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

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

author	Jim Procter <j.procter@dundee.ac.uk>
	Fri, 11 Feb 2022 15:27:51 +0000 (15:27 +0000)
committer	Jim Procter <j.procter@dundee.ac.uk>
	Fri, 11 Feb 2022 15:38:20 +0000 (15:38 +0000)
commit	cb8e52fbbc5f725e3f7f48c672cdddb0690bd978
tree	cb6b14c381701d87ff2c59b2eabff76a72135efd	tree \| snapshot
parent	1c721468246c2aafd86fc52d954512374f576b11	commit \| diff

JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

Conflicts:
src/jalview/bin/Jalview.java

99 files changed:

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/bin/Cache.java		diff \| blob \| history
src/jalview/bin/Console.java	[new file with mode: 0644]	blob
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/service/alphafold/AlphafoldRestClient.java		diff \| blob \| history
src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.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/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/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.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/BackupFiles.java		diff \| blob \| history
src/jalview/io/BackupFilesPresetEntry.java		diff \| blob \| history
src/jalview/io/EMBLLikeFlatFile.java		diff \| blob \| history
src/jalview/io/EmblFlatFile.java		diff \| blob \| history
src/jalview/io/FileParse.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/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/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/log/JLogger.java		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/MapList.java		diff \| blob \| history
src/jalview/util/MappingUtils.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/RestJobThread.java		diff \| blob \| history
src/jalview/ws/seqfetcher/ASequenceFetcher.java		diff \| blob \| history
test/jalview/gui/JAL1353bugdemo.java		diff \| blob \| history
test/jalview/gui/PopupMenuTest.java		diff \| blob \| history
test/jalview/io/EmblFlatFileTest.java		diff \| blob \| history
test/jalview/io/FileIOTester.java		diff \| blob \| history
test/jalview/io/GenBankFileTest.java		diff \| blob \| history
test/jalview/io/vcf/VCFLoaderTest.java		diff \| blob \| history
test/jalview/util/Log4jTest.java		diff \| blob \| history
test/jalview/util/MapListTest.java		diff \| blob \| history
test/jalview/util/MappingUtilsTest.java		diff \| blob \| history
test/jalview/ws/gui/Jws2ParamView.java		diff \| blob \| history
test/jalview/ws/jabaws/DisorderAnnotExportImport.java		diff \| blob \| history
test/jalview/ws/jabaws/RNAStructExportImport.java		diff \| blob \| history
test/jalview/ws/jws2/ParameterUtilsTest.java		diff \| blob \| history
test/jalview/ws/rest/ShmmrRSBSService.java		diff \| blob \| history
test/jalview/ws/seqfetcher/DbRefFetcherTest.java		diff \| blob \| history

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