileParse.java
- src/jalview/io/FormatAdapter.java
- src/jalview/io/GenBankFile.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/IntKeyStringValueEntry.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/ModellerDescription.java
- src/jalview/io/NewickFile.java
- src/jalview/io/PContactPredictionFile.java
- src/jalview/io/PDBFeatureSettings.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/ScoreMatrixFile.java
- src/jalview/io/SequenceAnnotationReport.java
- src/jalview/io/SimpleBlastFile.java
- src/jalview/io/StockholmFile.java
- src/jalview/io/StructureFile.java
- src/jalview/io/TCoffeeScoreFile.java
- src/jalview/io/VamsasAppDatastore.java
- src/jalview/io/WSWUBlastClient.java
- src/jalview/io/cache/AppCache.java
- src/jalview/io/cache/JvCacheableInputBox.java
- src/jalview/io/exceptions/ImageOutputException.java
- src/jalview/io/gff/ExonerateHelper.java
- src/jalview/io/gff/Gff2Helper.java
- src/jalview/io/gff/Gff3Helper.java
- src/jalview/io/gff/GffConstants.java
- src/jalview/io/gff/GffHelperBase.java
- src/jalview/io/gff/GffHelperFactory.java
- src/jalview/io/gff/GffHelperI.java
- src/jalview/io/gff/InterProScanHelper.java
- src/jalview/io/gff/SequenceOntologyFactory.java
- src/jalview/io/gff/SequenceOntologyI.java
- src/jalview/io/gff/SequenceOntologyLite.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/io/vcf/VCFLoader.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/javascript/json/JSON.java
- src/jalview/javascript/web/Client.java
- src/jalview/javascript/web/ClientResponse.java
- src/jalview/javascript/web/WebResource.java
- src/jalview/jbgui/FilterOption.java
- src/jalview/jbgui/GAlignFrame.java
- src/jalview/jbgui/GAlignmentPanel.java
- src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
- src/jalview/jbgui/GCutAndPasteTransfer.java
- src/jalview/jbgui/GDesktop.java
- src/jalview/jbgui/GFinder.java
- src/jalview/jbgui/GFontChooser.java
- src/jalview/jbgui/GPCAPanel.java
- src/jalview/jbgui/GPaSiMapPanel.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/GStructureChooser.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/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/log/JLogger.java
- src/jalview/log/JLoggerI.java
- src/jalview/log/JLoggerLog4j.java
- src/jalview/log/JalviewAppender.java
- src/jalview/math/AlignmentDimension.java
- src/jalview/math/Matrix.java
- src/jalview/math/MatrixI.java
- src/jalview/math/MiscMath.java
- src/jalview/math/RotatableMatrix.java
- src/jalview/math/SameLengthException.java
- src/jalview/math/SparseMatrix.java
- src/jalview/project/Jalview2XML.java
- src/jalview/renderer/AnnotationRenderer.java
- src/jalview/renderer/AnnotationRendererFactory.java
- src/jalview/renderer/AwtRenderPanelI.java
- src/jalview/renderer/ContactGeometry.java
- src/jalview/renderer/ContactMapRenderer.java
- src/jalview/renderer/OverviewRenderer.java
- src/jalview/renderer/OverviewResColourFinder.java
- src/jalview/renderer/ResidueColourFinder.java
- src/jalview/renderer/ResidueShader.java
- src/jalview/renderer/ResidueShaderI.java
- src/jalview/renderer/ScaleRenderer.java
- src/jalview/renderer/api/AnnotationRendererFactoryI.java
- src/jalview/renderer/api/AnnotationRowRendererI.java
- src/jalview/renderer/seqfeatures/FeatureColourFinder.java
- src/jalview/renderer/seqfeatures/FeatureRenderer.java
- src/jalview/rest/RestHandler.java
- src/jalview/schemes/AnnotationColourGradient.java
- src/jalview/schemes/BlossomColourScheme.java
- src/jalview/schemes/Blosum62ColourScheme.java
- src/jalview/schemes/BuriedColourScheme.java
- src/jalview/schemes/ClustalxColourScheme.java
- src/jalview/schemes/ColourSchemeI.java
- src/jalview/schemes/ColourSchemeLoader.java
- src/jalview/schemes/ColourSchemeProperty.java
- src/jalview/schemes/ColourSchemes.java
- src/jalview/schemes/Consensus.java
- src/jalview/schemes/CovariationColourScheme.java
- src/jalview/schemes/FeatureColour.java
- src/jalview/schemes/FeatureSettingsAdapter.java
- src/jalview/schemes/FlowerColourScheme.java
- src/jalview/schemes/FollowerColourScheme.java
- src/jalview/schemes/HelixColourScheme.java
- src/jalview/schemes/HydrophobicColourScheme.java
- src/jalview/schemes/IdColourScheme.java
- src/jalview/schemes/JalviewColourScheme.java
- src/jalview/schemes/NucleotideAmbiguityColourScheme.java
- src/jalview/schemes/NucleotideColourScheme.java
- src/jalview/schemes/OceanColourScheme.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/StrandColourScheme.java
- src/jalview/schemes/SunsetColourScheme.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/AtomSpecModel.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/StructureCommand.java
- src/jalview/structure/StructureCommandI.java
- src/jalview/structure/StructureCommandsBase.java
- src/jalview/structure/StructureCommandsI.java
- src/jalview/structure/StructureImportSettings.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/urls/CustomUrlProvider.java
- src/jalview/urls/IdOrgSettings.java
- src/jalview/urls/IdentifiersUrlProvider.java
- src/jalview/urls/UrlLinkDisplay.java
- src/jalview/urls/UrlLinkTableModel.java
- src/jalview/urls/UrlProvider.java
- src/jalview/urls/UrlProviderImpl.java
- src/jalview/urls/api/UrlProviderFactoryI.java
- src/jalview/urls/api/UrlProviderI.java
- src/jalview/urls/applet/AppletUrlProviderFactory.java
- src/jalview/urls/desktop/DesktopUrlProviderFactory.java
- src/jalview/util/AWTConsole.java
- src/jalview/util/ArgParserUtils.java
- src/jalview/util/ArrayUtils.java
- src/jalview/util/BrowserLauncher.java
- src/jalview/util/CaseInsensitiveString.java
- src/jalview/util/ChannelProperties.java
- src/jalview/util/ColorUtils.java
- src/jalview/util/Comparison.java
- src/jalview/util/Constants.java
- src/jalview/util/DBRefUtils.java
- src/jalview/util/DnaUtils.java
- src/jalview/util/ErrorLog.java
- src/jalview/util/FileUtils.java
- src/jalview/util/Format.java
- src/jalview/util/GroupUrlLink.java
- src/jalview/util/HttpUtils.java
- src/jalview/util/ImageMaker.java
- src/jalview/util/IntRangeComparator.java
- src/jalview/util/JSONUtils.java
- src/jalview/util/LaunchUtils.java
- src/jalview/util/LinkedIdentityHashSet.java
- src/jalview/util/Log4j.java
- src/jalview/util/MapList.java
- src/jalview/util/MapUtils.java
- src/jalview/util/MappingUtils.java
- src/jalview/util/MathUtils.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/SetUtils.java
- src/jalview/util/ShiftList.java
- src/jalview/util/ShortcutKeyMaskExWrapper.java
- src/jalview/util/ShortcutKeyMaskExWrapper11.java
- src/jalview/util/ShortcutKeyMaskExWrapper8.java
- src/jalview/util/ShortcutKeyMaskExWrapperI.java
- src/jalview/util/SparseCount.java
- src/jalview/util/StringUtils.java
- src/jalview/util/TableSorter.java
- src/jalview/util/UrlConstants.java
- src/jalview/util/UrlLink.java
- src/jalview/util/UserAgent.java
- src/jalview/util/dialogrunner/DialogRunnerI.java
- src/jalview/util/imagemaker/BitmapImageSizing.java
- src/jalview/util/jarInputStreamProvider.java
- src/jalview/util/matcher/Condition.java
- src/jalview/util/matcher/Matcher.java
- src/jalview/util/matcher/MatcherI.java
- src/jalview/viewmodel/AlignmentViewport.java
- src/jalview/viewmodel/OverviewDimensions.java
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- src/jalview/viewmodel/OverviewDimensionsShowHidden.java
- src/jalview/viewmodel/PCAModel.java
- src/jalview/viewmodel/PaSiMapModel.java
- src/jalview/viewmodel/ViewportListenerI.java
- src/jalview/viewmodel/ViewportProperties.java
- src/jalview/viewmodel/ViewportRanges.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/AlignmentAnnotationFactory.java
- src/jalview/workers/AnnotationProviderI.java
- src/jalview/workers/AnnotationWorker.java
- src/jalview/workers/ColumnCounterSetWorker.java
- src/jalview/workers/ComplementConsensusThread.java
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- src/jalview/workers/ConservationThread.java
- src/jalview/workers/FeatureSetCounterI.java
- src/jalview/workers/SecondaryStructureConsensusThread.java
- src/jalview/workers/StrucConsensusThread.java
- src/jalview/ws/AWSThread.java
- src/jalview/ws/AWsJob.java
- src/jalview/ws/DBRefFetcher.java
- src/jalview/ws/HttpClientUtils.java
- src/jalview/ws/JobStateSummary.java
- src/jalview/ws/SequenceFetcher.java
- src/jalview/ws/SequenceFetcherFactory.java
- src/jalview/ws/WSClient.java
- src/jalview/ws/WSClientI.java
- src/jalview/ws/WSMenuEntryProviderI.java
- src/jalview/ws/datamodel/MappableContactMatrixI.java
- src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
- src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
- src/jalview/ws/dbsources/EBIAlfaFold.java
- src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
- src/jalview/ws/dbsources/EmblCdsSource.java
- src/jalview/ws/dbsources/EmblFlatfileSource.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/TDBeacons.java
- src/jalview/ws/dbsources/Uniprot.java
- src/jalview/ws/dbsources/UniprotName.java
- src/jalview/ws/dbsources/Xfam.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/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/sifts/MappingOutputPojo.java
- src/jalview/ws/sifts/SiftsClient.java
- src/jalview/ws/sifts/SiftsException.java
- src/jalview/ws/sifts/SiftsSettings.java
- src/jalview/ws/uimodel/AlignAnalysisUIText.java
- src/jalview/ws/utils/UrlDownloadClient.java
- src/mc_view/AppletPDBCanvas.java
- src/mc_view/AppletPDBViewer.java
- src/mc_view/Atom.java
- src/mc_view/Bond.java
- src/mc_view/MCMatrix.java
- src/mc_view/PDBCanvas.java
- src/mc_view/PDBChain.java
- src/mc_view/PDBfile.java
- src/mc_view/Residue.java
- src/mc_view/Zsort.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/jalview/analysis/AAFrequencyTest.java
- test/jalview/analysis/AlignSeqTest.java
- test/jalview/analysis/AlignmentAnnotationUtilsTest.java
- test/jalview/analysis/AlignmentGenerator.java
- test/jalview/analysis/AlignmentSorterTest.java
- test/jalview/analysis/AlignmentUtilsTests.java
- test/jalview/analysis/AnnotationSorterTest.java
- test/jalview/analysis/AverageDistanceEngineTest.java
- test/jalview/analysis/CodingUtilsTest.java
- test/jalview/analysis/ConservationTest.java
- test/jalview/analysis/CrossRefTest.java
- test/jalview/analysis/DnaTest.java
- test/jalview/analysis/FinderTest.java
- test/jalview/analysis/GeneticCodesTest.java
- test/jalview/analysis/GroupingTest.java
- test/jalview/analysis/ParsePropertiesTest.java
- test/jalview/analysis/RnaTest.java
- test/jalview/analysis/SeqsetUtilsTest.java
- test/jalview/analysis/SequenceIdMatcherTest.java
- test/jalview/analysis/TestAlignSeq.java
- test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
- test/jalview/analysis/scoremodels/PIDModelTest.java
- test/jalview/analysis/scoremodels/ScoreMatrixTest.java
- test/jalview/analysis/scoremodels/ScoreModelsTest.java
- test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java
- test/jalview/bin/ArgsParserTest.java
- test/jalview/bin/CacheTest.java
- test/jalview/bin/CommandLineOperations.java
- test/jalview/bin/CommandLineOperationsNG.java
- test/jalview/bin/CommandsTest.java
- test/jalview/bin/CommandsTest2.java
- test/jalview/bin/HiDPISettingTest1.java
- test/jalview/bin/HiDPISettingTest2.java
- test/jalview/bin/JalviewLiteTest.java
- test/jalview/bin/MemorySettingTest.java
- test/jalview/bin/argparser/ArgParserTest.java
- test/jalview/commands/EditCommandTest.java
- test/jalview/commands/TrimRegionCommandTest.java
- test/jalview/controller/AlignViewControllerTest.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/AllColsIteratorTest.java
- test/jalview/datamodel/AllRowsIteratorTest.java
- test/jalview/datamodel/CigarArrayTest.java
- test/jalview/datamodel/ColumnSelectionTest.java
- test/jalview/datamodel/ConcurrentModificationTest.java
- test/jalview/datamodel/ContactMatrixTest.java
- test/jalview/datamodel/ContactRangeTest.java
- test/jalview/datamodel/DBRefEntryTest.java
- test/jalview/datamodel/HiddenColumnsCursorTest.java
- test/jalview/datamodel/HiddenColumnsTest.java
- test/jalview/datamodel/HiddenSequencesTest.java
- test/jalview/datamodel/MappedFeaturesTest.java
- test/jalview/datamodel/MappingTest.java
- test/jalview/datamodel/MappingTypeTest.java
- test/jalview/datamodel/MatchTest.java
- test/jalview/datamodel/PAEContactMatrixTest.java
- test/jalview/datamodel/PDBEntryTest.java
- test/jalview/datamodel/RangeElementsIteratorTest.java
- test/jalview/datamodel/ResidueCountTest.java
- test/jalview/datamodel/SearchResultsTest.java
- test/jalview/datamodel/SeqCigarTest.java
- test/jalview/datamodel/SequenceDummyTest.java
- test/jalview/datamodel/SequenceFeatureTest.java
- test/jalview/datamodel/SequenceGroupTest.java
- test/jalview/datamodel/SequenceTest.java
- test/jalview/datamodel/StartRegionIteratorTest.java
- test/jalview/datamodel/VisibleContigsIteratorTest.java
- test/jalview/datamodel/VisibleRowsIteratorTest.java
- test/jalview/datamodel/features/FeatureAttributesTest.java
- test/jalview/datamodel/features/FeatureMatcherSetTest.java
- test/jalview/datamodel/features/FeatureMatcherTest.java
- test/jalview/datamodel/features/FeatureStoreTest.java
- test/jalview/datamodel/features/SequenceFeaturesTest.java
- test/jalview/ext/android/SparseDoubleArrayTest.java
- test/jalview/ext/android/SparseIntArrayTest.java
- test/jalview/ext/android/SparseShortArrayTest.java
- test/jalview/ext/ensembl/EnsemblCdnaTest.java
- test/jalview/ext/ensembl/EnsemblCdsTest.java
- test/jalview/ext/ensembl/EnsemblGeneTest.java
- test/jalview/ext/ensembl/EnsemblGenomeTest.java
- test/jalview/ext/ensembl/EnsemblProteinTest.java
- test/jalview/ext/ensembl/EnsemblRestClientTest.java
- test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
- test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
- test/jalview/ext/ensembl/EnsemblXrefTest.java
- test/jalview/ext/ensembl/SpeciesTest.java
- test/jalview/ext/htsjdk/TestHtsContigDb.java
- test/jalview/ext/htsjdk/VCFReaderTest.java
- test/jalview/ext/jmol/JmolCommandsTest.java
- test/jalview/ext/jmol/JmolParserTest.java
- test/jalview/ext/jmol/JmolViewerTest.java
- test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
- test/jalview/ext/paradise/TestAnnotate3D.java
- test/jalview/ext/pymol/PymolCommandsTest.java
- test/jalview/ext/pymol/PymolManagerTest.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/ChimeraXCommandsTest.java
- test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
- test/jalview/ext/so/SequenceOntologyTest.java
- test/jalview/fts/core/FTSRestClientTest.java
- test/jalview/fts/service/pdb/PDBFTSPanelTest.java
- test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
- test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
- test/jalview/fts/threedbeacons/TDBeaconsPanelTest.java
- test/jalview/gui/AlignFrameTest.java
- test/jalview/gui/AlignViewportTest.java
- test/jalview/gui/AlignmentPanelTest.java
- test/jalview/gui/AnnotationChooserTest.java
- test/jalview/gui/AnnotationColumnChooserTest.java
- test/jalview/gui/AnnotationLabelsTest.java
- test/jalview/gui/AnnotationLabelsTest2.java
- test/jalview/gui/AnnotationPanelTest.java
- test/jalview/gui/AnnotationRowFilterTest.java
- test/jalview/gui/AppVarnaTest.java
- test/jalview/gui/AssociatePDBFileTest.java
- test/jalview/gui/CalculationChooserTest.java
- test/jalview/gui/ColourMenuHelperTest.java
- test/jalview/gui/DesktopTests.java
- test/jalview/gui/FeatureSettingsTest.java
- test/jalview/gui/FontChooserTest.java
- test/jalview/gui/FreeUpMemoryTest.java
- test/jalview/gui/HelpTest.java
- test/jalview/gui/JAL1353bugdemo.java
- test/jalview/gui/JvOptionPaneTest.java
- test/jalview/gui/JvSwingUtilsTest.java
- test/jalview/gui/MouseEventDemo.java
- test/jalview/gui/PaintRefresherTest.java
- test/jalview/gui/PairwiseAlignmentPanelTest.java
- test/jalview/gui/PopupMenuTest.java
- test/jalview/gui/ProgressBarTest.java
- test/jalview/gui/QuitHandlerTest.java
- test/jalview/gui/ScalePanelTest.java
- test/jalview/gui/SeqCanvasTest.java
- test/jalview/gui/SeqPanelTest.java
- test/jalview/gui/SequenceRendererTest.java
- test/jalview/gui/StructureChooserTest.java
- test/jalview/gui/StructureViewerTest.java
- test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
- test/jalview/io/AnnotatedPDBFileInputTest.java
- test/jalview/io/AnnotationExporterTest.java
- test/jalview/io/AnnotationFileIOTest.java
- test/jalview/io/BackupFilesTest.java
- test/jalview/io/BioJsHTMLOutputTest.java
- test/jalview/io/ClustalFileTest.java
- test/jalview/io/CrossRef2xmlTests.java
- test/jalview/io/EmblFlatFileTest.java
- test/jalview/io/FeaturesFileTest.java
- test/jalview/io/FileFormatsTest.java
- test/jalview/io/FileIOTester.java
- test/jalview/io/FileLoaderTest.java
- test/jalview/io/FormatAdapterTest.java
- test/jalview/io/GenBankFileTest.java
- test/jalview/io/HtmlFileTest.java
- test/jalview/io/IdentifyFileTest.java
- test/jalview/io/JSONFileTest.java
- test/jalview/io/Jalview2xmlBase.java
- test/jalview/io/JalviewExportPropertiesTests.java
- test/jalview/io/JalviewFileViewTest.java
- test/jalview/io/NewickFileTests.java
- test/jalview/io/PfamFormatInputTest.java
- test/jalview/io/PhylipFileTests.java
- test/jalview/io/RNAMLfileTest.java
- test/jalview/io/ScoreMatrixFileTest.java
- test/jalview/io/SequenceAnnotationReportTest.java
- test/jalview/io/StockholmFileTest.java
- test/jalview/io/TCoffeeScoreFileTest.java
- test/jalview/io/WindowsFileLoadAndSaveTest.java
- test/jalview/io/cache/AppCacheTest.java
- test/jalview/io/cache/JvCacheableInputBoxTest.java
- test/jalview/io/gff/ExonerateHelperTest.java
- test/jalview/io/gff/Gff3HelperTest.java
- test/jalview/io/gff/GffHelperBaseTest.java
- test/jalview/io/gff/GffHelperFactoryTest.java
- test/jalview/io/gff/GffTests.java
- test/jalview/io/gff/InterProScanHelperTest.java
- test/jalview/io/gff/SequenceOntologyLiteTest.java
- test/jalview/io/vcf/VCFLoaderTest.java
- test/jalview/math/MatrixTest.java
- test/jalview/math/RotatableMatrixTest.java
- test/jalview/math/SparseMatrixTest.java
- test/jalview/project/Jalview2xmlTests.java
- test/jalview/renderer/ContactGeometryTest.java
- test/jalview/renderer/OverviewRendererTest.java
- test/jalview/renderer/OverviewResColourFinderTest.java
- test/jalview/renderer/ResidueColourFinderTest.java
- test/jalview/renderer/ResidueShaderTest.java
- test/jalview/renderer/ScaleRendererTest.java
- test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
- test/jalview/renderer/seqfeatures/FeatureRendererTest.java
- test/jalview/schemes/AnnotationColourGradientTest.java
- test/jalview/schemes/Blosum62ColourSchemeTest.java
- test/jalview/schemes/BuriedColourSchemeTest.java
- test/jalview/schemes/ClustalxColourSchemeTest.java
- test/jalview/schemes/ColourSchemePropertyTest.java
- test/jalview/schemes/ColourSchemesTest.java
- test/jalview/schemes/FeatureColourTest.java
- test/jalview/schemes/HelixColourSchemeTest.java
- test/jalview/schemes/HydrophobicColourSchemeTest.java
- test/jalview/schemes/JalviewColourSchemeTest.java
- test/jalview/schemes/PIDColourSchemeTest.java
- test/jalview/schemes/ResidueColourSchemeTest.java
- test/jalview/schemes/ResiduePropertiesTest.java
- test/jalview/schemes/StrandColourSchemeTest.java
- test/jalview/schemes/TurnColourSchemeTest.java
- test/jalview/schemes/UserColourSchemeTest.java
- test/jalview/structure/AtomSpecModelTest.java
- test/jalview/structure/AtomSpecTest.java
- test/jalview/structure/Mapping.java
- test/jalview/structure/StructureCommandTest.java
- test/jalview/structure/StructureMappingTest.java
- test/jalview/structure/StructureSelectionManagerTest.java
- test/jalview/structures/models/AAStructureBindingModelTest.java
- test/jalview/urls/AppletUrlProviderFactoryTest.java
- test/jalview/urls/CustomUrlProviderTest.java
- test/jalview/urls/DesktopUrlProviderFactoryTest.java
- test/jalview/urls/IdentifiersUrlProviderTest.java
- test/jalview/urls/UrlLinkDisplayTest.java
- test/jalview/urls/UrlLinkTableModelTest.java
- test/jalview/urls/UrlProviderTest.java
- test/jalview/util/ArrayUtilsTest.java
- test/jalview/util/CaseInsensitiveStringTest.java
- test/jalview/util/ColorUtilsTest.java
- test/jalview/util/ComparisonTest.java
- test/jalview/util/DBRefUtilsTest.java
- test/jalview/util/DnaUtilsTest.java
- test/jalview/util/FileUtilsTest.java
- test/jalview/util/FormatTest.java
- test/jalview/util/ImageMakerTest.java
- test/jalview/util/JSONUtilsTest.java
- test/jalview/util/Log4jTest.java
- test/jalview/util/MapListTest.java
- test/jalview/util/MappingUtilsTest.java
- test/jalview/util/MathUtilsTest.java
- test/jalview/util/MessageManagerTest.java
- test/jalview/util/ParseHtmlBodyAndLinksTest.java
- test/jalview/util/PlatformTest.java
- test/jalview/util/QuickSortTest.java
- test/jalview/util/SetUtilsTest.java
- test/jalview/util/ShiftListTest.java
- test/jalview/util/SparseCountTest.java
- test/jalview/util/StringUtilsTest.java
- test/jalview/util/UrlLinkTest.java
- test/jalview/util/dialogrunner/DialogRunnerTest.java
- test/jalview/util/imagemaker/BitmapImageSizeTest.java
- test/jalview/util/matcher/ConditionTest.java
- test/jalview/util/matcher/MatcherTest.java
- test/jalview/viewmodel/OverviewDimensionsHideHiddenTest.java
- test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
- test/jalview/viewmodel/ViewportRangesTest.java
- test/jalview/viewmodel/styles/ViewStyleTest.java
- test/jalview/workers/AlignCalcManagerTest.java
- test/jalview/ws/PDBSequenceFetcherTest.java
- test/jalview/ws/SequenceFetcherTest.java
- test/jalview/ws/dbsources/EmblXmlSourceTest.java
- test/jalview/ws/dbsources/PfamFullTest.java
- test/jalview/ws/dbsources/PfamSeedTest.java
- test/jalview/ws/dbsources/RemoteFormatTest.java
- test/jalview/ws/dbsources/RfamFullTest.java
- test/jalview/ws/dbsources/RfamSeedTest.java
- test/jalview/ws/dbsources/UniprotTest.java
- test/jalview/ws/dbsources/XfamFetcherTest.java
- test/jalview/ws/ebi/EBIFetchClientTest.java
- test/jalview/ws/gui/Jws2ParamView.java
- test/jalview/ws/jabaws/DisorderAnnotExportImport.java
- test/jalview/ws/jabaws/JalviewJabawsTestUtils.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/DbRefFetcherTest.java
- test/jalview/ws/sifts/SiftsClientTest.java
- test/jalview/ws/utils/UrlDownloadClientTest.java
- test/mc_view/AtomTest.java
- test/mc_view/BondTest.java
- test/mc_view/PDBChainTest.java
- test/mc_view/PDBfileTest.java
- test/mc_view/ResidueTest.java
- utils/BufferedLineReader.java
- utils/HelpLinksChecker.java
- utils/MessageBundleChecker.java
- utils/getJavaVersion.java
- utils/help2Website.java
- utils/showJVMVersion.java
- utils/test/JalviewJSTest.java
- utils/test/Test_Applet_Scroll.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/java-team/jalview/-/commit/ea14fe6f7f1161ec0d5c6d40fe35d9a98d08b670

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View it on GitLab: https://salsa.debian.org/java-team/jalview/-/commit/ea14fe6f7f1161ec0d5c6d40fe35d9a98d08b670
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