JAL-2446 merged to spike branch
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Fri, 9 Jun 2017 15:28:28 +0000 (16:28 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Fri, 9 Jun 2017 15:28:28 +0000 (16:28 +0100)
commit136c0793b90b72b928c4d77dc109dd5c644e00d3
tree53131544aa73290b4bedd7925b203e746ce9fd34
parent8677e6e34e291edc58c1da2fc9c958473754143f
JAL-2446 merged to spike branch
491 files changed:
.classpath
examples/appletParameters.html
examples/example.json
examples/exampleFeatures.txt
examples/groovy/colourConserved.groovy [new file with mode: 0644]
examples/groovy/colourSchemes.groovy [new file with mode: 0644]
examples/groovy/colourUnconserved.groovy [new file with mode: 0644]
examples/groovy/featuresCounter.groovy [new file with mode: 0644]
examples/groovy/visibleFeaturesCounter.groovy [new file with mode: 0644]
examples/testdata/example_annot_file.jva
help/help.jhm
help/helpTOC.xml
help/html/colourSchemes/clustal.html
help/html/colourSchemes/user.html
help/html/colourSchemes/userDefined_java7.gif
help/html/features/chimera.html
help/html/features/groovy.html
help/html/features/overview.html
help/html/features/preferences.html
help/html/features/splitView.html
help/html/groovy/featuresCounter.html [new file with mode: 0644]
help/html/io/tcoffeescores.html
help/html/menus/desktopMenu.html
help/html/menus/popupMenu.html
help/html/releases.html
help/html/webServices/JABAWS.html
help/html/webServices/jnet.html
help/html/webServices/jnetprediction.gif [changed mode: 0755->0644]
help/html/webServices/msaclient.html
help/html/webServices/proteinDisorder.html
help/html/webServices/urllinks.html
help/html/whatsNew.html
lib/jabaws-min-client-2.2.0.jar [new file with mode: 0644]
resources/lang/Messages.properties
resources/lang/Messages_es.properties
resources/scoreModel/blosum62.scm [new file with mode: 0644]
resources/scoreModel/blosum80.scm [new file with mode: 0644]
resources/scoreModel/dna.scm [new file with mode: 0644]
resources/scoreModel/pam250.scm [new file with mode: 0644]
resources/uniprot_mapping.xml
src/MCview/AppletPDBCanvas.java
src/MCview/AppletPDBViewer.java
src/MCview/PDBCanvas.java
src/MCview/PDBChain.java
src/MCview/PDBViewer.java [deleted file]
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/AverageDistanceTree.java [new file with mode: 0644]
src/jalview/analysis/Conservation.java
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/analysis/NJTree.java
src/jalview/analysis/PCA.java
src/jalview/analysis/Rna.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/analysis/TreeBuilder.java [new file with mode: 0644]
src/jalview/analysis/TreeModel.java [new file with mode: 0644]
src/jalview/analysis/scoremodels/DistanceScoreModel.java [new file with mode: 0644]
src/jalview/analysis/scoremodels/FeatureDistanceModel.java [new file with mode: 0644]
src/jalview/analysis/scoremodels/FeatureScoreModel.java [deleted file]
src/jalview/analysis/scoremodels/PIDModel.java [new file with mode: 0644]
src/jalview/analysis/scoremodels/PIDScoreModel.java [deleted file]
src/jalview/analysis/scoremodels/ScoreMatrix.java [new file with mode: 0644]
src/jalview/analysis/scoremodels/ScoreModels.java [new file with mode: 0644]
src/jalview/analysis/scoremodels/SimilarityParams.java [new file with mode: 0644]
src/jalview/analysis/scoremodels/SimilarityScoreModel.java [new file with mode: 0644]
src/jalview/analysis/scoremodels/SmithWatermanModel.java [moved from src/jalview/analysis/scoremodels/SWScoreModel.java with 63% similarity]
src/jalview/api/AlignViewportI.java
src/jalview/api/AlignmentColsCollectionI.java [new file with mode: 0644]
src/jalview/api/AlignmentRowsCollectionI.java [new file with mode: 0644]
src/jalview/api/ComplexAlignFile.java
src/jalview/api/FeatureRenderer.java
src/jalview/api/FeaturesDisplayedI.java
src/jalview/api/SequenceRenderer.java
src/jalview/api/SiftsClientI.java
src/jalview/api/ViewStyleI.java
src/jalview/api/analysis/PairwiseScoreModelI.java [new file with mode: 0644]
src/jalview/api/analysis/ScoreModelI.java
src/jalview/api/analysis/SimilarityParamsI.java [new file with mode: 0644]
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/ExtJmol.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/OverviewCanvas.java [new file with mode: 0644]
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/PCAPanel.java
src/jalview/appletgui/RedundancyPanel.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/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/commands/EditCommand.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/AllColsCollection.java [new file with mode: 0644]
src/jalview/datamodel/AllColsIterator.java [new file with mode: 0644]
src/jalview/datamodel/AllRowsCollection.java [new file with mode: 0644]
src/jalview/datamodel/AllRowsIterator.java [new file with mode: 0644]
src/jalview/datamodel/AnnotatedCollectionI.java
src/jalview/datamodel/Annotation.java
src/jalview/datamodel/BinarySequence.java
src/jalview/datamodel/CigarArray.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/ContiguousI.java [new file with mode: 0644]
src/jalview/datamodel/HiddenColumns.java [new file with mode: 0644]
src/jalview/datamodel/HiddenSequences.java
src/jalview/datamodel/Mapping.java
src/jalview/datamodel/Range.java [new file with mode: 0644]
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/SeqCigar.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceCollectionI.java
src/jalview/datamodel/SequenceCursor.java [new file with mode: 0644]
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/SequenceNode.java
src/jalview/datamodel/VisibleColsCollection.java [new file with mode: 0644]
src/jalview/datamodel/VisibleColsIterator.java [new file with mode: 0644]
src/jalview/datamodel/VisibleRowsCollection.java [new file with mode: 0644]
src/jalview/datamodel/VisibleRowsIterator.java [new file with mode: 0644]
src/jalview/datamodel/features/FeatureLocationI.java [new file with mode: 0644]
src/jalview/datamodel/features/FeatureStore.java [new file with mode: 0644]
src/jalview/datamodel/features/NCList.java [new file with mode: 0644]
src/jalview/datamodel/features/NCNode.java [new file with mode: 0644]
src/jalview/datamodel/features/RangeComparator.java [new file with mode: 0644]
src/jalview/datamodel/features/SequenceFeatures.java [new file with mode: 0644]
src/jalview/datamodel/features/SequenceFeaturesI.java [new file with mode: 0644]
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/datamodel/xdb/uniprot/UniprotEntry.java [new file with mode: 0755]
src/jalview/datamodel/xdb/uniprot/UniprotFeature.java [new file with mode: 0644]
src/jalview/datamodel/xdb/uniprot/UniprotFile.java [new file with mode: 0755]
src/jalview/datamodel/xdb/uniprot/UniprotProteinName.java [new file with mode: 0755]
src/jalview/datamodel/xdb/uniprot/UniprotSequence.java [new file with mode: 0755]
src/jalview/ext/android/ContainerHelpers.java
src/jalview/ext/android/SparseDoubleArray.java [new file with mode: 0644]
src/jalview/ext/ensembl/EnsemblCdna.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblRestClient.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolCommands.java
src/jalview/ext/rbvi/chimera/AtomSpecModel.java
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/ext/varna/VarnaCommands.java
src/jalview/fts/api/GFTSPanelI.java
src/jalview/fts/core/GFTSPanel.java
src/jalview/fts/service/pdb/PDBFTSPanel.java
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
src/jalview/fts/service/uniprot/UniprotFTSPanel.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.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/CalculationChooser.java [new file with mode: 0644]
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/ColourMenuHelper.java [new file with mode: 0644]
src/jalview/gui/ComboBoxTooltipRenderer.java [new file with mode: 0644]
src/jalview/gui/Console.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/FontChooser.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/IdPanel.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/JalviewDialog.java
src/jalview/gui/OverviewCanvas.java [new file with mode: 0644]
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/RedundancyPanel.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/SplitFrame.java
src/jalview/gui/StructureChooser.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/VamsasApplication.java
src/jalview/gui/WsParamSetManager.java
src/jalview/gui/WsPreferences.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileFormat.java
src/jalview/io/FileFormats.java
src/jalview/io/FileLoader.java
src/jalview/io/FormatAdapter.java
src/jalview/io/HTMLOutput.java
src/jalview/io/HtmlFile.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JSONFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/ScoreMatrixFile.java [new file with mode: 0644]
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/io/StructureFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/cache/AppCache.java [new file with mode: 0644]
src/jalview/io/cache/JvCacheableInputBox.java [new file with mode: 0644]
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/JalviewDataset.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/io/vamsas/Sequencefeature.java
src/jalview/io/vamsas/Tree.java
src/jalview/javascript/JsSelectionSender.java
src/jalview/javascript/MouseOverStructureListener.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GFinder.java
src/jalview/jbgui/GFontChooser.java
src/jalview/jbgui/GPCAPanel.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GSequenceLink.java
src/jalview/jbgui/GSliderPanel.java
src/jalview/jbgui/GStructureChooser.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/jbgui/GUserDefinedColours.java
src/jalview/math/Matrix.java
src/jalview/math/MatrixI.java [new file with mode: 0644]
src/jalview/math/SparseMatrix.java [new file with mode: 0644]
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/OverviewRenderer.java [new file with mode: 0644]
src/jalview/renderer/ResidueShader.java [new file with mode: 0644]
src/jalview/renderer/ResidueShaderI.java [new file with mode: 0644]
src/jalview/renderer/ScaleRenderer.java
src/jalview/renderer/seqfeatures/FeatureColourFinder.java [new file with mode: 0644]
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/Blosum62ColourScheme.java
src/jalview/schemes/BuriedColourScheme.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/schemes/ColourSchemeI.java
src/jalview/schemes/ColourSchemeLoader.java [new file with mode: 0644]
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/ColourSchemes.java [new file with mode: 0644]
src/jalview/schemes/CovariationColourScheme.java
src/jalview/schemes/FeatureColour.java
src/jalview/schemes/FollowerColourScheme.java
src/jalview/schemes/HelixColourScheme.java
src/jalview/schemes/HydrophobicColourScheme.java
src/jalview/schemes/JalviewColourScheme.java [new file with mode: 0644]
src/jalview/schemes/NucleotideColourScheme.java
src/jalview/schemes/PIDColourScheme.java
src/jalview/schemes/PurinePyrimidineColourScheme.java
src/jalview/schemes/RNAHelicesColour.java
src/jalview/schemes/RNAHelicesColourChooser.java
src/jalview/schemes/RNAInteractionColourScheme.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/ScoreColourScheme.java
src/jalview/schemes/ScoreMatrix.java [deleted file]
src/jalview/schemes/StrandColourScheme.java
src/jalview/schemes/TCoffeeColourScheme.java
src/jalview/schemes/TaylorColourScheme.java
src/jalview/schemes/TurnColourScheme.java
src/jalview/schemes/UserColourScheme.java
src/jalview/schemes/ZappoColourScheme.java
src/jalview/structure/SelectionListener.java
src/jalview/structure/StructureListener.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/urls/CustomUrlProvider.java [new file with mode: 0644]
src/jalview/urls/IdOrgSettings.java [new file with mode: 0644]
src/jalview/urls/IdentifiersUrlProvider.java [new file with mode: 0644]
src/jalview/urls/UrlLinkDisplay.java [new file with mode: 0644]
src/jalview/urls/UrlLinkTableModel.java [new file with mode: 0644]
src/jalview/urls/UrlProvider.java [new file with mode: 0644]
src/jalview/urls/UrlProviderImpl.java [new file with mode: 0644]
src/jalview/urls/api/UrlProviderFactoryI.java [new file with mode: 0644]
src/jalview/urls/api/UrlProviderI.java [new file with mode: 0644]
src/jalview/urls/applet/AppletUrlProviderFactory.java [new file with mode: 0644]
src/jalview/urls/desktop/DesktopUrlProviderFactory.java [new file with mode: 0644]
src/jalview/util/ColorUtils.java
src/jalview/util/Comparison.java
src/jalview/util/ImageMaker.java
src/jalview/util/IntRangeComparator.java [new file with mode: 0644]
src/jalview/util/LinkedIdentityHashSet.java
src/jalview/util/MappingUtils.java
src/jalview/util/ParseHtmlBodyAndLinks.java
src/jalview/util/SetUtils.java [new file with mode: 0644]
src/jalview/util/UrlConstants.java
src/jalview/util/UrlLink.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/OverviewDimensions.java [new file with mode: 0644]
src/jalview/viewmodel/OverviewDimensionsHideHidden.java [new file with mode: 0644]
src/jalview/viewmodel/OverviewDimensionsShowHidden.java [new file with mode: 0644]
src/jalview/viewmodel/PCAModel.java
src/jalview/viewmodel/ViewportListenerI.java [new file with mode: 0644]
src/jalview/viewmodel/ViewportProperties.java [new file with mode: 0644]
src/jalview/viewmodel/ViewportRanges.java [new file with mode: 0644]
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
src/jalview/viewmodel/styles/ViewStyle.java
src/jalview/workers/AlignmentAnnotationFactory.java
src/jalview/workers/ColumnCounterSetWorker.java [moved from src/jalview/workers/ColumnCounterWorker.java with 60% similarity]
src/jalview/workers/ConsensusThread.java
src/jalview/workers/ConservationThread.java
src/jalview/workers/FeatureSetCounterI.java [moved from src/jalview/workers/FeatureCounterI.java with 76% similarity]
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/DasSequenceFeatureFetcher.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws1/MsaWSThread.java
src/jalview/ws/jws1/SeqSearchWSThread.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/jws2/JPred301Client.java [deleted file]
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/MsaWSThread.java
src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
src/jalview/ws/rest/RestClient.java
src/jalview/ws/rest/RestJobThread.java
src/jalview/ws/rest/params/Alignment.java
src/jalview/ws/sifts/SiftsClient.java
src/jalview/ws/utils/UrlDownloadClient.java [new file with mode: 0644]
test/MCview/PDBChainTest.java
test/jalview/analysis/AlignSeqTest.java
test/jalview/analysis/AlignmentSorterTest.java [new file with mode: 0644]
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/DnaTest.java
test/jalview/analysis/RnaTest.java
test/jalview/analysis/SeqsetUtilsTest.java
test/jalview/analysis/TestAlignSeq.java
test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java [new file with mode: 0644]
test/jalview/analysis/scoremodels/FeatureScoreModelTest.java [deleted file]
test/jalview/analysis/scoremodels/PIDModelTest.java [new file with mode: 0644]
test/jalview/analysis/scoremodels/ScoreMatrixTest.java [new file with mode: 0644]
test/jalview/analysis/scoremodels/ScoreModelsTest.java [new file with mode: 0644]
test/jalview/commands/EditCommandTest.java
test/jalview/datamodel/AlignmentAnnotationTests.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/datamodel/AlignmentViewTest.java
test/jalview/datamodel/AllColsIteratorTest.java [new file with mode: 0644]
test/jalview/datamodel/AllRowsIteratorTest.java [new file with mode: 0644]
test/jalview/datamodel/ColumnSelectionTest.java
test/jalview/datamodel/HiddenColumnsTest.java [new file with mode: 0644]
test/jalview/datamodel/HiddenSequencesTest.java
test/jalview/datamodel/SequenceFeatureTest.java
test/jalview/datamodel/SequenceGroupTest.java [new file with mode: 0644]
test/jalview/datamodel/SequenceTest.java
test/jalview/datamodel/VisibleColsIteratorTest.java [new file with mode: 0644]
test/jalview/datamodel/VisibleRowsIteratorTest.java [new file with mode: 0644]
test/jalview/datamodel/features/FeatureStoreTest.java [new file with mode: 0644]
test/jalview/datamodel/features/NCListTest.java [new file with mode: 0644]
test/jalview/datamodel/features/NCNodeTest.java [new file with mode: 0644]
test/jalview/datamodel/features/RangeComparatorTest.java [new file with mode: 0644]
test/jalview/datamodel/features/SequenceFeaturesTest.java [new file with mode: 0644]
test/jalview/ext/android/SparseDoubleArrayTest.java [new file with mode: 0644]
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/EnsemblSeqProxyTest.java
test/jalview/ext/jmol/JmolCommandsTest.java
test/jalview/ext/jmol/JmolParserTest.java
test/jalview/ext/jmol/JmolViewerTest.java
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
test/jalview/fts/service/pdb/PDBFTSPanelTest.java
test/jalview/gui/AlignFrameTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/gui/AlignmentPanelTest.java [new file with mode: 0644]
test/jalview/gui/AnnotationChooserTest.java
test/jalview/gui/AnnotationRowFilterTest.java [new file with mode: 0644]
test/jalview/gui/PopupMenuTest.java
test/jalview/gui/SeqPanelTest.java [new file with mode: 0644]
test/jalview/gui/SequenceRendererTest.java
test/jalview/gui/StructureChooserTest.java
test/jalview/io/AnnotatedPDBFileInputTest.java
test/jalview/io/AnnotationFileIOTest.java
test/jalview/io/FeaturesFileTest.java
test/jalview/io/FileFormatsTest.java
test/jalview/io/FileLoaderTest.java [new file with mode: 0644]
test/jalview/io/IdentifyFileTest.java
test/jalview/io/JSONFileTest.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/JalviewFileViewTest.java
test/jalview/io/NewickFileTests.java
test/jalview/io/PhylipFileTests.java
test/jalview/io/RNAMLfileTest.java
test/jalview/io/ScoreMatrixFileTest.java [new file with mode: 0644]
test/jalview/io/SequenceAnnotationReportTest.java
test/jalview/io/StockholmFileTest.java
test/jalview/io/cache/AppCacheTest.java [new file with mode: 0644]
test/jalview/io/cache/JvCacheableInputBoxTest.java [new file with mode: 0644]
test/jalview/io/gff/Gff3HelperTest.java
test/jalview/io/gff/InterProScanHelperTest.java
test/jalview/io/testProps.jvprops
test/jalview/math/MatrixTest.java
test/jalview/math/SparseMatrixTest.java [new file with mode: 0644]
test/jalview/renderer/ResidueShaderTest.java [new file with mode: 0644]
test/jalview/renderer/ScaleRendererTest.java [new file with mode: 0644]
test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java [new file with mode: 0644]
test/jalview/renderer/seqfeatures/FeatureRendererTest.java [new file with mode: 0644]
test/jalview/schemes/AnnotationColourGradientTest.java [new file with mode: 0644]
test/jalview/schemes/Blosum62ColourSchemeTest.java [new file with mode: 0644]
test/jalview/schemes/ClustalxColourSchemeTest.java [new file with mode: 0644]
test/jalview/schemes/ColourSchemePropertyTest.java [new file with mode: 0644]
test/jalview/schemes/ColourSchemesTest.java [new file with mode: 0644]
test/jalview/schemes/FeatureColourTest.java
test/jalview/schemes/JalviewColourSchemeTest.java [new file with mode: 0644]
test/jalview/schemes/PIDColourSchemeTest.java [new file with mode: 0644]
test/jalview/schemes/ResidueColourSchemeTest.java
test/jalview/schemes/ScoreMatrixPrinter.java [deleted file]
test/jalview/schemes/UserColourSchemeTest.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/structures/models/AAStructureBindingModelTest.java
test/jalview/urls/AppletUrlProviderFactoryTest.java [new file with mode: 0644]
test/jalview/urls/CustomUrlProviderTest.java [new file with mode: 0644]
test/jalview/urls/DesktopUrlProviderFactoryTest.java [new file with mode: 0644]
test/jalview/urls/IdentifiersUrlProviderTest.java [new file with mode: 0644]
test/jalview/urls/UrlLinkDisplayTest.java [new file with mode: 0644]
test/jalview/urls/UrlLinkTableModelTest.java [new file with mode: 0644]
test/jalview/urls/UrlProviderTest.java [new file with mode: 0644]
test/jalview/util/ColorUtilsTest.java
test/jalview/util/ComparisonTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/util/SetUtilsTest.java [new file with mode: 0644]
test/jalview/util/UrlLinkTest.java
test/jalview/viewmodel/OverviewDimensionsHideHiddenTest.java [new file with mode: 0644]
test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java [new file with mode: 0644]
test/jalview/viewmodel/ViewportRangesTest.java [new file with mode: 0644]
test/jalview/ws/dbsources/RemoteFormatTest.java [new file with mode: 0644]
test/jalview/ws/dbsources/UniprotTest.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/JpredJabaStructExportImport.java [deleted file]
test/jalview/ws/jabaws/MinJabawsClientTests.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/jws2/ParameterUtilsTest.java
test/jalview/ws/seqfetcher/DasSequenceFetcher.java
test/jalview/ws/seqfetcher/DbRefFetcherTest.java
test/jalview/ws/sifts/SiftsClientTest.java
test/jalview/ws/utils/UrlDownloadClientTest.java [new file with mode: 0644]
test/junit/extensions/PA.java [new file with mode: 0644]
test/junit/extensions/PrivilegedAccessor.java [new file with mode: 0644]