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

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

author	Ben Soares <b.soares@dundee.ac.uk>
	Fri, 11 Feb 2022 03:34:22 +0000 (03:34 +0000)
committer	Ben Soares <b.soares@dundee.ac.uk>
	Fri, 11 Feb 2022 03:34:22 +0000 (03:34 +0000)
commit	a1984b1c8c273ed33c7ce9283039f4027dcae2de
tree	12489ebfb2760d3e423a68fcfd70507fce6a55d3	tree \| snapshot
parent	c4e814d2930b175c789c2a004801b7b8a1dacd32	commit \| diff

JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls for this. Removal of jalview.javascript.log4j. Improvements to the Java Console (controllable autoscrolling).

119 files changed:

gradle.properties		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/GeneticCodes.java		diff \| blob \| history
src/jalview/analysis/PCA.java		diff \| blob \| history
src/jalview/analysis/TreeModel.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblLookup.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSeqProxy.java		diff \| blob \| history
src/jalview/ext/htsjdk/VCFReader.java		diff \| blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/pymol/PymolManager.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/fts/core/GFTSPanel.java		diff \| blob \| history
src/jalview/fts/service/alphafold/AlphafoldRestClient.java		diff \| blob \| history
src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java		diff \| blob \| history
src/jalview/gui/APQHandlers.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/AppJmol.java		diff \| blob \| history
src/jalview/gui/AppJmolBinding.java		diff \| blob \| history
src/jalview/gui/BlogReader.java		diff \| blob \| history
src/jalview/gui/ChimeraViewFrame.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/Desktop.java		diff \| blob \| history
src/jalview/gui/FeatureTypeSettings.java		diff \| blob \| history
src/jalview/gui/OOMWarning.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/PromptUserConfig.java		diff \| blob \| history
src/jalview/gui/PymolBindingModel.java		diff \| blob \| history
src/jalview/gui/PymolViewer.java		diff \| blob \| history
src/jalview/gui/RotatableCanvas.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.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/TreePanel.java		diff \| blob \| history
src/jalview/gui/UserQuestionnaireCheck.java		diff \| blob \| history
src/jalview/gui/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/gui/WsParamSetManager.java		diff \| blob \| history
src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java		diff \| blob \| history
src/jalview/io/BackupFilesPresetEntry.java		diff \| blob \| history
src/jalview/io/BioJsHTMLOutput.java		diff \| blob \| history
src/jalview/io/EMBLLikeFlatFile.java		diff \| blob \| history
src/jalview/io/EmblFlatFile.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/HtmlSvgOutput.java		diff \| blob \| history
src/jalview/io/ModellerDescription.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/VamsasAppDatastore.java		diff \| blob \| history
src/jalview/io/vamsas/DatastoreItem.java		diff \| blob \| history
src/jalview/io/vamsas/DatastoreRegistry.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/io/vcf/VCFLoader.java		diff \| blob \| history
src/jalview/javascript/MouseOverListener.java		diff \| blob \| history
src/jalview/javascript/log4j/Appender.java	[deleted file]	blob \| history
src/jalview/javascript/log4j/ConsoleAppender.java	[deleted file]	blob \| history
src/jalview/javascript/log4j/Layout.java	[deleted file]	blob \| history
src/jalview/javascript/log4j/Level.java	[deleted file]	blob \| history
src/jalview/javascript/log4j/Logger.java	[deleted file]	blob \| history
src/jalview/javascript/log4j/Priority.java	[deleted file]	blob \| history
src/jalview/javascript/log4j/SimpleLayout.java	[deleted file]	blob \| history
src/jalview/javascript/log4j/WriterAppender.java	[deleted file]	blob \| history
src/jalview/javascript/log4j/spi/LoggingEvent.java	[deleted file]	blob \| history
src/jalview/javascript/log4j/spi/OptionHandler.java	[deleted file]	blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GWsPreferences.java		diff \| blob \| history
src/jalview/log/JLogger.java	[new file with mode: 0644]	blob
src/jalview/log/JLoggerI.java	[new file with mode: 0644]	blob
src/jalview/log/JLoggerLog4j.java	[new file with mode: 0644]	blob
src/jalview/log/JalviewAppender.java	[moved from src/jalview/gui/JalviewAppender.java with 72% similarity]	diff \| blob \| history
src/jalview/project/Jalview2XML.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/structures/models/AAStructureBindingModel.java		diff \| blob \| history
src/jalview/urls/UrlLinkTableModel.java		diff \| blob \| history
src/jalview/util/BrowserLauncher.java		diff \| blob \| history
src/jalview/util/Log4j.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/ws/AWSThread.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/dbsources/EmblFlatfileSource.java		diff \| blob \| history
src/jalview/ws/dbsources/EmblXmlSource.java		diff \| blob \| history
src/jalview/ws/dbsources/Xfam.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/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/jws2/AADisorderClient.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/Jws2Client.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/rest/HttpResultSet.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
test/jalview/util/Log4jTest.java	[new file with mode: 0644]	blob
test/jalview/util/log4jTestProps.jvprops	[new file with mode: 0644]	blob

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