JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...
authorBen Soares <b.soares@dundee.ac.uk>
Tue, 21 Sep 2021 23:08:45 +0000 (00:08 +0100)
committerBen Soares <b.soares@dundee.ac.uk>
Tue, 21 Sep 2021 23:08:45 +0000 (00:08 +0100)
commit9d2408483e451285fd555c3cd6e0273977acbaa7
tree1c5cd8afc87826f3ec3a69d653f9e6578ef17a7a
parent214ad7e089fdf9cde66ac5e5d56d498101bbe2c3
JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately
103 files changed:
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/AnnotationSorter.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/Finder.java
src/jalview/analysis/GeneticCodes.java
src/jalview/analysis/SequenceIdMatcher.java
src/jalview/bin/HiDPISetting.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/bin/Launcher.java
src/jalview/bin/MemorySetting.java
src/jalview/commands/ChangeCaseCommand.java
src/jalview/commands/EditCommand.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/DBRefSource.java
src/jalview/datamodel/MappedFeatures.java
src/jalview/datamodel/features/FeatureMatcher.java
src/jalview/datamodel/features/FeatureMatcherSet.java
src/jalview/ext/ensembl/EnsemblInfo.java
src/jalview/ext/jmol/JmolParser.java
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
src/jalview/fts/core/FTSRestClient.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AppJmol.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/JDatabaseTree.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/WebserviceInfo.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/io/AppletFormatAdapter.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileFormats.java
src/jalview/io/FormatAdapter.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JPredFile.java
src/jalview/io/JalviewFileFilter.java
src/jalview/io/JalviewFileView.java
src/jalview/io/JnetAnnotationMaker.java
src/jalview/io/MSFfile.java
src/jalview/io/NewickFile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/io/gff/ExonerateHelper.java
src/jalview/io/packed/ParsePackedSet.java
src/jalview/io/vcf/VCFLoader.java
src/jalview/javascript/log4j/Level.java
src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
src/jalview/project/Jalview2XML.java
src/jalview/schemes/ColourSchemeLoader.java
src/jalview/schemes/ColourSchemes.java
src/jalview/schemes/FeatureColour.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/UserColourScheme.java
src/jalview/structure/StructureImportSettings.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/util/CaseInsensitiveString.java
src/jalview/util/ColorUtils.java
src/jalview/util/DBRefUtils.java
src/jalview/util/MessageManager.java
src/jalview/util/ParseHtmlBodyAndLinks.java
src/jalview/util/StringUtils.java
src/jalview/util/matcher/Matcher.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/dbsources/EmblFlatfileSource.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/dbsources/TDBeacons.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/dbsources/Xfam.java
src/jalview/ws/ebi/EBIFetchClient.java
src/jalview/ws/io/mime/MimeTypes.java
src/jalview/ws/jws1/JPredClient.java
src/jalview/ws/jws1/MsaWSClient.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
src/jalview/ws/rest/InputType.java
src/jalview/ws/rest/RestJobThread.java
src/jalview/ws/sifts/SiftsClient.java
test/jalview/analysis/AlignmentGenerator.java
test/jalview/analysis/RnaTest.java
test/jalview/commands/EditCommandTest.java
test/jalview/datamodel/ResidueCountTest.java
test/jalview/datamodel/SequenceTest.java
test/jalview/ext/ensembl/EnsemblCdnaTest.java
test/jalview/ext/ensembl/EnsemblGeneTest.java
test/jalview/ext/paradise/TestAnnotate3D.java
test/jalview/io/FileFormatsTest.java
test/jalview/ws/gui/Jws2ParamView.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/jws2/ParameterUtilsTest.java
test/junit/extensions/PrivilegedAccessor.java