JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...
authorBen Soares <b.soares@dundee.ac.uk>
Thu, 10 Aug 2023 15:31:15 +0000 (16:31 +0100)
committerBen Soares <b.soares@dundee.ac.uk>
Thu, 10 Aug 2023 15:31:15 +0000 (16:31 +0100)
commitc932f0e85a8852824cdd8ce790af68682732c85c
tree620fe588b1aa29b6e6773cee381f37c649b9309b
parent8bcbf5c32f8091f2d5871e7eec4d4727c26d5c63
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
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/analysis/GeneticCodes.java
src/jalview/analysis/Grouping.java
src/jalview/analysis/ParseProperties.java
src/jalview/analysis/Rna.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/analysis/StructureFrequency.java
src/jalview/analysis/TreeEngine.java
src/jalview/analysis/TreeModel.java
src/jalview/analysis/scoremodels/FeatureDistanceModel.java
src/jalview/analysis/scoremodels/ScoreMatrix.java
src/jalview/analysis/scoremodels/ScoreModels.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/ExtJmol.java
src/jalview/appletgui/PCAPanel.java
src/jalview/appletgui/PairwiseAlignPanel.java
src/jalview/appletgui/RedundancyPanel.java
src/jalview/appletgui/RotatableCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/TreePanel.java
src/jalview/bin/Cache.java
src/jalview/bin/Console.java
src/jalview/bin/GetMemory.java
src/jalview/bin/HiDPISetting.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/bin/JalviewLiteURLRetrieve.java
src/jalview/bin/JalviewTaskbar.java
src/jalview/bin/Launcher.java
src/jalview/bin/MemorySetting.java
src/jalview/bin/argparser/BootstrapArgs.java
src/jalview/commands/EditCommand.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/HiddenSequences.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/features/FeatureMatcher.java
src/jalview/datamodel/features/FeatureMatcherSet.java
src/jalview/datamodel/features/FeatureStore.java
src/jalview/datamodel/features/SequenceFeatures.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblLookup.java
src/jalview/ext/ensembl/EnsemblMap.java
src/jalview/ext/ensembl/EnsemblRestClient.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
src/jalview/ext/htsjdk/HtsContigDb.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolParser.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/ext/pymol/PymolManager.java
src/jalview/ext/rbvi/chimera/ChimeraListener.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/fts/core/FTSDataColumnPreferences.java
src/jalview/fts/service/alphafold/AlphafoldRestClient.java
src/jalview/fts/service/pdb/PDBFTSRestClient.java
src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/AppJmol.java
src/jalview/gui/AppVarna.java
src/jalview/gui/AppVarnaBinding.java
src/jalview/gui/BlogReader.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/ColourMenuHelper.java
src/jalview/gui/Console.java
src/jalview/gui/CrossRefAction.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/FeatureTypeSettings.java
src/jalview/gui/Help.java
src/jalview/gui/JDatabaseTree.java
src/jalview/gui/JvOptionPane.java
src/jalview/gui/OptsAndParamsPage.java
src/jalview/gui/PaintRefresher.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/ProgressBar.java
src/jalview/gui/PymolBindingModel.java
src/jalview/gui/RedundancyPanel.java
src/jalview/gui/RestInputParamEditDialog.java
src/jalview/gui/RestServiceEditorPane.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqCanvas.java.broken
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/StructureViewerBase.java
src/jalview/gui/TreePanel.java
src/jalview/gui/VamsasApplication.java
src/jalview/gui/WebserviceInfo.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
src/jalview/gui/structurechooser/StructureChooserQuerySource.java
src/jalview/gui/structurechooser/TDBResultAnalyser.java
src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
src/jalview/httpserver/AbstractRequestHandler.java
src/jalview/httpserver/HttpServer.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BackupFilenameFilter.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/ClustalFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileFormats.java
src/jalview/io/FileLoader.java
src/jalview/io/FileParse.java
src/jalview/io/HTMLOutput.java
src/jalview/io/HtmlSvgOutput.java
src/jalview/io/JPredFile.java
src/jalview/io/JSONFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/JalviewFileView.java
src/jalview/io/MSFfile.java
src/jalview/io/NewickFile.java
src/jalview/io/PIRFile.java
src/jalview/io/PfamFile.java
src/jalview/io/PhylipFile.java
src/jalview/io/RnamlFile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/SimpleBlastFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/StructureFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/WSWUBlastClient.java
src/jalview/io/cache/JvCacheableInputBox.java
src/jalview/io/gff/ExonerateHelper.java
src/jalview/io/gff/Gff3Helper.java
src/jalview/io/gff/GffHelperBase.java
src/jalview/io/gff/SequenceOntologyLite.java
src/jalview/io/packed/JalviewDataset.java
src/jalview/io/packed/ParsePackedSet.java
src/jalview/io/vamsas/Sequencemapping.java
src/jalview/io/vamsas/Tree.java
src/jalview/io/vcf/VCFLoader.java
src/jalview/javascript/JSFunctionExec.java
src/jalview/javascript/JsSelectionSender.java
src/jalview/javascript/MouseOverListener.java
src/jalview/javascript/MouseOverStructureListener.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GStructureChooser.java
src/jalview/log/JLogger.java
src/jalview/math/Matrix.java
src/jalview/math/RotatableMatrix.java
src/jalview/project/Jalview2XML.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/rest/RestHandler.java
src/jalview/schemes/ColourSchemeLoader.java
src/jalview/schemes/ColourSchemes.java
src/jalview/schemes/Consensus.java
src/jalview/schemes/CovariationColourScheme.java
src/jalview/schemes/FeatureColour.java
src/jalview/schemes/RNAHelicesColour.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/UserColourScheme.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/urls/IdentifiersUrlProvider.java
src/jalview/urls/UrlProvider.java
src/jalview/util/AWTConsole.java
src/jalview/util/ChannelProperties.java
src/jalview/util/DBRefUtils.java
src/jalview/util/GroupUrlLink.java
src/jalview/util/HttpUtils.java
src/jalview/util/LaunchUtils.java
src/jalview/util/Log4j.java
src/jalview/util/Platform.java
src/jalview/util/StringUtils.java
src/jalview/util/UrlLink.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/ViewportRanges.java
src/jalview/workers/AlignCalcManager.java
src/jalview/workers/AlignmentAnnotationFactory.java
src/jalview/workers/ConsensusThread.java
src/jalview/ws/AWSThread.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/JobStateSummary.java
src/jalview/ws/dbsources/EBIAlfaFold.java
src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/ebi/EBIFetchClient.java
src/jalview/ws/jws1/Annotate3D.java
src/jalview/ws/jws1/Discoverer.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws1/MsaWSThread.java
src/jalview/ws/jws1/SeqSearchWSThread.java
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
src/jalview/ws/jws2/JabaParamStore.java
src/jalview/ws/jws2/JabaWsServerQuery.java
src/jalview/ws/jws2/JabawsCalcWorker.java
src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/MsaWSThread.java
src/jalview/ws/jws2/ParameterUtils.java
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
src/jalview/ws/rest/InputType.java
src/jalview/ws/rest/RestClient.java
src/jalview/ws/rest/RestJobThread.java
src/jalview/ws/seqfetcher/ASequenceFetcher.java
src/jalview/ws/sifts/SiftsClient.java
src/jalview/ws/utils/UrlDownloadClient.java
test/jalview/bin/CommandLineOperations.java
test/jalview/bin/CommandLineOperationsNG.java
test/jalview/bin/CommandsTest.java
test/jalview/bin/uniref50-output.fa [new file with mode: 0644]