source.jalview.org Git - jalview.git/commit - src/jalview/util/LaunchUtils.java

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

author	Ben Soares <b.soares@dundee.ac.uk>
	Thu, 10 Aug 2023 15:31:15 +0000 (16:31 +0100)
committer	Ben Soares <b.soares@dundee.ac.uk>
	Thu, 10 Aug 2023 15:31:15 +0000 (16:31 +0100)
commit	c932f0e85a8852824cdd8ce790af68682732c85c
tree	620fe588b1aa29b6e6773cee381f37c649b9309b	tree \| snapshot
parent	8bcbf5c32f8091f2d5871e7eec4d4727c26d5c63	commit \| diff

JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console.errPrintln. Fix command line tests. Add test for STDOUT output file.

225 files changed:

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/Conservation.java		diff \| blob \| history
src/jalview/analysis/CrossRef.java		diff \| blob \| history
src/jalview/analysis/Dna.java		diff \| blob \| history
src/jalview/analysis/GeneticCodes.java		diff \| blob \| history
src/jalview/analysis/Grouping.java		diff \| blob \| history
src/jalview/analysis/ParseProperties.java		diff \| blob \| history
src/jalview/analysis/Rna.java		diff \| blob \| history
src/jalview/analysis/SeqsetUtils.java		diff \| blob \| history
src/jalview/analysis/StructureFrequency.java		diff \| blob \| history
src/jalview/analysis/TreeEngine.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/ScoreMatrix.java		diff \| blob \| history
src/jalview/analysis/scoremodels/ScoreModels.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/AppletJmol.java		diff \| blob \| history
src/jalview/appletgui/ExtJmol.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/SeqPanel.java		diff \| blob \| history
src/jalview/appletgui/TreePanel.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/Console.java		diff \| blob \| history
src/jalview/bin/GetMemory.java		diff \| blob \| history
src/jalview/bin/HiDPISetting.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/bin/JalviewTaskbar.java		diff \| blob \| history
src/jalview/bin/Launcher.java		diff \| blob \| history
src/jalview/bin/MemorySetting.java		diff \| blob \| history
src/jalview/bin/argparser/BootstrapArgs.java		diff \| blob \| history
src/jalview/commands/EditCommand.java		diff \| blob \| history
src/jalview/datamodel/AlignedCodonFrame.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AlignmentView.java		diff \| blob \| history
src/jalview/datamodel/HiddenSequences.java		diff \| blob \| history
src/jalview/datamodel/SearchResults.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureMatcher.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureMatcherSet.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/htsjdk/HtsContigDb.java		diff \| blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.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/pymol/PymolManager.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/alphafold/AlphafoldRestClient.java		diff \| blob \| history
src/jalview/fts/service/pdb/PDBFTSRestClient.java		diff \| blob \| history
src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java		diff \| blob \| history
src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java		diff \| blob \| history
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignmentPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/AppVarna.java		diff \| blob \| history
src/jalview/gui/AppVarnaBinding.java		diff \| blob \| history
src/jalview/gui/BlogReader.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/Desktop.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/FeatureTypeSettings.java		diff \| blob \| history
src/jalview/gui/Help.java		diff \| blob \| history
src/jalview/gui/JDatabaseTree.java		diff \| blob \| history
src/jalview/gui/JvOptionPane.java		diff \| blob \| history
src/jalview/gui/OptsAndParamsPage.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/ProgressBar.java		diff \| blob \| history
src/jalview/gui/PymolBindingModel.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/SeqCanvas.java		diff \| blob \| history
src/jalview/gui/SeqCanvas.java.broken		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SplashScreen.java		diff \| blob \| history
src/jalview/gui/StructureChooser.java		diff \| blob \| history
src/jalview/gui/StructureViewerBase.java		diff \| blob \| history
src/jalview/gui/TreePanel.java		diff \| blob \| history
src/jalview/gui/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/WebserviceInfo.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java		diff \| blob \| history
src/jalview/gui/structurechooser/StructureChooserQuerySource.java		diff \| blob \| history
src/jalview/gui/structurechooser/TDBResultAnalyser.java		diff \| blob \| history
src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java		diff \| blob \| history
src/jalview/httpserver/AbstractRequestHandler.java		diff \| blob \| history
src/jalview/httpserver/HttpServer.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/FileFormats.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/FileParse.java		diff \| blob \| history
src/jalview/io/HTMLOutput.java		diff \| blob \| history
src/jalview/io/HtmlSvgOutput.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/MSFfile.java		diff \| blob \| history
src/jalview/io/NewickFile.java		diff \| blob \| history
src/jalview/io/PIRFile.java		diff \| blob \| history
src/jalview/io/PfamFile.java		diff \| blob \| history
src/jalview/io/PhylipFile.java		diff \| blob \| history
src/jalview/io/RnamlFile.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/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/SequenceOntologyLite.java		diff \| blob \| history
src/jalview/io/packed/JalviewDataset.java		diff \| blob \| history
src/jalview/io/packed/ParsePackedSet.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		diff \| blob \| history
src/jalview/javascript/JSFunctionExec.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/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GStructureChooser.java		diff \| blob \| history
src/jalview/log/JLogger.java		diff \| blob \| history
src/jalview/math/Matrix.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/rest/RestHandler.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/RNAHelicesColour.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/schemes/UserColourScheme.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/urls/UrlProvider.java		diff \| blob \| history
src/jalview/util/AWTConsole.java		diff \| blob \| history
src/jalview/util/ChannelProperties.java		diff \| blob \| history
src/jalview/util/DBRefUtils.java		diff \| blob \| history
src/jalview/util/GroupUrlLink.java		diff \| blob \| history
src/jalview/util/HttpUtils.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/StringUtils.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/workers/AlignmentAnnotationFactory.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/JobStateSummary.java		diff \| blob \| history
src/jalview/ws/dbsources/EBIAlfaFold.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/Annotate3D.java		diff \| blob \| history
src/jalview/ws/jws1/Discoverer.java		diff \| blob \| history
src/jalview/ws/jws1/JPredThread.java		diff \| blob \| history
src/jalview/ws/jws1/MsaWSThread.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/JabaParamStore.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/MsaWSThread.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/InputType.java		diff \| blob \| history
src/jalview/ws/rest/RestClient.java		diff \| blob \| history
src/jalview/ws/rest/RestJobThread.java		diff \| blob \| history
src/jalview/ws/seqfetcher/ASequenceFetcher.java		diff \| blob \| history
src/jalview/ws/sifts/SiftsClient.java		diff \| blob \| history
src/jalview/ws/utils/UrlDownloadClient.java		diff \| blob \| history
test/jalview/bin/CommandLineOperations.java		diff \| blob \| history
test/jalview/bin/CommandLineOperationsNG.java		diff \| blob \| history
test/jalview/bin/CommandsTest.java		diff \| blob \| history
test/jalview/bin/uniref50-output.fa	[new file with mode: 0644]	blob

RSS Atom