git://source.jalview.org / jalview.git / commit
? search:
summary | shortlog | log | commit | commitdiff | tree
(parent: 7c70cb0) | patch
JAL-2418 source formatting
authorJim Procter <jprocter@issues.jalview.org>
Wed, 16 Aug 2017 21:22:11 +0000 (22:22 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Wed, 16 Aug 2017 21:36:25 +0000 (22:36 +0100)
commit3d0101179759ef157b088ea135423cd909512d9f
tree10420a0a73ef4d55424282fe7d12e9425dacfbebtree | snapshot
parent7c70cb09e9de68ab567e38520d6d09f0c17a3939commit | diff
JAL-2418 source formatting
465 files changed:
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/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/SmithWatermanModel.java diff | blob | history
src/jalview/api/DBRefEntryI.java diff | blob | history
src/jalview/api/analysis/ScoreModelI.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/OverviewPanel.java diff | blob | history
src/jalview/appletgui/PCAPanel.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/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/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/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/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/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/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/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/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/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/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/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/FastaFile.java diff | blob | history
src/jalview/io/FeaturesFile.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 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/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/ResidueShader.java diff | blob | history
src/jalview/renderer/ResidueShaderI.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/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/SparseCount.java diff | blob | history
src/jalview/util/StringUtils.java diff | blob | history
src/jalview/util/TableSorter.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/OverviewDimensionsShowHidden.java diff | blob | history
src/jalview/viewmodel/PCAModel.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/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/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/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/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