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

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

author	James Procter <j.procter@dundee.ac.uk>
	Fri, 3 Nov 2023 07:29:04 +0000 (07:29 +0000)
committer	James Procter <j.procter@dundee.ac.uk>
	Fri, 3 Nov 2023 07:29:04 +0000 (07:29 +0000)
commit	eb3e681d6e82ccdd5d312d1981dfb306e7f479f0
tree	812fd3011239f3b0070c8fa8e76b26813a41cb90	tree \| snapshot
parent	cb31e23d9138e481479623374aed7767bf8934d2	commit \| diff

JAL-4090 JAL-1551 spotlessApply

213 files changed:

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/AverageDistanceEngine.java		diff \| blob \| history
src/jalview/analysis/CrossRef.java		diff \| blob \| history
src/jalview/analysis/GeneticCodes.java		diff \| blob \| history
src/jalview/analysis/Rna.java		diff \| blob \| history
src/jalview/analysis/TreeEngine.java		diff \| blob \| history
src/jalview/analysis/TreeModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/ScoreModels.java		diff \| blob \| history
src/jalview/api/SequenceRenderer.java		diff \| blob \| history
src/jalview/api/structures/JalviewStructureDisplayI.java		diff \| blob \| history
src/jalview/appletgui/APopupMenu.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/appletgui/RedundancyPanel.java		diff \| blob \| history
src/jalview/appletgui/SeqCanvas.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/bin/JalviewLiteURLRetrieve.java		diff \| blob \| history
src/jalview/commands/EditCommand.java		diff \| blob \| history
src/jalview/datamodel/AlignedCodonFrame.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/ContactListImpl.java		diff \| blob \| history
src/jalview/datamodel/ContactMapHolder.java		diff \| blob \| history
src/jalview/datamodel/ContactMatrix.java		diff \| blob \| history
src/jalview/datamodel/ContactMatrixI.java		diff \| blob \| history
src/jalview/datamodel/DBRefSource.java		diff \| blob \| history
src/jalview/datamodel/FloatContactMatrix.java		diff \| blob \| history
src/jalview/datamodel/GroupSet.java		diff \| blob \| history
src/jalview/datamodel/SearchResultMatchI.java		diff \| blob \| history
src/jalview/datamodel/SearchResults.java		diff \| blob \| history
src/jalview/datamodel/SearchResultsI.java		diff \| blob \| history
src/jalview/datamodel/SeqDistanceContactMatrix.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureStore.java		diff \| blob \| history
src/jalview/datamodel/features/SequenceFeatures.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblGene.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblLookup.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblMap.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/jmol/JmolParser.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/fts/core/FTSDataColumnPreferences.java		diff \| blob \| history
src/jalview/fts/service/pdb/PDBFTSRestClient.java		diff \| blob \| history
src/jalview/fts/service/threedbeacons/TDB_FTSData.java		diff \| blob \| history
src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java		diff \| blob \| history
src/jalview/gui/AlignFrame.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/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AppVarna.java		diff \| blob \| history
src/jalview/gui/AppVarnaBinding.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/FeatureEditor.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/FeatureTypeSettings.java		diff \| blob \| history
src/jalview/gui/IdCanvas.java		diff \| blob \| history
src/jalview/gui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/QuitHandler.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/StructureChooser.java		diff \| blob \| history
src/jalview/gui/StructureViewerBase.java		diff \| blob \| history
src/jalview/gui/TreeCanvas.java		diff \| blob \| history
src/jalview/gui/TreePanel.java		diff \| blob \| history
src/jalview/gui/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/io/AnnotationFile.java		diff \| blob \| history
src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
src/jalview/io/BackupFilenameFilter.java		diff \| blob \| history
src/jalview/io/BioJsHTMLOutput.java		diff \| blob \| history
src/jalview/io/ClustalFile.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/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/MSFfile.java		diff \| blob \| history
src/jalview/io/PfamFile.java		diff \| blob \| history
src/jalview/io/RnamlFile.java		diff \| blob \| history
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/VamsasAppDatastore.java		diff \| blob \| history
src/jalview/io/WSWUBlastClient.java		diff \| blob \| history
src/jalview/io/exceptions/ImageOutputException.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/packed/ParsePackedSet.java		diff \| blob \| history
src/jalview/io/vamsas/Tree.java		diff \| blob \| history
src/jalview/io/vcf/VCFLoader.java		diff \| blob \| history
src/jalview/javascript/JSFunctionExec.java		diff \| blob \| history
src/jalview/javascript/JsSelectionSender.java		diff \| blob \| history
src/jalview/javascript/MouseOverStructureListener.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/math/RotatableMatrix.java		diff \| blob \| history
src/jalview/project/Jalview2XML.java		diff \| blob \| history
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/ContactGeometry.java		diff \| blob \| history
src/jalview/renderer/ContactMapRenderer.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeLoader.java		diff \| blob \| history
src/jalview/schemes/ColourSchemes.java		diff \| blob \| history
src/jalview/schemes/Consensus.java		diff \| blob \| history
src/jalview/schemes/CovariationColourScheme.java		diff \| blob \| history
src/jalview/schemes/FeatureColour.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/structure/StructureCommand.java		diff \| blob \| history
src/jalview/structure/StructureCommandI.java		diff \| blob \| history
src/jalview/structure/StructureCommandsBase.java		diff \| blob \| history
src/jalview/structure/StructureCommandsI.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/structures/models/AAStructureBindingModel.java		diff \| blob \| history
src/jalview/urls/IdentifiersUrlProvider.java		diff \| blob \| history
src/jalview/util/ChannelProperties.java		diff \| blob \| history
src/jalview/util/ColorUtils.java		diff \| blob \| history
src/jalview/util/Format.java		diff \| blob \| history
src/jalview/util/GroupUrlLink.java		diff \| blob \| history
src/jalview/util/LaunchUtils.java		diff \| blob \| history
src/jalview/util/Log4j.java		diff \| blob \| history
src/jalview/util/Platform.java		diff \| blob \| history
src/jalview/util/UrlLink.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/ViewportRanges.java		diff \| blob \| history
src/jalview/workers/AlignCalcManager.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/JobStateSummary.java		diff \| blob \| history
src/jalview/ws/datamodel/MappableContactMatrixI.java		diff \| blob \| history
src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java		diff \| blob \| history
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java		diff \| blob \| history
src/jalview/ws/dbsources/EbiFileRetrievedProxy.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/ebi/EBIFetchClient.java		diff \| blob \| history
src/jalview/ws/jws1/SeqSearchWSThread.java		diff \| blob \| history
src/jalview/ws/jws2/AbstractJabaCalcWorker.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/Jws2Discoverer.java		diff \| blob \| history
src/jalview/ws/jws2/ParameterUtils.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2Instance.java		diff \| blob \| history
src/jalview/ws/rest/RestClient.java		diff \| blob \| history
src/jalview/ws/sifts/SiftsClient.java		diff \| blob \| history
src/jalview/ws/utils/UrlDownloadClient.java		diff \| blob \| history
src/jalview/xml/binding/jalview/AlcodonFrame.java		diff \| blob \| history
src/jalview/xml/binding/jalview/Annotation.java		diff \| blob \| history
src/jalview/xml/binding/jalview/AnnotationColourScheme.java		diff \| blob \| history
src/jalview/xml/binding/jalview/AnnotationElement.java		diff \| blob \| history
src/jalview/xml/binding/jalview/DoubleMatrix.java		diff \| blob \| history
src/jalview/xml/binding/jalview/DoubleVector.java		diff \| blob \| history
src/jalview/xml/binding/jalview/Feature.java		diff \| blob \| history
src/jalview/xml/binding/jalview/FeatureMatcher.java		diff \| blob \| history
src/jalview/xml/binding/jalview/FeatureMatcherSet.java		diff \| blob \| history
src/jalview/xml/binding/jalview/FilterBy.java		diff \| blob \| history
src/jalview/xml/binding/jalview/JalviewModel.java		diff \| blob \| history
src/jalview/xml/binding/jalview/JalviewUserColours.java		diff \| blob \| history
src/jalview/xml/binding/jalview/MapListType.java		diff \| blob \| history
src/jalview/xml/binding/jalview/MapOnAMatrixType.java		diff \| blob \| history
src/jalview/xml/binding/jalview/Mapping.java		diff \| blob \| history
src/jalview/xml/binding/jalview/MatrixType.java		diff \| blob \| history
src/jalview/xml/binding/jalview/NoValueColour.java		diff \| blob \| history
src/jalview/xml/binding/jalview/ObjectFactory.java		diff \| blob \| history
src/jalview/xml/binding/jalview/PcaDataType.java		diff \| blob \| history
src/jalview/xml/binding/jalview/Pdbentry.java		diff \| blob \| history
src/jalview/xml/binding/jalview/Property.java		diff \| blob \| history
src/jalview/xml/binding/jalview/Sequence.java		diff \| blob \| history
src/jalview/xml/binding/jalview/SequenceSet.java		diff \| blob \| history
src/jalview/xml/binding/jalview/SequenceType.java		diff \| blob \| history
src/jalview/xml/binding/jalview/ThresholdType.java		diff \| blob \| history
src/jalview/xml/binding/jalview/VAMSAS.java		diff \| blob \| history
src/jalview/xml/binding/jalview/WebServiceParameterSet.java		diff \| blob \| history
src/jalview/xml/binding/jalview/package-info.java		diff \| blob \| history
test/jalview/analysis/TestAlignSeq.java		diff \| blob \| history
test/jalview/bin/CommandsTest.java		diff \| blob \| history
test/jalview/datamodel/AlignmentAnnotationTests.java		diff \| blob \| history
test/jalview/datamodel/PAEContactMatrixTest.java		diff \| blob \| history
test/jalview/datamodel/SearchResultsTest.java		diff \| blob \| history
test/jalview/datamodel/SequenceTest.java		diff \| blob \| history
test/jalview/fts/service/pdb/PDBFTSRestClientTest.java		diff \| blob \| history
test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java		diff \| blob \| history
test/jalview/gui/AlignViewportTest.java		diff \| blob \| history
test/jalview/gui/AlignmentPanelTest.java		diff \| blob \| history
test/jalview/gui/FeatureSettingsTest.java		diff \| blob \| history
test/jalview/gui/ScalePanelTest.java		diff \| blob \| history
test/jalview/gui/SeqPanelTest.java		diff \| blob \| history
test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java		diff \| blob \| history
test/jalview/io/RNAMLfileTest.java		diff \| blob \| history
test/jalview/io/SequenceAnnotationReportTest.java		diff \| blob \| history
test/jalview/io/cache/JvCacheableInputBoxTest.java		diff \| blob \| history
test/jalview/project/Jalview2xmlTests.java		diff \| blob \| history
test/jalview/renderer/ContactGeometryTest.java		diff \| blob \| history
test/jalview/ws/sifts/SiftsClientTest.java		diff \| blob \| history

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