source.jalview.org Git - jalview.git/commit

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

author	gmungoc <g.m.carstairs@dundee.ac.uk>
	Fri, 9 Jun 2017 15:28:28 +0000 (16:28 +0100)
committer	gmungoc <g.m.carstairs@dundee.ac.uk>
	Fri, 9 Jun 2017 15:28:28 +0000 (16:28 +0100)
commit	136c0793b90b72b928c4d77dc109dd5c644e00d3
tree	53131544aa73290b4bedd7925b203e746ce9fd34	tree \| snapshot
parent	8677e6e34e291edc58c1da2fc9c958473754143f	commit \| diff

JAL-2446 merged to spike branch

491 files changed:

.classpath		diff \| blob \| history
examples/appletParameters.html		diff \| blob \| history
examples/example.json		diff \| blob \| history
examples/exampleFeatures.txt		diff \| blob \| history
examples/groovy/colourConserved.groovy	[new file with mode: 0644]	blob
examples/groovy/colourSchemes.groovy	[new file with mode: 0644]	blob
examples/groovy/colourUnconserved.groovy	[new file with mode: 0644]	blob
examples/groovy/featuresCounter.groovy	[new file with mode: 0644]	blob
examples/groovy/visibleFeaturesCounter.groovy	[new file with mode: 0644]	blob
examples/testdata/example_annot_file.jva		diff \| blob \| history
help/help.jhm		diff \| blob \| history
help/helpTOC.xml		diff \| blob \| history
help/html/colourSchemes/clustal.html		diff \| blob \| history
help/html/colourSchemes/user.html		diff \| blob \| history
help/html/colourSchemes/userDefined_java7.gif		diff \| blob \| history
help/html/features/chimera.html		diff \| blob \| history
help/html/features/groovy.html		diff \| blob \| history
help/html/features/overview.html		diff \| blob \| history
help/html/features/preferences.html		diff \| blob \| history
help/html/features/splitView.html		diff \| blob \| history
help/html/groovy/featuresCounter.html	[new file with mode: 0644]	blob
help/html/io/tcoffeescores.html		diff \| blob \| history
help/html/menus/desktopMenu.html		diff \| blob \| history
help/html/menus/popupMenu.html		diff \| blob \| history
help/html/releases.html		diff \| blob \| history
help/html/webServices/JABAWS.html		diff \| blob \| history
help/html/webServices/jnet.html		diff \| blob \| history
help/html/webServices/jnetprediction.gif	[changed mode: 0755->0644]	diff \| blob \| history
help/html/webServices/msaclient.html		diff \| blob \| history
help/html/webServices/proteinDisorder.html		diff \| blob \| history
help/html/webServices/urllinks.html		diff \| blob \| history
help/html/whatsNew.html		diff \| blob \| history
lib/jabaws-min-client-2.2.0.jar	[new file with mode: 0644]	blob
resources/lang/Messages.properties		diff \| blob \| history
resources/lang/Messages_es.properties		diff \| blob \| history
resources/scoreModel/blosum62.scm	[new file with mode: 0644]	blob
resources/scoreModel/blosum80.scm	[new file with mode: 0644]	blob
resources/scoreModel/dna.scm	[new file with mode: 0644]	blob
resources/scoreModel/pam250.scm	[new file with mode: 0644]	blob
resources/uniprot_mapping.xml		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/PDBViewer.java	[deleted file]	blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentSorter.java		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/AverageDistanceTree.java	[new file with mode: 0644]	blob
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/NJTree.java		diff \| blob \| history
src/jalview/analysis/PCA.java		diff \| blob \| history
src/jalview/analysis/Rna.java		diff \| blob \| history
src/jalview/analysis/SeqsetUtils.java		diff \| blob \| history
src/jalview/analysis/TreeBuilder.java	[new file with mode: 0644]	blob
src/jalview/analysis/TreeModel.java	[new file with mode: 0644]	blob
src/jalview/analysis/scoremodels/DistanceScoreModel.java	[new file with mode: 0644]	blob
src/jalview/analysis/scoremodels/FeatureDistanceModel.java	[new file with mode: 0644]	blob
src/jalview/analysis/scoremodels/FeatureScoreModel.java	[deleted file]	blob \| history
src/jalview/analysis/scoremodels/PIDModel.java	[new file with mode: 0644]	blob
src/jalview/analysis/scoremodels/PIDScoreModel.java	[deleted file]	blob \| history
src/jalview/analysis/scoremodels/ScoreMatrix.java	[new file with mode: 0644]	blob
src/jalview/analysis/scoremodels/ScoreModels.java	[new file with mode: 0644]	blob
src/jalview/analysis/scoremodels/SimilarityParams.java	[new file with mode: 0644]	blob
src/jalview/analysis/scoremodels/SimilarityScoreModel.java	[new file with mode: 0644]	blob
src/jalview/analysis/scoremodels/SmithWatermanModel.java	[moved from src/jalview/analysis/scoremodels/SWScoreModel.java with 63% similarity]	diff \| blob \| history
src/jalview/api/AlignViewportI.java		diff \| blob \| history
src/jalview/api/AlignmentColsCollectionI.java	[new file with mode: 0644]	blob
src/jalview/api/AlignmentRowsCollectionI.java	[new file with mode: 0644]	blob
src/jalview/api/ComplexAlignFile.java		diff \| blob \| history
src/jalview/api/FeatureRenderer.java		diff \| blob \| history
src/jalview/api/FeaturesDisplayedI.java		diff \| blob \| history
src/jalview/api/SequenceRenderer.java		diff \| blob \| history
src/jalview/api/SiftsClientI.java		diff \| blob \| history
src/jalview/api/ViewStyleI.java		diff \| blob \| history
src/jalview/api/analysis/PairwiseScoreModelI.java	[new file with mode: 0644]	blob
src/jalview/api/analysis/ScoreModelI.java		diff \| blob \| history
src/jalview/api/analysis/SimilarityParamsI.java	[new file with mode: 0644]	blob
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/ExtJmol.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/OverviewCanvas.java	[new file with mode: 0644]	blob
src/jalview/appletgui/OverviewPanel.java		diff \| blob \| history
src/jalview/appletgui/PCAPanel.java		diff \| blob \| history
src/jalview/appletgui/RedundancyPanel.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/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/commands/EditCommand.java		diff \| blob \| history
src/jalview/controller/AlignViewController.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/AlignmentView.java		diff \| blob \| history
src/jalview/datamodel/AllColsCollection.java	[new file with mode: 0644]	blob
src/jalview/datamodel/AllColsIterator.java	[new file with mode: 0644]	blob
src/jalview/datamodel/AllRowsCollection.java	[new file with mode: 0644]	blob
src/jalview/datamodel/AllRowsIterator.java	[new file with mode: 0644]	blob
src/jalview/datamodel/AnnotatedCollectionI.java		diff \| blob \| history
src/jalview/datamodel/Annotation.java		diff \| blob \| history
src/jalview/datamodel/BinarySequence.java		diff \| blob \| history
src/jalview/datamodel/CigarArray.java		diff \| blob \| history
src/jalview/datamodel/ColumnSelection.java		diff \| blob \| history
src/jalview/datamodel/ContiguousI.java	[new file with mode: 0644]	blob
src/jalview/datamodel/HiddenColumns.java	[new file with mode: 0644]	blob
src/jalview/datamodel/HiddenSequences.java		diff \| blob \| history
src/jalview/datamodel/Mapping.java		diff \| blob \| history
src/jalview/datamodel/Range.java	[new file with mode: 0644]	blob
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/SequenceCollectionI.java		diff \| blob \| history
src/jalview/datamodel/SequenceCursor.java	[new file with mode: 0644]	blob
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/SequenceNode.java		diff \| blob \| history
src/jalview/datamodel/VisibleColsCollection.java	[new file with mode: 0644]	blob
src/jalview/datamodel/VisibleColsIterator.java	[new file with mode: 0644]	blob
src/jalview/datamodel/VisibleRowsCollection.java	[new file with mode: 0644]	blob
src/jalview/datamodel/VisibleRowsIterator.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/FeatureLocationI.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/FeatureStore.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/NCList.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/NCNode.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/RangeComparator.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/SequenceFeatures.java	[new file with mode: 0644]	blob
src/jalview/datamodel/features/SequenceFeaturesI.java	[new file with mode: 0644]	blob
src/jalview/datamodel/xdb/embl/EmblEntry.java		diff \| blob \| history
src/jalview/datamodel/xdb/uniprot/UniprotEntry.java	[new file with mode: 0755]	blob
src/jalview/datamodel/xdb/uniprot/UniprotFeature.java	[new file with mode: 0644]	blob
src/jalview/datamodel/xdb/uniprot/UniprotFile.java	[new file with mode: 0755]	blob
src/jalview/datamodel/xdb/uniprot/UniprotProteinName.java	[new file with mode: 0755]	blob
src/jalview/datamodel/xdb/uniprot/UniprotSequence.java	[new file with mode: 0755]	blob
src/jalview/ext/android/ContainerHelpers.java		diff \| blob \| history
src/jalview/ext/android/SparseDoubleArray.java	[new file with mode: 0644]	blob
src/jalview/ext/ensembl/EnsemblCdna.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblGene.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblRestClient.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSeqProxy.java		diff \| blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/jmol/JmolCommands.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/JalviewChimeraBinding.java		diff \| blob \| history
src/jalview/ext/varna/VarnaCommands.java		diff \| blob \| history
src/jalview/fts/api/GFTSPanelI.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/uniprot/UniProtFTSRestClient.java		diff \| blob \| history
src/jalview/fts/service/uniprot/UniprotFTSPanel.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/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/CalculationChooser.java	[new file with mode: 0644]	blob
src/jalview/gui/ChimeraViewFrame.java		diff \| blob \| history
src/jalview/gui/ColourMenuHelper.java	[new file with mode: 0644]	blob
src/jalview/gui/ComboBoxTooltipRenderer.java	[new file with mode: 0644]	blob
src/jalview/gui/Console.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/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/IdCanvas.java		diff \| blob \| history
src/jalview/gui/IdPanel.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/JalviewDialog.java		diff \| blob \| history
src/jalview/gui/OverviewCanvas.java	[new file with mode: 0644]	blob
src/jalview/gui/OverviewPanel.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/RedundancyPanel.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/SplitFrame.java		diff \| blob \| history
src/jalview/gui/StructureChooser.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/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/WsParamSetManager.java		diff \| blob \| history
src/jalview/gui/WsPreferences.java		diff \| blob \| history
src/jalview/io/AnnotationFile.java		diff \| blob \| history
src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
src/jalview/io/FeaturesFile.java		diff \| blob \| history
src/jalview/io/FileFormat.java		diff \| blob \| history
src/jalview/io/FileFormats.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/FormatAdapter.java		diff \| blob \| history
src/jalview/io/HTMLOutput.java		diff \| blob \| history
src/jalview/io/HtmlFile.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/JSONFile.java		diff \| blob \| history
src/jalview/io/JalviewFileChooser.java		diff \| blob \| history
src/jalview/io/ScoreMatrixFile.java	[new file with mode: 0644]	blob
src/jalview/io/SequenceAnnotationReport.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/cache/AppCache.java	[new file with mode: 0644]	blob
src/jalview/io/cache/JvCacheableInputBox.java	[new file with mode: 0644]	blob
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/JalviewDataset.java		diff \| blob \| history
src/jalview/io/vamsas/Datasetsequence.java		diff \| blob \| history
src/jalview/io/vamsas/Sequencefeature.java		diff \| blob \| history
src/jalview/io/vamsas/Tree.java		diff \| blob \| history
src/jalview/javascript/JsSelectionSender.java		diff \| blob \| history
src/jalview/javascript/MouseOverStructureListener.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GFinder.java		diff \| blob \| history
src/jalview/jbgui/GFontChooser.java		diff \| blob \| history
src/jalview/jbgui/GPCAPanel.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GSequenceLink.java		diff \| blob \| history
src/jalview/jbgui/GSliderPanel.java		diff \| blob \| history
src/jalview/jbgui/GStructureChooser.java		diff \| blob \| history
src/jalview/jbgui/GStructureViewer.java		diff \| blob \| history
src/jalview/jbgui/GUserDefinedColours.java		diff \| blob \| history
src/jalview/math/Matrix.java		diff \| blob \| history
src/jalview/math/MatrixI.java	[new file with mode: 0644]	blob
src/jalview/math/SparseMatrix.java	[new file with mode: 0644]	blob
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/OverviewRenderer.java	[new file with mode: 0644]	blob
src/jalview/renderer/ResidueShader.java	[new file with mode: 0644]	blob
src/jalview/renderer/ResidueShaderI.java	[new file with mode: 0644]	blob
src/jalview/renderer/ScaleRenderer.java		diff \| blob \| history
src/jalview/renderer/seqfeatures/FeatureColourFinder.java	[new file with mode: 0644]	blob
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/BuriedColourScheme.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	[new file with mode: 0644]	blob
src/jalview/schemes/ColourSchemeProperty.java		diff \| blob \| history
src/jalview/schemes/ColourSchemes.java	[new file with mode: 0644]	blob
src/jalview/schemes/CovariationColourScheme.java		diff \| blob \| history
src/jalview/schemes/FeatureColour.java		diff \| blob \| history
src/jalview/schemes/FollowerColourScheme.java		diff \| blob \| history
src/jalview/schemes/HelixColourScheme.java		diff \| blob \| history
src/jalview/schemes/HydrophobicColourScheme.java		diff \| blob \| history
src/jalview/schemes/JalviewColourScheme.java	[new file with mode: 0644]	blob
src/jalview/schemes/NucleotideColourScheme.java		diff \| blob \| history
src/jalview/schemes/PIDColourScheme.java		diff \| blob \| history
src/jalview/schemes/PurinePyrimidineColourScheme.java		diff \| blob \| history
src/jalview/schemes/RNAHelicesColour.java		diff \| blob \| history
src/jalview/schemes/RNAHelicesColourChooser.java		diff \| blob \| history
src/jalview/schemes/RNAInteractionColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/schemes/ScoreColourScheme.java		diff \| blob \| history
src/jalview/schemes/ScoreMatrix.java	[deleted file]	blob \| history
src/jalview/schemes/StrandColourScheme.java		diff \| blob \| history
src/jalview/schemes/TCoffeeColourScheme.java		diff \| blob \| history
src/jalview/schemes/TaylorColourScheme.java		diff \| blob \| history
src/jalview/schemes/TurnColourScheme.java		diff \| blob \| history
src/jalview/schemes/UserColourScheme.java		diff \| blob \| history
src/jalview/schemes/ZappoColourScheme.java		diff \| blob \| history
src/jalview/structure/SelectionListener.java		diff \| blob \| history
src/jalview/structure/StructureListener.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/structures/models/AAStructureBindingModel.java		diff \| blob \| history
src/jalview/urls/CustomUrlProvider.java	[new file with mode: 0644]	blob
src/jalview/urls/IdOrgSettings.java	[new file with mode: 0644]	blob
src/jalview/urls/IdentifiersUrlProvider.java	[new file with mode: 0644]	blob
src/jalview/urls/UrlLinkDisplay.java	[new file with mode: 0644]	blob
src/jalview/urls/UrlLinkTableModel.java	[new file with mode: 0644]	blob
src/jalview/urls/UrlProvider.java	[new file with mode: 0644]	blob
src/jalview/urls/UrlProviderImpl.java	[new file with mode: 0644]	blob
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test/jalview/schemes/Blosum62ColourSchemeTest.java	[new file with mode: 0644]	blob
test/jalview/schemes/ClustalxColourSchemeTest.java	[new file with mode: 0644]	blob
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