JAL-2738 copy to spikes/mungo
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 3 Oct 2017 10:25:45 +0000 (11:25 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 3 Oct 2017 10:25:45 +0000 (11:25 +0100)
commitf4766a7bbcfae845fc95923b01fa14ff83d589ff
treec5dd7f88e2b0fd5957b3437e656ea339f354bcd4
parent163ed5b997bbda48e4cdd950e87a8fe01baae7fb
JAL-2738 copy to spikes/mungo
569 files changed:
.ant-targets-build.xml [new file with mode: 0644]
.gitignore
RELEASE
benchmarking/.classpath [new file with mode: 0644]
benchmarking/.gitignore [new file with mode: 0644]
benchmarking/.settings/org.eclipse.core.resources.prefs [new file with mode: 0644]
benchmarking/.settings/org.eclipse.jdt.core.prefs [new file with mode: 0644]
benchmarking/.settings/org.eclipse.m2e.core.prefs [new file with mode: 0644]
benchmarking/README [new file with mode: 0644]
benchmarking/pom.xml [new file with mode: 0644]
benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java [new file with mode: 0644]
build.xml
examples/exampleFeatures.txt
examples/testdata/AGC_DMPK.pdb [new file with mode: 0644]
examples/testdata/agc_dmpk_frag.fa [new file with mode: 0644]
help/help.jhm
help/helpTOC.xml
help/html/calculations/calculatedialog.png [new file with mode: 0644]
help/html/calculations/calculations.html [new file with mode: 0644]
help/html/calculations/pca.html
help/html/calculations/tree.html
help/html/features/overview.html
help/html/features/overview.png [new file with mode: 0644]
help/html/features/preferences.html
help/html/features/search.html
help/html/features/search.png [new file with mode: 0644]
help/html/features/searchclearhist.png [new file with mode: 0644]
help/html/features/searchhist.png [new file with mode: 0644]
help/html/features/splitView.html
help/html/features/viewingpdbs.html
help/html/menus/alignmentMenu.html
help/html/menus/alwcalculate.html
help/html/releases.html
help/html/whatsNew.html
lib/jabaws-min-client-2.2.0.jar
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/MCview/AppletPDBCanvas.java
src/MCview/AppletPDBViewer.java
src/MCview/PDBCanvas.java
src/MCview/PDBChain.java
src/MCview/PDBfile.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/AverageDistanceTree.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/TreeBuilder.java
src/jalview/analysis/TreeModel.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/SimilarityParams.java
src/jalview/analysis/scoremodels/SimilarityScoreModel.java
src/jalview/analysis/scoremodels/SmithWatermanModel.java
src/jalview/api/AlignmentColsCollectionI.java
src/jalview/api/AlignmentRowsCollectionI.java
src/jalview/api/DBRefEntryI.java
src/jalview/api/RendererListenerI.java [new file with mode: 0644]
src/jalview/api/analysis/PairwiseScoreModelI.java
src/jalview/api/analysis/ScoreModelI.java
src/jalview/api/analysis/SimilarityParamsI.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/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/Tooltip.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/TreePanel.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/bin/JalviewLiteURLRetrieve.java
src/jalview/binding/Alignment.java
src/jalview/binding/Annotation.java
src/jalview/binding/AnnotationElement.java
src/jalview/binding/Colour.java
src/jalview/binding/Feature.java
src/jalview/binding/FeatureSettings.java
src/jalview/binding/Features.java
src/jalview/binding/JGroup.java
src/jalview/binding/JSeq.java
src/jalview/binding/JalviewModel.java
src/jalview/binding/JalviewModelSequence.java
src/jalview/binding/JalviewUserColours.java
src/jalview/binding/Pdbentry.java
src/jalview/binding/PdbentryItem.java
src/jalview/binding/Pdbids.java
src/jalview/binding/Property.java
src/jalview/binding/Sequence.java
src/jalview/binding/SequenceSet.java
src/jalview/binding/SequenceType.java
src/jalview/binding/Setting.java
src/jalview/binding/Tree.java
src/jalview/binding/UserColourScheme.java
src/jalview/binding/UserColours.java
src/jalview/binding/VAMSAS.java
src/jalview/binding/VamsasModel.java
src/jalview/binding/Viewport.java
src/jalview/commands/EditCommand.java
src/jalview/commands/RemoveGapColCommand.java
src/jalview/commands/RemoveGapsCommand.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentOrder.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/AllColsCollection.java
src/jalview/datamodel/AllColsIterator.java
src/jalview/datamodel/AllRowsCollection.java
src/jalview/datamodel/AllRowsIterator.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/ColumnSelection.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/FeatureProperties.java
src/jalview/datamodel/GeneLociI.java [new file with mode: 0644]
src/jalview/datamodel/GraphLine.java
src/jalview/datamodel/HiddenColumns.java
src/jalview/datamodel/HiddenSequences.java
src/jalview/datamodel/Mapping.java
src/jalview/datamodel/PDBEntry.java
src/jalview/datamodel/Profile.java
src/jalview/datamodel/Profiles.java
src/jalview/datamodel/ResidueCount.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/SeqCigar.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/VisibleColsCollection.java
src/jalview/datamodel/VisibleColsIterator.java
src/jalview/datamodel/VisibleRowsCollection.java
src/jalview/datamodel/VisibleRowsIterator.java
src/jalview/datamodel/features/FeatureStore.java
src/jalview/datamodel/features/SequenceFeatures.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/datamodel/xdb/embl/EmblFile.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblMap.java [new file with mode: 0644]
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/Species.java
src/jalview/ext/htsjdk/HtsContigDb.java
src/jalview/ext/htsjdk/VCFReader.java [new file with mode: 0644]
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/rbvi/chimera/AtomSpecModel.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/so/SequenceOntology.java
src/jalview/ext/varna/JalviewVarnaBinding.java
src/jalview/ext/varna/VarnaCommands.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/pdb/PDBFTSPanel.java
src/jalview/fts/service/pdb/PDBFTSRestClient.java
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
src/jalview/fts/service/uniprot/UniprotFTSPanel.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/CalculationChooser.java
src/jalview/gui/ChimeraViewFrame.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/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/EPSOptions.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/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/JalviewChimeraBindingModel.java
src/jalview/gui/JvOptionPane.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OOMWarning.java
src/jalview/gui/OptsAndParamsPage.java
src/jalview/gui/OverviewCanvas.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PaintRefresher.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/ProgressBar.java
src/jalview/gui/ProgressPanel.java [new file with mode: 0644]
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/AlignFile.java
src/jalview/io/AlignmentFileReaderI.java
src/jalview/io/AlignmentFileWriterI.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/ClustalFile.java
src/jalview/io/DataSourceType.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/HTMLOutput.java [changed mode: 0755->0644]
src/jalview/io/HtmlSvgOutput.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JPredFile.java
src/jalview/io/JSONFile.java
src/jalview/io/JalviewFileChooser.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/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/gff/ExonerateHelper.java
src/jalview/io/gff/Gff3Helper.java
src/jalview/io/gff/GffHelperBase.java
src/jalview/io/gff/InterProScanHelper.java
src/jalview/io/packed/ParsePackedSet.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/io/vamsas/DatastoreItem.java
src/jalview/io/vamsas/Dbref.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 [new file with mode: 0644]
src/jalview/javascript/JSFunctionExec.java
src/jalview/javascript/JalviewLiteJsApi.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/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/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/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/BioJSRepositoryPojo.java
src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
src/jalview/json/binding/biojson/v1/AlignmentPojo.java
src/jalview/json/binding/biojson/v1/AnnotationPojo.java
src/jalview/json/binding/biojson/v1/SequencePojo.java
src/jalview/math/Matrix.java
src/jalview/math/MatrixI.java
src/jalview/math/RotatableMatrix.java
src/jalview/math/SparseMatrix.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/OverviewRenderer.java
src/jalview/renderer/OverviewResColourFinder.java [new file with mode: 0644]
src/jalview/renderer/ResidueColourFinder.java [new file with mode: 0644]
src/jalview/renderer/ResidueShader.java
src/jalview/renderer/ResidueShaderI.java
src/jalview/renderer/seqfeatures/FeatureColourFinder.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/Blosum62ColourScheme.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/CovariationColourScheme.java
src/jalview/schemes/FeatureColour.java
src/jalview/schemes/JalviewColourScheme.java
src/jalview/schemes/PIDColourScheme.java
src/jalview/schemes/RNAHelicesColour.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/TCoffeeColourScheme.java
src/jalview/schemes/UserColourScheme.java
src/jalview/structure/SecondaryStructureListener.java
src/jalview/structure/SelectionListener.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/structures/models/SequenceStructureBindingModel.java
src/jalview/urls/CustomUrlProvider.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/util/AWTConsole.java
src/jalview/util/BrowserLauncher.java
src/jalview/util/CaseInsensitiveString.java
src/jalview/util/ColorUtils.java
src/jalview/util/Comparison.java
src/jalview/util/DBRefUtils.java
src/jalview/util/Format.java
src/jalview/util/GroupUrlLink.java
src/jalview/util/ImageMaker.java
src/jalview/util/MapList.java
src/jalview/util/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/SetUtils.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/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/OverviewDimensions.java
src/jalview/viewmodel/OverviewDimensionsHideHidden.java
src/jalview/viewmodel/OverviewDimensionsShowHidden.java
src/jalview/viewmodel/PCAModel.java
src/jalview/viewmodel/ViewportListenerI.java
src/jalview/viewmodel/ViewportRanges.java
src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/viewmodel/styles/ViewStyle.java
src/jalview/workers/AlignCalcManager.java
src/jalview/workers/AlignmentAnnotationFactory.java
src/jalview/workers/AnnotationWorker.java
src/jalview/workers/ConsensusThread.java
src/jalview/ws/AWSThread.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/dbsources/EmblXmlSource.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/RfamFull.java
src/jalview/ws/dbsources/RfamSeed.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/dbsources/Xfam.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/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/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/jws2/AAConClient.java
src/jalview/ws/jws2/AADisorderClient.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/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/ParamManager.java
src/jalview/ws/params/simple/BooleanOption.java
src/jalview/ws/params/simple/IntegerParameter.java
src/jalview/ws/params/simple/Parameter.java
src/jalview/ws/rest/HttpResultSet.java
src/jalview/ws/rest/InputType.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/DbSourceProxyImpl.java
src/jalview/ws/sifts/MappingOutputPojo.java
src/jalview/ws/sifts/SiftsClient.java
src/jalview/ws/utils/UrlDownloadClient.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/datamodel/SequenceTest.java
test/jalview/datamodel/features/SequenceFeaturesTest.java
test/jalview/ext/htsjdk/VCFReaderTest.java [new file with mode: 0644]
test/jalview/gui/AlignFrameTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/gui/PopupMenuTest.java
test/jalview/gui/SequenceRendererTest.java
test/jalview/io/CrossRef2xmlTests.java
test/jalview/io/FeaturesFileTest.java
test/jalview/io/testProps.jvprops
test/jalview/io/vcf/VCFLoaderTest.java [new file with mode: 0644]
test/jalview/renderer/OverviewResColourFinderTest.java [new file with mode: 0644]
test/jalview/renderer/ResidueColourFinderTest.java [new file with mode: 0644]
test/jalview/renderer/ResidueShaderTest.java
test/jalview/renderer/seqfeatures/FeatureRendererTest.java
test/jalview/structures/models/AAStructureBindingModelTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/viewmodel/OverviewDimensionsHideHiddenTest.java
test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
test/jalview/viewmodel/ViewportRangesTest.java
test/jalview/ws/dbsources/XfamFetcherTest.java
test/jalview/ws/ebi/EBIFetchClientTest.java
utils/InstallAnywhere/Jalview.iap_xml
utils/checkstyle/import-control.xml
utils/eclipse/JalviewCodeStyle.xml
utils/eclipse/README [new file with mode: 0644]