source.jalview.org Git - jalview.git/commit - examples/exampleFeatures.txt

git://source.jalview.org / jalview.git / commit

author	gmungoc <g.m.carstairs@dundee.ac.uk>
	Tue, 3 Oct 2017 10:25:45 +0000 (11:25 +0100)
committer	gmungoc <g.m.carstairs@dundee.ac.uk>
	Tue, 3 Oct 2017 10:25:45 +0000 (11:25 +0100)
commit	f4766a7bbcfae845fc95923b01fa14ff83d589ff
tree	c5dd7f88e2b0fd5957b3437e656ea339f354bcd4	tree \| snapshot
parent	163ed5b997bbda48e4cdd950e87a8fe01baae7fb	commit \| diff

JAL-2738 copy to spikes/mungo

569 files changed:

.ant-targets-build.xml	[new file with mode: 0644]	blob
.gitignore		diff \| blob \| history
RELEASE		diff \| blob \| history
benchmarking/.classpath	[new file with mode: 0644]	blob
benchmarking/.gitignore	[new file with mode: 0644]	blob
benchmarking/.settings/org.eclipse.core.resources.prefs	[new file with mode: 0644]	blob
benchmarking/.settings/org.eclipse.jdt.core.prefs	[new file with mode: 0644]	blob
benchmarking/.settings/org.eclipse.m2e.core.prefs	[new file with mode: 0644]	blob
benchmarking/README	[new file with mode: 0644]	blob
benchmarking/pom.xml	[new file with mode: 0644]	blob
benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java	[new file with mode: 0644]	blob
build.xml		diff \| blob \| history
examples/exampleFeatures.txt		diff \| blob \| history
examples/testdata/AGC_DMPK.pdb	[new file with mode: 0644]	blob
examples/testdata/agc_dmpk_frag.fa	[new file with mode: 0644]	blob
help/help.jhm		diff \| blob \| history
help/helpTOC.xml		diff \| blob \| history
help/html/calculations/calculatedialog.png	[new file with mode: 0644]	blob
help/html/calculations/calculations.html	[new file with mode: 0644]	blob
help/html/calculations/pca.html		diff \| blob \| history
help/html/calculations/tree.html		diff \| blob \| history
help/html/features/overview.html		diff \| blob \| history
help/html/features/overview.png	[new file with mode: 0644]	blob
help/html/features/preferences.html		diff \| blob \| history
help/html/features/search.html		diff \| blob \| history
help/html/features/search.png	[new file with mode: 0644]	blob
help/html/features/searchclearhist.png	[new file with mode: 0644]	blob
help/html/features/searchhist.png	[new file with mode: 0644]	blob
help/html/features/splitView.html		diff \| blob \| history
help/html/features/viewingpdbs.html		diff \| blob \| history
help/html/menus/alignmentMenu.html		diff \| blob \| history
help/html/menus/alwcalculate.html		diff \| blob \| history
help/html/releases.html		diff \| blob \| history
help/html/whatsNew.html		diff \| blob \| history
lib/jabaws-min-client-2.2.0.jar		diff \| blob \| history
resources/lang/Messages.properties		diff \| blob \| history
resources/lang/Messages_es.properties		diff \| blob \| history
src/MCview/AppletPDBCanvas.java		diff \| blob \| history
src/MCview/AppletPDBViewer.java		diff \| blob \| history
src/MCview/PDBCanvas.java		diff \| blob \| history
src/MCview/PDBChain.java		diff \| blob \| history
src/MCview/PDBfile.java		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentAnnotationUtils.java		diff \| blob \| history
src/jalview/analysis/AlignmentSorter.java		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/AnnotationSorter.java		diff \| blob \| history
src/jalview/analysis/AverageDistanceTree.java		diff \| blob \| history
src/jalview/analysis/Conservation.java		diff \| blob \| history
src/jalview/analysis/CrossRef.java		diff \| blob \| history
src/jalview/analysis/Dna.java		diff \| blob \| history
src/jalview/analysis/Finder.java		diff \| blob \| history
src/jalview/analysis/Grouping.java		diff \| blob \| history
src/jalview/analysis/NJTree.java		diff \| blob \| history
src/jalview/analysis/PCA.java		diff \| blob \| history
src/jalview/analysis/ParseProperties.java		diff \| blob \| history
src/jalview/analysis/Rna.java		diff \| blob \| history
src/jalview/analysis/SecStrConsensus.java		diff \| blob \| history
src/jalview/analysis/SeqsetUtils.java		diff \| blob \| history
src/jalview/analysis/SequenceIdMatcher.java		diff \| blob \| history
src/jalview/analysis/StructureFrequency.java		diff \| blob \| history
src/jalview/analysis/TreeBuilder.java		diff \| blob \| history
src/jalview/analysis/TreeModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/DistanceScoreModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/FeatureDistanceModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/PIDModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/ScoreMatrix.java		diff \| blob \| history
src/jalview/analysis/scoremodels/ScoreModels.java		diff \| blob \| history
src/jalview/analysis/scoremodels/SimilarityParams.java		diff \| blob \| history
src/jalview/analysis/scoremodels/SimilarityScoreModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/SmithWatermanModel.java		diff \| blob \| history
src/jalview/api/AlignmentColsCollectionI.java		diff \| blob \| history
src/jalview/api/AlignmentRowsCollectionI.java		diff \| blob \| history
src/jalview/api/DBRefEntryI.java		diff \| blob \| history
src/jalview/api/RendererListenerI.java	[new file with mode: 0644]	blob
src/jalview/api/analysis/PairwiseScoreModelI.java		diff \| blob \| history
src/jalview/api/analysis/ScoreModelI.java		diff \| blob \| history
src/jalview/api/analysis/SimilarityParamsI.java		diff \| blob \| history
src/jalview/appletgui/APopupMenu.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignViewport.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/appletgui/AnnotationColumnChooser.java		diff \| blob \| history
src/jalview/appletgui/AnnotationLabels.java		diff \| blob \| history
src/jalview/appletgui/AnnotationPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationRowFilter.java		diff \| blob \| history
src/jalview/appletgui/AppletJmol.java		diff \| blob \| history
src/jalview/appletgui/AppletJmolBinding.java		diff \| blob \| history
src/jalview/appletgui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/appletgui/EmbmenuFrame.java		diff \| blob \| history
src/jalview/appletgui/ExtJmol.java		diff \| blob \| history
src/jalview/appletgui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/appletgui/FeatureRenderer.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/Finder.java		diff \| blob \| history
src/jalview/appletgui/FontChooser.java		diff \| blob \| history
src/jalview/appletgui/IdCanvas.java		diff \| blob \| history
src/jalview/appletgui/IdPanel.java		diff \| blob \| history
src/jalview/appletgui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/appletgui/JVDialog.java		diff \| blob \| history
src/jalview/appletgui/OverviewCanvas.java		diff \| blob \| history
src/jalview/appletgui/OverviewPanel.java		diff \| blob \| history
src/jalview/appletgui/PCAPanel.java		diff \| blob \| history
src/jalview/appletgui/PaintRefresher.java		diff \| blob \| history
src/jalview/appletgui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/appletgui/RedundancyPanel.java		diff \| blob \| history
src/jalview/appletgui/RotatableCanvas.java		diff \| blob \| history
src/jalview/appletgui/ScalePanel.java		diff \| blob \| history
src/jalview/appletgui/SeqCanvas.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/appletgui/SequenceRenderer.java		diff \| blob \| history
src/jalview/appletgui/SliderPanel.java		diff \| blob \| history
src/jalview/appletgui/SplitFrame.java		diff \| blob \| history
src/jalview/appletgui/Tooltip.java		diff \| blob \| history
src/jalview/appletgui/TreeCanvas.java		diff \| blob \| history
src/jalview/appletgui/TreePanel.java		diff \| blob \| history
src/jalview/appletgui/UserDefinedColours.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/bin/JalviewLiteURLRetrieve.java		diff \| blob \| history
src/jalview/binding/Alignment.java		diff \| blob \| history
src/jalview/binding/Annotation.java		diff \| blob \| history
src/jalview/binding/AnnotationElement.java		diff \| blob \| history
src/jalview/binding/Colour.java		diff \| blob \| history
src/jalview/binding/Feature.java		diff \| blob \| history
src/jalview/binding/FeatureSettings.java		diff \| blob \| history
src/jalview/binding/Features.java		diff \| blob \| history
src/jalview/binding/JGroup.java		diff \| blob \| history
src/jalview/binding/JSeq.java		diff \| blob \| history
src/jalview/binding/JalviewModel.java		diff \| blob \| history
src/jalview/binding/JalviewModelSequence.java		diff \| blob \| history
src/jalview/binding/JalviewUserColours.java		diff \| blob \| history
src/jalview/binding/Pdbentry.java		diff \| blob \| history
src/jalview/binding/PdbentryItem.java		diff \| blob \| history
src/jalview/binding/Pdbids.java		diff \| blob \| history
src/jalview/binding/Property.java		diff \| blob \| history
src/jalview/binding/Sequence.java		diff \| blob \| history
src/jalview/binding/SequenceSet.java		diff \| blob \| history
src/jalview/binding/SequenceType.java		diff \| blob \| history
src/jalview/binding/Setting.java		diff \| blob \| history
src/jalview/binding/Tree.java		diff \| blob \| history
src/jalview/binding/UserColourScheme.java		diff \| blob \| history
src/jalview/binding/UserColours.java		diff \| blob \| history
src/jalview/binding/VAMSAS.java		diff \| blob \| history
src/jalview/binding/VamsasModel.java		diff \| blob \| history
src/jalview/binding/Viewport.java		diff \| blob \| history
src/jalview/commands/EditCommand.java		diff \| blob \| history
src/jalview/commands/RemoveGapColCommand.java		diff \| blob \| history
src/jalview/commands/RemoveGapsCommand.java		diff \| blob \| history
src/jalview/controller/AlignViewController.java		diff \| blob \| history
src/jalview/datamodel/AlignedCodonFrame.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AlignmentI.java		diff \| blob \| history
src/jalview/datamodel/AlignmentOrder.java		diff \| blob \| history
src/jalview/datamodel/AlignmentView.java		diff \| blob \| history
src/jalview/datamodel/AllColsCollection.java		diff \| blob \| history
src/jalview/datamodel/AllColsIterator.java		diff \| blob \| history
src/jalview/datamodel/AllRowsCollection.java		diff \| blob \| history
src/jalview/datamodel/AllRowsIterator.java		diff \| blob \| history
src/jalview/datamodel/Annotation.java		diff \| blob \| history
src/jalview/datamodel/BinaryNode.java		diff \| blob \| history
src/jalview/datamodel/BinarySequence.java		diff \| blob \| history
src/jalview/datamodel/CigarArray.java		diff \| blob \| history
src/jalview/datamodel/CigarBase.java		diff \| blob \| history
src/jalview/datamodel/CigarCigar.java		diff \| blob \| history
src/jalview/datamodel/ColumnSelection.java		diff \| blob \| history
src/jalview/datamodel/DBRefEntry.java		diff \| blob \| history
src/jalview/datamodel/FeatureProperties.java		diff \| blob \| history
src/jalview/datamodel/GeneLociI.java	[new file with mode: 0644]	blob
src/jalview/datamodel/GraphLine.java		diff \| blob \| history
src/jalview/datamodel/HiddenColumns.java		diff \| blob \| history
src/jalview/datamodel/HiddenSequences.java		diff \| blob \| history
src/jalview/datamodel/Mapping.java		diff \| blob \| history
src/jalview/datamodel/PDBEntry.java		diff \| blob \| history
src/jalview/datamodel/Profile.java		diff \| blob \| history
src/jalview/datamodel/Profiles.java		diff \| blob \| history
src/jalview/datamodel/ResidueCount.java		diff \| blob \| history
src/jalview/datamodel/SearchResults.java		diff \| blob \| history
src/jalview/datamodel/SeqCigar.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceFeature.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/datamodel/VisibleColsCollection.java		diff \| blob \| history
src/jalview/datamodel/VisibleColsIterator.java		diff \| blob \| history
src/jalview/datamodel/VisibleRowsCollection.java		diff \| blob \| history
src/jalview/datamodel/VisibleRowsIterator.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureStore.java		diff \| blob \| history
src/jalview/datamodel/features/SequenceFeatures.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblEntry.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblFile.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblGene.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblMap.java	[new file with mode: 0644]	blob
src/jalview/ext/ensembl/EnsemblRestClient.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSeqProxy.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSymbol.java		diff \| blob \| history
src/jalview/ext/ensembl/Species.java		diff \| blob \| history
src/jalview/ext/htsjdk/HtsContigDb.java		diff \| blob \| history
src/jalview/ext/htsjdk/VCFReader.java	[new file with mode: 0644]	blob
src/jalview/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/jmol/JmolCommands.java		diff \| blob \| history
src/jalview/ext/jmol/JmolParser.java		diff \| blob \| history
src/jalview/ext/paradise/Annotate3D.java		diff \| blob \| history
src/jalview/ext/rbvi/chimera/AtomSpecModel.java		diff \| blob \| history
src/jalview/ext/rbvi/chimera/ChimeraCommands.java		diff \| blob \| history
src/jalview/ext/rbvi/chimera/ChimeraListener.java		diff \| blob \| history
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java		diff \| blob \| history
src/jalview/ext/so/SequenceOntology.java		diff \| blob \| history
src/jalview/ext/varna/JalviewVarnaBinding.java		diff \| blob \| history
src/jalview/ext/varna/VarnaCommands.java		diff \| blob \| history
src/jalview/fts/core/DecimalFormatTableCellRenderer.java		diff \| blob \| history
src/jalview/fts/core/FTSDataColumnPreferences.java		diff \| blob \| history
src/jalview/fts/core/FTSRestClient.java		diff \| blob \| history
src/jalview/fts/core/FTSRestRequest.java		diff \| blob \| history
src/jalview/fts/core/FTSRestResponse.java		diff \| blob \| history
src/jalview/fts/core/GFTSPanel.java		diff \| blob \| history
src/jalview/fts/service/pdb/PDBFTSPanel.java		diff \| blob \| history
src/jalview/fts/service/pdb/PDBFTSRestClient.java		diff \| blob \| history
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java		diff \| blob \| history
src/jalview/fts/service/uniprot/UniprotFTSPanel.java		diff \| blob \| history
src/jalview/gui/AlignExportSettings.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AlignmentPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationColumnChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationExporter.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationRowFilter.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/AppJmolBinding.java		diff \| blob \| history
src/jalview/gui/AppVarna.java		diff \| blob \| history
src/jalview/gui/AppVarnaBinding.java		diff \| blob \| history
src/jalview/gui/AssociatePdbFileWithSeq.java		diff \| blob \| history
src/jalview/gui/BlogReader.java		diff \| blob \| history
src/jalview/gui/CalculationChooser.java		diff \| blob \| history
src/jalview/gui/ChimeraViewFrame.java		diff \| blob \| history
src/jalview/gui/ColourMenuHelper.java		diff \| blob \| history
src/jalview/gui/ComboBoxTooltipRenderer.java		diff \| blob \| history
src/jalview/gui/Console.java		diff \| blob \| history
src/jalview/gui/CrossRefAction.java		diff \| blob \| history
src/jalview/gui/CutAndPasteHtmlTransfer.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/DasSourceBrowser.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/EPSOptions.java		diff \| blob \| history
src/jalview/gui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/gui/FeatureRenderer.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/Finder.java		diff \| blob \| history
src/jalview/gui/FontChooser.java		diff \| blob \| history
src/jalview/gui/HTMLOptions.java		diff \| blob \| history
src/jalview/gui/IdCanvas.java		diff \| blob \| history
src/jalview/gui/IdPanel.java		diff \| blob \| history
src/jalview/gui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/gui/JDatabaseTree.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/Jalview2XML_V1.java		diff \| blob \| history
src/jalview/gui/JalviewChimeraBindingModel.java		diff \| blob \| history
src/jalview/gui/JvOptionPane.java		diff \| blob \| history
src/jalview/gui/JvSwingUtils.java		diff \| blob \| history
src/jalview/gui/OOMWarning.java		diff \| blob \| history
src/jalview/gui/OptsAndParamsPage.java		diff \| blob \| history
src/jalview/gui/OverviewCanvas.java		diff \| blob \| history
src/jalview/gui/OverviewPanel.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PaintRefresher.java		diff \| blob \| history
src/jalview/gui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/ProgressBar.java		diff \| blob \| history
src/jalview/gui/ProgressPanel.java	[new file with mode: 0644]	blob
src/jalview/gui/PromptUserConfig.java		diff \| blob \| history
src/jalview/gui/RedundancyPanel.java		diff \| blob \| history
src/jalview/gui/RestInputParamEditDialog.java		diff \| blob \| history
src/jalview/gui/RestServiceEditorPane.java		diff \| blob \| history
src/jalview/gui/RotatableCanvas.java		diff \| blob \| history
src/jalview/gui/SVGOptions.java		diff \| blob \| history
src/jalview/gui/ScalePanel.java		diff \| blob \| history
src/jalview/gui/SeqCanvas.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SequenceRenderer.java		diff \| blob \| history
src/jalview/gui/SliderPanel.java		diff \| blob \| history
src/jalview/gui/SplashScreen.java		diff \| blob \| history
src/jalview/gui/SplitFrame.java		diff \| blob \| history
src/jalview/gui/StructureChooser.java		diff \| blob \| history
src/jalview/gui/StructureViewer.java		diff \| blob \| history
src/jalview/gui/StructureViewerBase.java		diff \| blob \| history
src/jalview/gui/TextColourChooser.java		diff \| blob \| history
src/jalview/gui/TreeCanvas.java		diff \| blob \| history
src/jalview/gui/TreePanel.java		diff \| blob \| history
src/jalview/gui/UserDefinedColours.java		diff \| blob \| history
src/jalview/gui/UserQuestionnaireCheck.java		diff \| blob \| history
src/jalview/gui/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/ViewSelectionMenu.java		diff \| blob \| history
src/jalview/gui/WebserviceInfo.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/gui/WsParamSetManager.java		diff \| blob \| history
src/jalview/gui/WsPreferences.java		diff \| blob \| history
src/jalview/httpserver/AbstractRequestHandler.java		diff \| blob \| history
src/jalview/httpserver/HttpServer.java		diff \| blob \| history
src/jalview/io/AlignFile.java		diff \| blob \| history
src/jalview/io/AlignmentFileReaderI.java		diff \| blob \| history
src/jalview/io/AlignmentFileWriterI.java		diff \| blob \| history
src/jalview/io/AnnotationFile.java		diff \| blob \| history
src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
src/jalview/io/BioJsHTMLOutput.java		diff \| blob \| history
src/jalview/io/ClustalFile.java		diff \| blob \| history
src/jalview/io/DataSourceType.java		diff \| blob \| history
src/jalview/io/FastaFile.java		diff \| blob \| history
src/jalview/io/FeaturesFile.java		diff \| blob \| history
src/jalview/io/FileFormat.java		diff \| blob \| history
src/jalview/io/FileFormatException.java		diff \| blob \| history
src/jalview/io/FileFormatI.java		diff \| blob \| history
src/jalview/io/FileFormats.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/FileParse.java		diff \| blob \| history
src/jalview/io/FormatAdapter.java		diff \| blob \| history
src/jalview/io/HTMLOutput.java	[changed mode: 0755->0644]	diff \| blob \| history
src/jalview/io/HtmlSvgOutput.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/JPredFile.java		diff \| blob \| history
src/jalview/io/JSONFile.java		diff \| blob \| history
src/jalview/io/JalviewFileChooser.java		diff \| blob \| history
src/jalview/io/JalviewFileView.java		diff \| blob \| history
src/jalview/io/JnetAnnotationMaker.java		diff \| blob \| history
src/jalview/io/MSFfile.java		diff \| blob \| history
src/jalview/io/ModellerDescription.java		diff \| blob \| history
src/jalview/io/NewickFile.java		diff \| blob \| history
src/jalview/io/PfamFile.java		diff \| blob \| history
src/jalview/io/PhylipFile.java		diff \| blob \| history
src/jalview/io/PileUpfile.java		diff \| blob \| history
src/jalview/io/RnamlFile.java		diff \| blob \| history
src/jalview/io/ScoreMatrixFile.java		diff \| blob \| history
src/jalview/io/SequenceAnnotationReport.java		diff \| blob \| history
src/jalview/io/SimpleBlastFile.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/StructureFile.java		diff \| blob \| history
src/jalview/io/TCoffeeScoreFile.java		diff \| blob \| history
src/jalview/io/VamsasAppDatastore.java		diff \| blob \| history
src/jalview/io/WSWUBlastClient.java		diff \| blob \| history
src/jalview/io/cache/AppCache.java		diff \| blob \| history
src/jalview/io/cache/JvCacheableInputBox.java		diff \| blob \| history
src/jalview/io/gff/ExonerateHelper.java		diff \| blob \| history
src/jalview/io/gff/Gff3Helper.java		diff \| blob \| history
src/jalview/io/gff/GffHelperBase.java		diff \| blob \| history
src/jalview/io/gff/InterProScanHelper.java		diff \| blob \| history
src/jalview/io/packed/ParsePackedSet.java		diff \| blob \| history
src/jalview/io/vamsas/Datasetsequence.java		diff \| blob \| history
src/jalview/io/vamsas/DatastoreItem.java		diff \| blob \| history
src/jalview/io/vamsas/Dbref.java		diff \| blob \| history
src/jalview/io/vamsas/Rangetype.java		diff \| blob \| history
src/jalview/io/vamsas/Sequencefeature.java		diff \| blob \| history
src/jalview/io/vamsas/Sequencemapping.java		diff \| blob \| history
src/jalview/io/vamsas/Tree.java		diff \| blob \| history
src/jalview/io/vcf/VCFLoader.java	[new file with mode: 0644]	blob
src/jalview/javascript/JSFunctionExec.java		diff \| blob \| history
src/jalview/javascript/JalviewLiteJsApi.java		diff \| blob \| history
src/jalview/javascript/JsSelectionSender.java		diff \| blob \| history
src/jalview/javascript/MouseOverListener.java		diff \| blob \| history
src/jalview/javascript/MouseOverStructureListener.java		diff \| blob \| history
src/jalview/jbgui/GAlignExportSettings.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java		diff \| blob \| history
src/jalview/jbgui/GCutAndPasteTransfer.java		diff \| blob \| history
src/jalview/jbgui/GDasSourceBrowser.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GFinder.java		diff \| blob \| history
src/jalview/jbgui/GPCAPanel.java		diff \| blob \| history
src/jalview/jbgui/GPairwiseAlignPanel.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GRestInputParamEditDialog.java		diff \| blob \| history
src/jalview/jbgui/GRestServiceEditorPane.java		diff \| blob \| history
src/jalview/jbgui/GSequenceLink.java		diff \| blob \| history
src/jalview/jbgui/GSliderPanel.java		diff \| blob \| history
src/jalview/jbgui/GSplitFrame.java		diff \| blob \| history
src/jalview/jbgui/GStructureChooser.java		diff \| blob \| history
src/jalview/jbgui/GStructureViewer.java		diff \| blob \| history
src/jalview/jbgui/GTreePanel.java		diff \| blob \| history
src/jalview/jbgui/GUserDefinedColours.java		diff \| blob \| history
src/jalview/jbgui/GWebserviceInfo.java		diff \| blob \| history
src/jalview/jbgui/GWsPreferences.java		diff \| blob \| history
src/jalview/json/binding/biojs/BioJSRepositoryPojo.java		diff \| blob \| history
src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java		diff \| blob \| history
src/jalview/json/binding/biojson/v1/AlignmentPojo.java		diff \| blob \| history
src/jalview/json/binding/biojson/v1/AnnotationPojo.java		diff \| blob \| history
src/jalview/json/binding/biojson/v1/SequencePojo.java		diff \| blob \| history
src/jalview/math/Matrix.java		diff \| blob \| history
src/jalview/math/MatrixI.java		diff \| blob \| history
src/jalview/math/RotatableMatrix.java		diff \| blob \| history
src/jalview/math/SparseMatrix.java		diff \| blob \| history
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/OverviewRenderer.java		diff \| blob \| history
src/jalview/renderer/OverviewResColourFinder.java	[new file with mode: 0644]	blob
src/jalview/renderer/ResidueColourFinder.java	[new file with mode: 0644]	blob
src/jalview/renderer/ResidueShader.java		diff \| blob \| history
src/jalview/renderer/ResidueShaderI.java		diff \| blob \| history
src/jalview/renderer/seqfeatures/FeatureColourFinder.java		diff \| blob \| history
src/jalview/renderer/seqfeatures/FeatureRenderer.java		diff \| blob \| history
src/jalview/schemes/AnnotationColourGradient.java		diff \| blob \| history
src/jalview/schemes/Blosum62ColourScheme.java		diff \| blob \| history
src/jalview/schemes/ClustalxColourScheme.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeI.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeLoader.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeProperty.java		diff \| blob \| history
src/jalview/schemes/ColourSchemes.java		diff \| blob \| history
src/jalview/schemes/CovariationColourScheme.java		diff \| blob \| history
src/jalview/schemes/FeatureColour.java		diff \| blob \| history
src/jalview/schemes/JalviewColourScheme.java		diff \| blob \| history
src/jalview/schemes/PIDColourScheme.java		diff \| blob \| history
src/jalview/schemes/RNAHelicesColour.java		diff \| blob \| history
src/jalview/schemes/ResidueColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/schemes/TCoffeeColourScheme.java		diff \| blob \| history
src/jalview/schemes/UserColourScheme.java		diff \| blob \| history
src/jalview/structure/SecondaryStructureListener.java		diff \| blob \| history
src/jalview/structure/SelectionListener.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/structures/models/AAStructureBindingModel.java		diff \| blob \| history
src/jalview/structures/models/SequenceStructureBindingModel.java		diff \| blob \| history
src/jalview/urls/CustomUrlProvider.java		diff \| blob \| history
src/jalview/urls/IdentifiersUrlProvider.java		diff \| blob \| history
src/jalview/urls/UrlLinkDisplay.java		diff \| blob \| history
src/jalview/urls/UrlLinkTableModel.java		diff \| blob \| history
src/jalview/urls/UrlProvider.java		diff \| blob \| history
src/jalview/urls/UrlProviderImpl.java		diff \| blob \| history
src/jalview/urls/api/UrlProviderFactoryI.java		diff \| blob \| history
src/jalview/util/AWTConsole.java		diff \| blob \| history
src/jalview/util/BrowserLauncher.java		diff \| blob \| history
src/jalview/util/CaseInsensitiveString.java		diff \| blob \| history
src/jalview/util/ColorUtils.java		diff \| blob \| history
src/jalview/util/Comparison.java		diff \| blob \| history
src/jalview/util/DBRefUtils.java		diff \| blob \| history
src/jalview/util/Format.java		diff \| blob \| history
src/jalview/util/GroupUrlLink.java		diff \| blob \| history
src/jalview/util/ImageMaker.java		diff \| blob \| history
src/jalview/util/MapList.java		diff \| blob \| history
src/jalview/util/MappingUtils.java		diff \| blob \| history
src/jalview/util/MessageManager.java		diff \| blob \| history
src/jalview/util/ParseHtmlBodyAndLinks.java		diff \| blob \| history
src/jalview/util/Platform.java		diff \| blob \| history
src/jalview/util/QuickSort.java		diff \| blob \| history
src/jalview/util/SetUtils.java		diff \| blob \| history
src/jalview/util/SparseCount.java		diff \| blob \| history
src/jalview/util/StringUtils.java		diff \| blob \| history
src/jalview/util/TableSorter.java		diff \| blob \| history
src/jalview/util/UrlConstants.java		diff \| blob \| history
src/jalview/util/UrlLink.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/OverviewDimensions.java		diff \| blob \| history
src/jalview/viewmodel/OverviewDimensionsHideHidden.java		diff \| blob \| history
src/jalview/viewmodel/OverviewDimensionsShowHidden.java		diff \| blob \| history
src/jalview/viewmodel/PCAModel.java		diff \| blob \| history
src/jalview/viewmodel/ViewportListenerI.java		diff \| blob \| history
src/jalview/viewmodel/ViewportRanges.java		diff \| blob \| history
src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java		diff \| blob \| history
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java		diff \| blob \| history
src/jalview/viewmodel/styles/ViewStyle.java		diff \| blob \| history
src/jalview/workers/AlignCalcManager.java		diff \| blob \| history
src/jalview/workers/AlignmentAnnotationFactory.java		diff \| blob \| history
src/jalview/workers/AnnotationWorker.java		diff \| blob \| history
src/jalview/workers/ConsensusThread.java		diff \| blob \| history
src/jalview/ws/AWSThread.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/DasSequenceFeatureFetcher.java		diff \| blob \| history
src/jalview/ws/HttpClientUtils.java		diff \| blob \| history
src/jalview/ws/JobStateSummary.java		diff \| blob \| history
src/jalview/ws/SequenceFetcher.java		diff \| blob \| history
src/jalview/ws/dbsources/EmblXmlSource.java		diff \| blob \| history
src/jalview/ws/dbsources/Pdb.java		diff \| blob \| history
src/jalview/ws/dbsources/Pfam.java		diff \| blob \| history
src/jalview/ws/dbsources/PfamFull.java		diff \| blob \| history
src/jalview/ws/dbsources/PfamSeed.java		diff \| blob \| history
src/jalview/ws/dbsources/RfamFull.java		diff \| blob \| history
src/jalview/ws/dbsources/RfamSeed.java		diff \| blob \| history
src/jalview/ws/dbsources/Uniprot.java		diff \| blob \| history
src/jalview/ws/dbsources/Xfam.java		diff \| blob \| history
src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java		diff \| blob \| history
src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java		diff \| blob \| history
src/jalview/ws/dbsources/das/datamodel/JalviewSource.java		diff \| blob \| history
src/jalview/ws/ebi/EBIFetchClient.java		diff \| blob \| history
src/jalview/ws/jws1/Annotate3D.java		diff \| blob \| history
src/jalview/ws/jws1/Discoverer.java		diff \| blob \| history
src/jalview/ws/jws1/JPredClient.java		diff \| blob \| history
src/jalview/ws/jws1/JPredThread.java		diff \| blob \| history
src/jalview/ws/jws1/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/jws1/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/jws1/SeqSearchWSClient.java		diff \| blob \| history
src/jalview/ws/jws1/SeqSearchWSThread.java		diff \| blob \| history
src/jalview/ws/jws1/WS1Client.java		diff \| blob \| history
src/jalview/ws/jws2/AAConClient.java		diff \| blob \| history
src/jalview/ws/jws2/AADisorderClient.java		diff \| blob \| history
src/jalview/ws/jws2/AbstractJabaCalcWorker.java		diff \| blob \| history
src/jalview/ws/jws2/JWs2Job.java		diff \| blob \| history
src/jalview/ws/jws2/JabaParamStore.java		diff \| blob \| history
src/jalview/ws/jws2/JabaPreset.java		diff \| blob \| history
src/jalview/ws/jws2/JabaWsServerQuery.java		diff \| blob \| history
src/jalview/ws/jws2/JabawsCalcWorker.java		diff \| blob \| history
src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Client.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Discoverer.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/jws2/ParameterUtils.java		diff \| blob \| history
src/jalview/ws/jws2/RNAalifoldClient.java		diff \| blob \| history
src/jalview/ws/jws2/SequenceAnnotationWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/dm/AAConSettings.java		diff \| blob \| history
src/jalview/ws/jws2/dm/JabaOption.java		diff \| blob \| history
src/jalview/ws/jws2/dm/JabaValueConstrain.java		diff \| blob \| history
src/jalview/ws/jws2/dm/JabaWsParamSet.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2Instance.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java		diff \| blob \| history
src/jalview/ws/params/ParamManager.java		diff \| blob \| history
src/jalview/ws/params/simple/BooleanOption.java		diff \| blob \| history
src/jalview/ws/params/simple/IntegerParameter.java		diff \| blob \| history
src/jalview/ws/params/simple/Parameter.java		diff \| blob \| history
src/jalview/ws/rest/HttpResultSet.java		diff \| blob \| history
src/jalview/ws/rest/InputType.java		diff \| blob \| history
src/jalview/ws/rest/RestClient.java		diff \| blob \| history
src/jalview/ws/rest/RestJob.java		diff \| blob \| history
src/jalview/ws/rest/RestJobThread.java		diff \| blob \| history
src/jalview/ws/rest/RestServiceDescription.java		diff \| blob \| history
src/jalview/ws/rest/params/Alignment.java		diff \| blob \| history
src/jalview/ws/rest/params/AnnotationFile.java		diff \| blob \| history
src/jalview/ws/rest/params/JobConstant.java		diff \| blob \| history
src/jalview/ws/rest/params/SeqGroupIndexVector.java		diff \| blob \| history
src/jalview/ws/rest/params/SeqIdVector.java		diff \| blob \| history
src/jalview/ws/rest/params/SeqVector.java		diff \| blob \| history
src/jalview/ws/rest/params/Tree.java		diff \| blob \| history
src/jalview/ws/seqfetcher/ASequenceFetcher.java		diff \| blob \| history
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java		diff \| blob \| history
src/jalview/ws/sifts/MappingOutputPojo.java		diff \| blob \| history
src/jalview/ws/sifts/SiftsClient.java		diff \| blob \| history
src/jalview/ws/utils/UrlDownloadClient.java		diff \| blob \| history
test/jalview/analysis/AlignmentUtilsTests.java		diff \| blob \| history
test/jalview/datamodel/SequenceTest.java		diff \| blob \| history
test/jalview/datamodel/features/SequenceFeaturesTest.java		diff \| blob \| history
test/jalview/ext/htsjdk/VCFReaderTest.java	[new file with mode: 0644]	blob
test/jalview/gui/AlignFrameTest.java		diff \| blob \| history
test/jalview/gui/AlignViewportTest.java		diff \| blob \| history
test/jalview/gui/PopupMenuTest.java		diff \| blob \| history
test/jalview/gui/SequenceRendererTest.java		diff \| blob \| history
test/jalview/io/CrossRef2xmlTests.java		diff \| blob \| history
test/jalview/io/FeaturesFileTest.java		diff \| blob \| history
test/jalview/io/testProps.jvprops		diff \| blob \| history
test/jalview/io/vcf/VCFLoaderTest.java	[new file with mode: 0644]	blob
test/jalview/renderer/OverviewResColourFinderTest.java	[new file with mode: 0644]	blob
test/jalview/renderer/ResidueColourFinderTest.java	[new file with mode: 0644]	blob
test/jalview/renderer/ResidueShaderTest.java		diff \| blob \| history
test/jalview/renderer/seqfeatures/FeatureRendererTest.java		diff \| blob \| history
test/jalview/structures/models/AAStructureBindingModelTest.java		diff \| blob \| history
test/jalview/util/MappingUtilsTest.java		diff \| blob \| history
test/jalview/viewmodel/OverviewDimensionsHideHiddenTest.java		diff \| blob \| history
test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java		diff \| blob \| history
test/jalview/viewmodel/ViewportRangesTest.java		diff \| blob \| history
test/jalview/ws/dbsources/XfamFetcherTest.java		diff \| blob \| history
test/jalview/ws/ebi/EBIFetchClientTest.java		diff \| blob \| history
utils/InstallAnywhere/Jalview.iap_xml		diff \| blob \| history
utils/checkstyle/import-control.xml		diff \| blob \| history
utils/eclipse/JalviewCodeStyle.xml		diff \| blob \| history
utils/eclipse/README	[new file with mode: 0644]	blob

RSS Atom