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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...
author
Ben Soares
<b.soares@dundee.ac.uk>
Tue, 21 Sep 2021 23:08:45 +0000
(
00:08
+0100)
committer
Ben Soares
<b.soares@dundee.ac.uk>
Tue, 21 Sep 2021 23:08:45 +0000
(
00:08
+0100)
103 files changed:
src/jalview/analysis/AlignSeq.java
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src/jalview/analysis/AlignmentUtils.java
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src/jalview/analysis/AnnotationSorter.java
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src/jalview/analysis/Conservation.java
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src/jalview/analysis/Finder.java
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src/jalview/analysis/GeneticCodes.java
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src/jalview/analysis/SequenceIdMatcher.java
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src/jalview/bin/HiDPISetting.java
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src/jalview/bin/Jalview.java
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src/jalview/bin/JalviewLite.java
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src/jalview/bin/Launcher.java
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src/jalview/bin/MemorySetting.java
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src/jalview/commands/ChangeCaseCommand.java
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src/jalview/commands/EditCommand.java
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src/jalview/datamodel/AlignmentAnnotation.java
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src/jalview/datamodel/DBRefEntry.java
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src/jalview/datamodel/DBRefSource.java
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src/jalview/datamodel/MappedFeatures.java
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src/jalview/datamodel/features/FeatureMatcher.java
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src/jalview/datamodel/features/FeatureMatcherSet.java
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src/jalview/ext/ensembl/EnsemblInfo.java
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src/jalview/ext/jmol/JmolParser.java
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src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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src/jalview/fts/core/FTSRestClient.java
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src/jalview/gui/AlignFrame.java
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src/jalview/gui/AnnotationExporter.java
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src/jalview/gui/AnnotationLabels.java
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src/jalview/gui/AppJmol.java
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src/jalview/gui/Desktop.java
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src/jalview/gui/FeatureSettings.java
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src/jalview/gui/Finder.java
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src/jalview/gui/JDatabaseTree.java
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src/jalview/gui/PopupMenu.java
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src/jalview/gui/StructureChooser.java
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src/jalview/gui/TreePanel.java
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src/jalview/gui/UserDefinedColours.java
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src/jalview/gui/WebserviceInfo.java
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src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
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src/jalview/gui/structurechooser/StructureChooserQuerySource.java
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src/jalview/gui/structurechooser/TDBResultAnalyser.java
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src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
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src/jalview/io/AppletFormatAdapter.java
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src/jalview/io/FeaturesFile.java
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src/jalview/io/FileFormats.java
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src/jalview/io/FormatAdapter.java
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src/jalview/io/IdentifyFile.java
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src/jalview/io/JPredFile.java
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src/jalview/io/JalviewFileFilter.java
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src/jalview/io/JalviewFileView.java
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src/jalview/io/JnetAnnotationMaker.java
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src/jalview/io/MSFfile.java
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src/jalview/io/NewickFile.java
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src/jalview/io/SequenceAnnotationReport.java
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src/jalview/io/StockholmFile.java
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src/jalview/io/gff/ExonerateHelper.java
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src/jalview/io/packed/ParsePackedSet.java
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src/jalview/io/vcf/VCFLoader.java
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src/jalview/javascript/log4j/Level.java
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src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
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src/jalview/project/Jalview2XML.java
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src/jalview/schemes/ColourSchemeLoader.java
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src/jalview/schemes/ColourSchemes.java
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src/jalview/schemes/FeatureColour.java
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src/jalview/schemes/ResidueProperties.java
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src/jalview/schemes/UserColourScheme.java
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src/jalview/structure/StructureImportSettings.java
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src/jalview/structures/models/AAStructureBindingModel.java
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src/jalview/util/CaseInsensitiveString.java
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src/jalview/util/ColorUtils.java
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src/jalview/util/DBRefUtils.java
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src/jalview/util/MessageManager.java
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src/jalview/util/ParseHtmlBodyAndLinks.java
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src/jalview/util/StringUtils.java
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src/jalview/util/matcher/Matcher.java
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src/jalview/ws/DBRefFetcher.java
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src/jalview/ws/dbsources/EmblFlatfileSource.java
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src/jalview/ws/dbsources/EmblXmlSource.java
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src/jalview/ws/dbsources/TDBeacons.java
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src/jalview/ws/dbsources/Uniprot.java
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src/jalview/ws/dbsources/Xfam.java
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src/jalview/ws/ebi/EBIFetchClient.java
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src/jalview/ws/io/mime/MimeTypes.java
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src/jalview/ws/jws1/JPredClient.java
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src/jalview/ws/jws1/MsaWSClient.java
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src/jalview/ws/jws2/MsaWSClient.java
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src/jalview/ws/jws2/SequenceAnnotationWSClient.java
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src/jalview/ws/rest/InputType.java
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src/jalview/ws/rest/RestJobThread.java
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src/jalview/ws/sifts/SiftsClient.java
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test/jalview/analysis/AlignmentGenerator.java
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test/jalview/analysis/RnaTest.java
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test/jalview/commands/EditCommandTest.java
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test/jalview/datamodel/ResidueCountTest.java
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test/jalview/datamodel/SequenceTest.java
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test/jalview/ext/ensembl/EnsemblCdnaTest.java
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test/jalview/ext/ensembl/EnsemblGeneTest.java
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test/jalview/ext/paradise/TestAnnotate3D.java
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test/jalview/io/FileFormatsTest.java
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test/jalview/ws/gui/Jws2ParamView.java
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test/jalview/ws/jabaws/DisorderAnnotExportImport.java
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test/jalview/ws/jabaws/RNAStructExportImport.java
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test/jalview/ws/jws2/ParameterUtilsTest.java
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test/junit/extensions/PrivilegedAccessor.java
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diff --git
a/src/jalview/analysis/AlignSeq.java
b/src/jalview/analysis/AlignSeq.java
index
1b2578e
..
2fb6ce1
100755
(executable)
--- a/
src/jalview/analysis/AlignSeq.java
+++ b/
src/jalview/analysis/AlignSeq.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
@@
-148,7
+150,7
@@
public class AlignSeq
public AlignSeq(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
{
public AlignSeq(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
{
- seqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
+ seqInit(s1, string1.toUpperCase(Locale.ROOT), s2, string2.toUpperCase(Locale.ROOT), type);
}
/**
}
/**
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
0c40873
..
23c5d64
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.commands.RemoveGapColCommand;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.commands.RemoveGapColCommand;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
@@
-181,9
+183,9
@@
public class AlignmentUtils
// TODO use Character.toLowerCase to avoid creating String objects?
char[] upstream = new String(ds
.getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
// TODO use Character.toLowerCase to avoid creating String objects?
char[] upstream = new String(ds
.getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
- .toLowerCase().toCharArray();
+ .toLowerCase(Locale.ROOT).toCharArray();
char[] downstream = new String(
char[] downstream = new String(
- ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase()
+ ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase(Locale.ROOT)
.toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
.toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
@@
-462,7
+464,7
@@
public class AlignmentUtils
if (cdnaLength != mappedLength && cdnaLength > 2)
{
String lastCodon = String.valueOf(cdnaSeqChars,
if (cdnaLength != mappedLength && cdnaLength > 2)
{
String lastCodon = String.valueOf(cdnaSeqChars,
- cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase();
+ cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(Locale.ROOT);
for (String stop : ResidueProperties.STOP_CODONS)
{
if (lastCodon.equals(stop))
for (String stop : ResidueProperties.STOP_CODONS)
{
if (lastCodon.equals(stop))
@@
-479,7
+481,7
@@
public class AlignmentUtils
*/
int startOffset = 0;
if (cdnaLength != mappedLength && cdnaLength > 2
*/
int startOffset = 0;
if (cdnaLength != mappedLength && cdnaLength > 2
- && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase()
+ && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase(Locale.ROOT)
.equals(ResidueProperties.START))
{
startOffset += CODON_LENGTH;
.equals(ResidueProperties.START))
{
startOffset += CODON_LENGTH;
diff --git
a/src/jalview/analysis/AnnotationSorter.java
b/src/jalview/analysis/AnnotationSorter.java
index
2f556f1
..
c9ed570
100644
(file)
--- a/
src/jalview/analysis/AnnotationSorter.java
+++ b/
src/jalview/analysis/AnnotationSorter.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
@@
-368,7
+370,7
@@
public class AnnotationSorter
{
return 1;
}
{
return 1;
}
- return label1.toUpperCase().compareTo(label2.toUpperCase());
+ return label1.toUpperCase(Locale.ROOT).compareTo(label2.toUpperCase(Locale.ROOT));
}
/**
}
/**
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
ff38c08
..
6cc9dd3
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.AlignmentAnnotation;
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.AlignmentAnnotation;
@@
-312,7
+314,7
@@
public class Conservation
protected static void recordConservation(Map<String, Integer> resultMap,
String res)
{
protected static void recordConservation(Map<String, Integer> resultMap,
String res)
{
- res = res.toUpperCase();
+ res = res.toUpperCase(Locale.ROOT);
for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
.entrySet())
{
for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
.entrySet())
{
diff --git
a/src/jalview/analysis/Finder.java
b/src/jalview/analysis/Finder.java
index
d52e42a
..
bf86a86
100644
(file)
--- a/
src/jalview/analysis/Finder.java
+++ b/
src/jalview/analysis/Finder.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
@@
-148,7
+150,7
@@
public class Finder implements FinderI
idMatches = new ArrayList<>();
String searchString = matchCase ? theSearchString
idMatches = new ArrayList<>();
String searchString = matchCase ? theSearchString
- : theSearchString.toUpperCase();
+ : theSearchString.toUpperCase(Locale.ROOT);
Regex searchPattern = new Regex(searchString);
searchPattern.setIgnoreCase(!matchCase);
Regex searchPattern = new Regex(searchString);
searchPattern.setIgnoreCase(!matchCase);
diff --git
a/src/jalview/analysis/GeneticCodes.java
b/src/jalview/analysis/GeneticCodes.java
index
df1dd82
..
8d69b0b
100644
(file)
--- a/
src/jalview/analysis/GeneticCodes.java
+++ b/
src/jalview/analysis/GeneticCodes.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.bin.Cache;
import java.io.BufferedReader;
import jalview.bin.Cache;
import java.io.BufferedReader;
@@
-198,13
+200,13
@@
public final class GeneticCodes
while (line != null)
{
line = readLine(dataIn);
while (line != null)
{
line = readLine(dataIn);
- if (line != null && !"DNA".equals(line.toUpperCase()))
+ if (line != null && !"DNA".equals(line.toUpperCase(Locale.ROOT)))
{
String[] tokens = line.split("\\t");
if (tokens.length == 2)
{
{
String[] tokens = line.split("\\t");
if (tokens.length == 2)
{
- ambiguityCodes.put(tokens[0].toUpperCase(),
- tokens[1].toUpperCase());
+ ambiguityCodes.put(tokens[0].toUpperCase(Locale.ROOT),
+ tokens[1].toUpperCase(Locale.ROOT));
}
else
{
}
else
{
@@
-341,13
+343,13
@@
public final class GeneticCodes
@Override
public String translateCanonical(String codon)
{
@Override
public String translateCanonical(String codon)
{
- return codons.get(codon.toUpperCase());
+ return codons.get(codon.toUpperCase(Locale.ROOT));
}
@Override
public String translate(String codon)
{
}
@Override
public String translate(String codon)
{
- String upper = codon.toUpperCase();
+ String upper = codon.toUpperCase(Locale.ROOT);
String peptide = translateCanonical(upper);
/*
String peptide = translateCanonical(upper);
/*
diff --git
a/src/jalview/analysis/SequenceIdMatcher.java
b/src/jalview/analysis/SequenceIdMatcher.java
index
a85c7f3
..
3ec162d
100755
(executable)
--- a/
src/jalview/analysis/SequenceIdMatcher.java
+++ b/
src/jalview/analysis/SequenceIdMatcher.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
@@
-289,7
+291,7
@@
public class SequenceIdMatcher
{
if (s != null)
{
{
if (s != null)
{
- id = s.toLowerCase();
+ id = s.toLowerCase(Locale.ROOT);
}
else
{
}
else
{
@@
-319,7
+321,7
@@
public class SequenceIdMatcher
{
if (s instanceof String)
{
{
if (s instanceof String)
{
- return this.stringequals(((String) s).toLowerCase());
+ return this.stringequals(((String) s).toLowerCase(Locale.ROOT));
}
}
}
}
diff --git
a/src/jalview/bin/HiDPISetting.java
b/src/jalview/bin/HiDPISetting.java
index
38b7587
..
6219179
100644
(file)
--- a/
src/jalview/bin/HiDPISetting.java
+++ b/
src/jalview/bin/HiDPISetting.java
@@
-1,5
+1,7
@@
package jalview.bin;
package jalview.bin;
+import java.util.Locale;
+
import java.awt.HeadlessException;
public class HiDPISetting
import java.awt.HeadlessException;
public class HiDPISetting
@@
-45,7
+47,7
@@
public class HiDPISetting
static
{
String system = System.getProperty("os.name") == null ? null
static
{
String system = System.getProperty("os.name") == null ? null
- : System.getProperty("os.name").toLowerCase();
+ : System.getProperty("os.name").toLowerCase(Locale.ROOT);
if (system != null)
{
isLinux = system.indexOf("linux") > -1;
if (system != null)
{
isLinux = system.indexOf("linux") > -1;
diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
0b5fafa
..
fe48283
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-20,6
+20,8
@@
*/
package jalview.bin;
*/
package jalview.bin;
+import java.util.Locale;
+
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
@@
-983,9
+985,9
@@
public class Jalview
for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
{
if (info.getName() != null && nameStartsWith
for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
{
if (info.getName() != null && nameStartsWith
- ? info.getName().toLowerCase()
- .startsWith(name.toLowerCase())
- : info.getName().toLowerCase().equals(name.toLowerCase()))
+ ? info.getName().toLowerCase(Locale.ROOT)
+ .startsWith(name.toLowerCase(Locale.ROOT))
+ : info.getName().toLowerCase(Locale.ROOT).equals(name.toLowerCase(Locale.ROOT)))
{
className = info.getClassName();
break;
{
className = info.getClassName();
break;
@@
-1042,7
+1044,7
@@
public class Jalview
System.setProperty("apple.laf.useScreenMenuBar", "true");
set = setQuaquaLookAndFeel();
if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
System.setProperty("apple.laf.useScreenMenuBar", "true");
set = setQuaquaLookAndFeel();
if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
- .toLowerCase().contains("quaqua"))
+ .toLowerCase(Locale.ROOT).contains("quaqua"))
{
set = setVaquaLookAndFeel();
}
{
set = setVaquaLookAndFeel();
}
diff --git
a/src/jalview/bin/JalviewLite.java
b/src/jalview/bin/JalviewLite.java
index
e7f2a53
..
871ca54
100644
(file)
--- a/
src/jalview/bin/JalviewLite.java
+++ b/
src/jalview/bin/JalviewLite.java
@@
-20,6
+20,8
@@
*/
package jalview.bin;
*/
package jalview.bin;
+import java.util.Locale;
+
import jalview.analysis.AlignmentUtils;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.analysis.AlignmentUtils;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
@@
-208,7
+210,7
@@
public class JalviewLite extends Applet
final int pos = apos;
// use vamsas listener to broadcast to all listeners in scope
if (alignedPosition != null && (alignedPosition.trim().length() == 0
final int pos = apos;
// use vamsas listener to broadcast to all listeners in scope
if (alignedPosition != null && (alignedPosition.trim().length() == 0
- || alignedPosition.toLowerCase().indexOf("false") > -1))
+ || alignedPosition.toLowerCase(Locale.ROOT).indexOf("false") > -1))
{
java.awt.EventQueue.invokeLater(new Runnable()
{
{
java.awt.EventQueue.invokeLater(new Runnable()
{
@@
-412,7
+414,7
@@
public class JalviewLite extends Applet
r--;
} catch (NumberFormatException ex)
{
r--;
} catch (NumberFormatException ex)
{
- if (cl.toLowerCase().equals("sequence"))
+ if (cl.toLowerCase(Locale.ROOT).equals("sequence"))
{
// we are in the dataset sequence's coordinate frame.
inseqpos = true;
{
// we are in the dataset sequence's coordinate frame.
inseqpos = true;
@@
-1440,7
+1442,7
@@
public class JalviewLite extends Applet
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
- useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT).equals(TRUE);
}
/**
* if true disable the check for jmol
}
/**
* if true disable the check for jmol
@@
-2691,7
+2693,7
@@
public class JalviewLite extends Applet
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
- // state.toLowerCase().equals("false"));
+ // state.toLowerCase(Locale.ROOT).equals("false"));
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
diff --git
a/src/jalview/bin/Launcher.java
b/src/jalview/bin/Launcher.java
index
b8d31c2
..
e13f2dd
100644
(file)
--- a/
src/jalview/bin/Launcher.java
+++ b/
src/jalview/bin/Launcher.java
@@
-20,6
+20,8
@@
*/
package jalview.bin;
*/
package jalview.bin;
+import java.util.Locale;
+
import java.io.File;
import java.io.IOException;
import java.lang.management.ManagementFactory;
import java.io.File;
import java.io.IOException;
import java.lang.management.ManagementFactory;
@@
-190,7
+192,7
@@
public class Launcher
process.waitFor();
} catch (IOException e)
{
process.waitFor();
} catch (IOException e)
{
- if (e.getMessage().toLowerCase().contains("memory"))
+ if (e.getMessage().toLowerCase(Locale.ROOT).contains("memory"))
{
System.out.println("Caught a memory exception: " + e.getMessage());
// Probably the "Cannot allocate memory" error, try without the memory
{
System.out.println("Caught a memory exception: " + e.getMessage());
// Probably the "Cannot allocate memory" error, try without the memory
diff --git
a/src/jalview/bin/MemorySetting.java
b/src/jalview/bin/MemorySetting.java
index
5d7f14c
..
52f0c9e
100644
(file)
--- a/
src/jalview/bin/MemorySetting.java
+++ b/
src/jalview/bin/MemorySetting.java
@@
-31,6
+31,8
@@
package jalview.bin;
* @author bsoares
*
*/
* @author bsoares
*
*/
+import java.util.Locale;
+
public class MemorySetting
{
public static final String MAX_HEAPSIZE_PERCENT_PROPERTY_NAME = "jvmmempc";
public class MemorySetting
{
public static final String MAX_HEAPSIZE_PERCENT_PROPERTY_NAME = "jvmmempc";
@@
-101,7
+103,7
@@
public class MemorySetting
if (jvmmemmax != null && jvmmemmax.length() > 0)
{
long multiplier = 1;
if (jvmmemmax != null && jvmmemmax.length() > 0)
{
long multiplier = 1;
- switch (jvmmemmax.toLowerCase().substring(jvmmemmax.length() - 1))
+ switch (jvmmemmax.toLowerCase(Locale.ROOT).substring(jvmmemmax.length() - 1))
{
case "t":
multiplier = 1099511627776L; // 2^40
{
case "t":
multiplier = 1099511627776L; // 2^40
diff --git
a/src/jalview/commands/ChangeCaseCommand.java
b/src/jalview/commands/ChangeCaseCommand.java
index
7f7142f
..
2d61705
100644
(file)
--- a/
src/jalview/commands/ChangeCaseCommand.java
+++ b/
src/jalview/commands/ChangeCaseCommand.java
@@
-20,6
+20,8
@@
*/
package jalview.commands;
*/
package jalview.commands;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
@@
-101,13
+103,13
@@
public class ChangeCaseCommand implements CommandI
if ((caseChange == TO_UPPER && doCommand)
|| (caseChange == TO_LOWER && !doCommand))
{
if ((caseChange == TO_UPPER && doCommand)
|| (caseChange == TO_LOWER && !doCommand))
{
- newSeq.append(sequence.substring(start, end).toUpperCase());
+ newSeq.append(sequence.substring(start, end).toUpperCase(Locale.ROOT));
}
else if ((caseChange == TO_LOWER && doCommand)
|| (caseChange == TO_UPPER && !doCommand))
{
}
else if ((caseChange == TO_LOWER && doCommand)
|| (caseChange == TO_UPPER && !doCommand))
{
- newSeq.append(sequence.substring(start, end).toLowerCase());
+ newSeq.append(sequence.substring(start, end).toLowerCase(Locale.ROOT));
}
else
}
else
diff --git
a/src/jalview/commands/EditCommand.java
b/src/jalview/commands/EditCommand.java
index
d0790c8
..
30595bc
100644
(file)
--- a/
src/jalview/commands/EditCommand.java
+++ b/
src/jalview/commands/EditCommand.java
@@
-20,6
+20,8
@@
*/
package jalview.commands;
*/
package jalview.commands;
+import java.util.Locale;
+
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
@@
-789,7
+791,7
@@
public class EditCommand implements CommandI
String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
- if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+ if (!nogaprep.toLowerCase(Locale.ROOT).equals(nogapold.toLowerCase(Locale.ROOT)))
{
// we may already have dataset and limits stashed...
if (newDSWasNeeded || newStartEndWasNeeded)
{
// we may already have dataset and limits stashed...
if (newDSWasNeeded || newStartEndWasNeeded)
@@
-838,7
+840,7
@@
public class EditCommand implements CommandI
// old ds and edited ds are different, so
// create the new dataset sequence
SequenceI newds = new Sequence(oldds);
// old ds and edited ds are different, so
// create the new dataset sequence
SequenceI newds = new Sequence(oldds);
- newds.setSequence(fullseq.toUpperCase());
+ newds.setSequence(fullseq.toUpperCase(Locale.ROOT));
if (command.oldds == null)
{
if (command.oldds == null)
{
@@
-891,7
+893,7
@@
public class EditCommand implements CommandI
// new
// start/end
String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
// new
// start/end
String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
- command.seqs[i].getSequenceAsString().toUpperCase());
+ command.seqs[i].getSequenceAsString().toUpperCase(Locale.ROOT));
int newStart = command.seqs[i].getDatasetSequence()
.getSequenceAsString().indexOf(nogapalseq);
if (newStart == -1)
int newStart = command.seqs[i].getDatasetSequence()
.getSequenceAsString().indexOf(nogapalseq);
if (newStart == -1)
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
2ee4503
..
d41cdd4
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import java.util.Locale;
+
import jalview.analysis.Rna;
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.analysis.WUSSParseException;
import jalview.analysis.Rna;
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.analysis.WUSSParseException;
@@
-1225,7
+1227,7
@@
public class AlignmentAnnotation
{
if (seqname && this.sequenceRef != null)
{
{
if (seqname && this.sequenceRef != null)
{
- int i = description.toLowerCase().indexOf("<html>");
+ int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
if (i > -1)
{
// move the html tag to before the sequence reference.
if (i > -1)
{
// move the html tag to before the sequence reference.
diff --git
a/src/jalview/datamodel/DBRefEntry.java
b/src/jalview/datamodel/DBRefEntry.java
index
511287b
..
4a5c888
100755
(executable)
--- a/
src/jalview/datamodel/DBRefEntry.java
+++ b/
src/jalview/datamodel/DBRefEntry.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import java.util.Locale;
+
import jalview.api.DBRefEntryI;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.api.DBRefEntryI;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
@@
-95,7
+97,7
@@
public class DBRefEntry implements DBRefEntryI
Mapping map,boolean isCanonical)
{
Mapping map,boolean isCanonical)
{
- this.source = source.toUpperCase();
+ this.source = source.toUpperCase(Locale.ROOT);
setVersion(version);
this.accessionId = accessionId;
this.map = map;
setVersion(version);
this.accessionId = accessionId;
this.map = map;
@@
-306,7
+308,7
@@
public class DBRefEntry implements DBRefEntryI
public void setAccessionId(String accessionId)
{
this.accessionId = accessionId;
public void setAccessionId(String accessionId)
{
this.accessionId = accessionId;
-// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
+// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(Locale.ROOT);
}
/**
}
/**
@@
-317,7
+319,7
@@
public class DBRefEntry implements DBRefEntryI
{
this.source = source;
{
this.source = source;
-// this.source = (source == null ? "" : source).toUpperCase();
+// this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
}
// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
}
@@
-326,7
+328,7
@@
public class DBRefEntry implements DBRefEntryI
public void setVersion(String version)
{
this.version = version;
public void setVersion(String version)
{
this.version = version;
- this.ucversion = (version == null ? null : version.toUpperCase());
+ this.ucversion = (version == null ? null : version.toUpperCase(Locale.ROOT));
}
@Override
}
@Override
diff --git
a/src/jalview/datamodel/DBRefSource.java
b/src/jalview/datamodel/DBRefSource.java
index
2f94884
..
2d2ae4f
100755
(executable)
--- a/
src/jalview/datamodel/DBRefSource.java
+++ b/
src/jalview/datamodel/DBRefSource.java
@@
-36,29
+36,31
@@
package jalview.datamodel;
* @author JimP
*
*/
* @author JimP
*
*/
+import java.util.Locale;
+
public class DBRefSource
{
public static final String UNIPROT = "UNIPROT";
public class DBRefSource
{
public static final String UNIPROT = "UNIPROT";
- public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
+ public static final String UP_NAME = "UNIPROT_NAME".toUpperCase(Locale.ROOT);
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
- public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+ public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase(Locale.ROOT);
public static final String ENSEMBL = "ENSEMBL";
public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
public static final String EMBL = "EMBL";
public static final String EMBLCDS = "EMBLCDS";
public static final String ENSEMBL = "ENSEMBL";
public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
public static final String EMBL = "EMBL";
public static final String EMBLCDS = "EMBLCDS";
- public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase();
+ public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase(Locale.ROOT);
public static final String PDB = "PDB";
public static final String PFAM = "PFAM";
public static final String RFAM = "RFAM";
public static final String PDB = "PDB";
public static final String PFAM = "PFAM";
public static final String RFAM = "RFAM";
- public static final String GENEDB = "GeneDB".toUpperCase();
+ public static final String GENEDB = "GeneDB".toUpperCase(Locale.ROOT);
public static final String PDB_CANONICAL_NAME = PDB;
public static final String PDB_CANONICAL_NAME = PDB;
@@
-146,7
+148,7
@@
public class DBRefSource
// see if there is a primary reference that derived this reference.
for (int i = allSources.length; --i >= 0;)
{
// see if there is a primary reference that derived this reference.
for (int i = allSources.length; --i >= 0;)
{
- if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
+ if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase(Locale.ROOT) unnecessary here for allSources
{
// by convention, many secondary references inherit the primary
// reference's
{
// by convention, many secondary references inherit the primary
// reference's
diff --git
a/src/jalview/datamodel/MappedFeatures.java
b/src/jalview/datamodel/MappedFeatures.java
index
d652a97
..
f145d93
100644
(file)
--- a/
src/jalview/datamodel/MappedFeatures.java
+++ b/
src/jalview/datamodel/MappedFeatures.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import java.util.Locale;
+
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@
-199,12
+201,12
@@
public class MappedFeatures
* e.g. C,G,T gives variants G and T for base C
*/
Set<String> variantPeptides = new HashSet<>();
* e.g. C,G,T gives variants G and T for base C
*/
Set<String> variantPeptides = new HashSet<>();
- String[] alleles = alls.toUpperCase().split(",");
+ String[] alleles = alls.toUpperCase(Locale.ROOT).split(",");
StringBuilder vars = new StringBuilder();
for (String allele : alleles)
{
StringBuilder vars = new StringBuilder();
for (String allele : alleles)
{
- allele = allele.trim().toUpperCase();
+ allele = allele.trim().toUpperCase(Locale.ROOT);
if (allele.length() > 1 || "-".equals(allele))
{
continue; // multi-locus variant
if (allele.length() > 1 || "-".equals(allele))
{
continue; // multi-locus variant
@@
-220,7
+222,7
@@
public class MappedFeatures
*/
final int i = cdsPos == codonPos[0] ? 0
: (cdsPos == codonPos[1] ? 1 : 2);
*/
final int i = cdsPos == codonPos[0] ? 0
: (cdsPos == codonPos[1] ? 1 : 2);
- variantCodon[i] = allele.toUpperCase().charAt(0);
+ variantCodon[i] = allele.toUpperCase(Locale.ROOT).charAt(0);
if (variantCodon[i] == baseCodon[i])
{
continue;
if (variantCodon[i] == baseCodon[i])
{
continue;
diff --git
a/src/jalview/datamodel/features/FeatureMatcher.java
b/src/jalview/datamodel/features/FeatureMatcher.java
index
e9fb9b2
..
69f80f2
100644
(file)
--- a/
src/jalview/datamodel/features/FeatureMatcher.java
+++ b/
src/jalview/datamodel/features/FeatureMatcher.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel.features;
*/
package jalview.datamodel.features;
+import java.util.Locale;
+
import jalview.datamodel.SequenceFeature;
import jalview.util.MessageManager;
import jalview.util.matcher.Condition;
import jalview.datamodel.SequenceFeature;
import jalview.util.MessageManager;
import jalview.util.matcher.Condition;
@@
-163,12
+165,12
@@
public class FeatureMatcher implements FeatureMatcherI
firstField = descriptor.substring(0, nextSpacePos);
leftToParse = descriptor.substring(nextSpacePos + 1).trim();
}
firstField = descriptor.substring(0, nextSpacePos);
leftToParse = descriptor.substring(nextSpacePos + 1).trim();
}
- String lower = firstField.toLowerCase();
- if (lower.startsWith(LABEL.toLowerCase()))
+ String lower = firstField.toLowerCase(Locale.ROOT);
+ if (lower.startsWith(LABEL.toLowerCase(Locale.ROOT)))
{
byLabel = true;
}
{
byLabel = true;
}
- else if (lower.startsWith(SCORE.toLowerCase()))
+ else if (lower.startsWith(SCORE.toLowerCase(Locale.ROOT)))
{
byScore = true;
}
{
byScore = true;
}
@@
-351,7
+353,7
@@
public class FeatureMatcher implements FeatureMatcherI
}
Condition condition = matcher.getCondition();
}
Condition condition = matcher.getCondition();
- sb.append(SPACE).append(condition.toString().toLowerCase());
+ sb.append(SPACE).append(condition.toString().toLowerCase(Locale.ROOT));
if (condition.isNumeric())
{
sb.append(SPACE).append(matcher.getPattern());
if (condition.isNumeric())
{
sb.append(SPACE).append(matcher.getPattern());
diff --git
a/src/jalview/datamodel/features/FeatureMatcherSet.java
b/src/jalview/datamodel/features/FeatureMatcherSet.java
index
3743278
..
ee4bf12
100644
(file)
--- a/
src/jalview/datamodel/features/FeatureMatcherSet.java
+++ b/
src/jalview/datamodel/features/FeatureMatcherSet.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel.features;
*/
package jalview.datamodel.features;
+import java.util.Locale;
+
import jalview.datamodel.SequenceFeature;
import jalview.util.MessageManager;
import jalview.datamodel.SequenceFeature;
import jalview.util.MessageManager;
@@
-257,7
+259,7
@@
public class FeatureMatcherSet implements FeatureMatcherSetI
if (!first)
{
String joiner = andConditions ? AND_18N : OR_I18N;
if (!first)
{
String joiner = andConditions ? AND_18N : OR_I18N;
- sb.append(SPACE).append(joiner.toLowerCase()).append(SPACE);
+ sb.append(SPACE).append(joiner.toLowerCase(Locale.ROOT)).append(SPACE);
}
first = false;
if (multiple)
}
first = false;
if (multiple)
diff --git
a/src/jalview/ext/ensembl/EnsemblInfo.java
b/src/jalview/ext/ensembl/EnsemblInfo.java
index
97ad242
..
e2d2725
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/
src/jalview/ext/ensembl/EnsemblInfo.java
@@
-20,6
+20,8
@@
*/
package jalview.ext.ensembl;
*/
package jalview.ext.ensembl;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.util.JSONUtils;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.util.JSONUtils;
@@
-94,7
+96,7
@@
public class EnsemblInfo extends EnsemblRestClient
{
fetchDivisions();
}
{
fetchDivisions();
}
- return divisions.get(division.toUpperCase());
+ return divisions.get(division.toUpperCase(Locale.ROOT));
}
/**
}
/**
@@
-108,7
+110,7
@@
public class EnsemblInfo extends EnsemblRestClient
/*
* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
*/
/*
* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
*/
- divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
+ divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT), ensemblDomain);
try
{
@SuppressWarnings("unchecked")
try
{
@SuppressWarnings("unchecked")
@@
-118,7
+120,7
@@
public class EnsemblInfo extends EnsemblRestClient
while (rvals.hasNext())
{
String division = rvals.next().toString();
while (rvals.hasNext())
{
String division = rvals.next().toString();
- divisions.put(division.toUpperCase(), ensemblGenomesDomain);
+ divisions.put(division.toUpperCase(Locale.ROOT), ensemblGenomesDomain);
}
} catch (IOException | ParseException | NumberFormatException e)
{
}
} catch (IOException | ParseException | NumberFormatException e)
{
diff --git
a/src/jalview/ext/jmol/JmolParser.java
b/src/jalview/ext/jmol/JmolParser.java
index
18d8e05
..
2a43244
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-20,6
+20,8
@@
*/
package jalview.ext.jmol;
*/
package jalview.ext.jmol;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
@@
-115,7
+117,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
// }
// ;
// instead, we distinguish .cif from non-.cif by filename
// }
// ;
// instead, we distinguish .cif from non-.cif by filename
- setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
+ setStructureFileType(getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
? PDBEntry.Type.MMCIF.toString()
: "PDB");
? PDBEntry.Type.MMCIF.toString()
: "PDB");
diff --git
a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index
ced22fa
..
02b7136
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@
-20,6
+20,8
@@
*/
package jalview.ext.rbvi.chimera;
*/
package jalview.ext.rbvi.chimera;
+import java.util.Locale;
+
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
@@
-181,7
+183,7
@@
public class ChimeraCommands extends StructureCommandsBase
* Chimera treats an attribute name ending in 'color' as colour-valued;
* Jalview doesn't, so prevent this by appending an underscore
*/
* Chimera treats an attribute name ending in 'color' as colour-valued;
* Jalview doesn't, so prevent this by appending an underscore
*/
- if (attName.toUpperCase().endsWith("COLOR"))
+ if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR"))
{
attName += "_";
}
{
attName += "_";
}
diff --git
a/src/jalview/fts/core/FTSRestClient.java
b/src/jalview/fts/core/FTSRestClient.java
index
b1cfc53
..
0bca070
100644
(file)
--- a/
src/jalview/fts/core/FTSRestClient.java
+++ b/
src/jalview/fts/core/FTSRestClient.java
@@
-20,6
+20,8
@@
*/
package jalview.fts.core;
*/
package jalview.fts.core;
+import java.util.Locale;
+
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
@@
-171,7
+173,7
@@
public abstract class FTSRestClient implements FTSRestClientI
public DataTypeI getDataType()
{
final String[] dataTypeString = lineData[2].split("\\|");
public DataTypeI getDataType()
{
final String[] dataTypeString = lineData[2].split("\\|");
- final String classString = dataTypeString[0].toUpperCase();
+ final String classString = dataTypeString[0].toUpperCase(Locale.ROOT);
return new DataTypeI()
{
return new DataTypeI()
{
@@
-182,7
+184,7
@@
public abstract class FTSRestClient implements FTSRestClientI
if (dataTypeString.length > 1
&& dataTypeString[1] != null)
{
if (dataTypeString.length > 1
&& dataTypeString[1] != null)
{
- switch (dataTypeString[1].toUpperCase())
+ switch (dataTypeString[1].toUpperCase(Locale.ROOT))
{
case "T":
case "TRUE":
{
case "T":
case "TRUE":
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
c5b90a9
..
8deff01
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
@@
-484,9
+486,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
});
}
}
});
- if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
.indexOf("devel") > -1
.indexOf("devel") > -1
- || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
.indexOf("test") > -1)
{
formatMenu.add(vsel);
.indexOf("test") > -1)
{
formatMenu.add(vsel);
@@
-4297,7
+4299,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
jws2servs.attachWSMenuEntry(webService, me);
for (Jws2Instance sv : jws2servs.getServices())
{
jws2servs.attachWSMenuEntry(webService, me);
for (Jws2Instance sv : jws2servs.getServices())
{
- if (sv.description.toLowerCase().contains("jpred"))
+ if (sv.description.toLowerCase(Locale.ROOT).contains("jpred"))
{
for (JMenuItem jmi : legacyItems)
{
{
for (JMenuItem jmi : legacyItems)
{
diff --git
a/src/jalview/gui/AnnotationExporter.java
b/src/jalview/gui/AnnotationExporter.java
index
d84287f
..
568ca47
100644
(file)
--- a/
src/jalview/gui/AnnotationExporter.java
+++ b/
src/jalview/gui/AnnotationExporter.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.api.FeatureRenderer;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.api.FeatureRenderer;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
@@
-337,7
+339,7
@@
public class AnnotationExporter extends JPanel
boolean nucleotide = ap.av.isNucleotide();
String complement = nucleotide
boolean nucleotide = ap.av.isNucleotide();
String complement = nucleotide
- ? MessageManager.getString("label.protein").toLowerCase()
+ ? MessageManager.getString("label.protein").toLowerCase(Locale.ROOT)
: "CDS";
JLabel label = new JLabel(
MessageManager.formatMessage("label.include_linked_features",
: "CDS";
JLabel label = new JLabel(
MessageManager.formatMessage("label.include_linked_features",
diff --git
a/src/jalview/gui/AnnotationLabels.java
b/src/jalview/gui/AnnotationLabels.java
index
5a681f1
..
21c45e9
100755
(executable)
--- a/
src/jalview/gui/AnnotationLabels.java
+++ b/
src/jalview/gui/AnnotationLabels.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentUtils;
import jalview.datamodel.Alignment;
import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentUtils;
import jalview.datamodel.Alignment;
@@
-754,12
+756,12
@@
public class AnnotationLabels extends JPanel
// jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
// tooltips
String desc = aa.getDescription(true).trim();
// jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
// tooltips
String desc = aa.getDescription(true).trim();
- if (!desc.toLowerCase().startsWith(HTML_START_TAG))
+ if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG))
{
tooltip.append(HTML_START_TAG);
desc = desc.replace("<", "<");
}
{
tooltip.append(HTML_START_TAG);
desc = desc.replace("<", "<");
}
- else if (desc.toLowerCase().endsWith(HTML_END_TAG))
+ else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG))
{
desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
}
{
desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
}
diff --git
a/src/jalview/gui/AppJmol.java
b/src/jalview/gui/AppJmol.java
index
458abc6
..
217d2b1
100644
(file)
--- a/
src/jalview/gui/AppJmol.java
+++ b/
src/jalview/gui/AppJmol.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
@@
-434,7
+436,7
@@
public class AppJmol extends StructureViewerBase
jmb.jmolViewer.renderScreenImage(g, width, height);
}
};
jmb.jmolViewer.renderScreenImage(g, width, height);
}
};
- String view = MessageManager.getString("action.view").toLowerCase();
+ String view = MessageManager.getString("action.view").toLowerCase(Locale.ROOT);
ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
exporter.doExport(null, this, width, height, view);
ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
exporter.doExport(null, this, width, height, view);
diff --git
a/src/jalview/gui/Desktop.java
b/src/jalview/gui/Desktop.java
index
67ef952
..
666fb4e
100644
(file)
--- a/
src/jalview/gui/Desktop.java
+++ b/
src/jalview/gui/Desktop.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
@@
-1055,7
+1057,7
@@
public class Desktop extends jalview.jbgui.GDesktop
String url = (history instanceof JTextField ? ((JTextField) history).getText()
: ((JComboBox<String>) history).getEditor().getItem().toString().trim());
String url = (history instanceof JTextField ? ((JTextField) history).getText()
: ((JComboBox<String>) history).getEditor().getItem().toString().trim());
- if (url.toLowerCase().endsWith(".jar")) {
+ if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) {
if (viewport != null) {
new FileLoader().LoadFile(viewport, url, DataSourceType.URL, FileFormat.Jalview);
} else {
if (viewport != null) {
new FileLoader().LoadFile(viewport, url, DataSourceType.URL, FileFormat.Jalview);
} else {
@@
-1181,7
+1183,7
@@
public class Desktop extends jalview.jbgui.GDesktop
// message.append("<br>...Checking latest version...</br>");
} else if (!latestVersion.equals(Cache.getProperty("VERSION"))) {
boolean red = false;
// message.append("<br>...Checking latest version...</br>");
} else if (!latestVersion.equals(Cache.getProperty("VERSION"))) {
boolean red = false;
- if (Cache.getProperty("VERSION").toLowerCase().indexOf("automated build") == -1) {
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT).indexOf("automated build") == -1) {
red = true;
// Displayed when code version and jnlp version do not match and code
// version is not a development build
red = true;
// Displayed when code version and jnlp version do not match and code
// version is not a development build
@@
-2669,7
+2671,7
@@
public class Desktop extends jalview.jbgui.GDesktop
continue;
}
java.net.URI uri = new java.net.URI(s);
continue;
}
java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase().startsWith("http")) {
+ if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http")) {
protocols.add(DataSourceType.URL);
files.add(uri.toString());
} else {
protocols.add(DataSourceType.URL);
files.add(uri.toString());
} else {
@@
-2706,7
+2708,7
@@
public class Desktop extends jalview.jbgui.GDesktop
// resolve any .lnk files in the file drop
for (int f = 0; f < files.size(); f++) {
// resolve any .lnk files in the file drop
for (int f = 0; f < files.size(); f++) {
- String source = files.get(f).toString().toLowerCase();
+ String source = files.get(f).toString().toLowerCase(Locale.ROOT);
if (protocols.get(f).equals(DataSourceType.FILE)
&& (source.endsWith(".lnk") || source.endsWith(".url") || source.endsWith(".site"))) {
try {
if (protocols.get(f).equals(DataSourceType.FILE)
&& (source.endsWith(".lnk") || source.endsWith(".url") || source.endsWith(".site"))) {
try {
diff --git
a/src/jalview/gui/FeatureSettings.java
b/src/jalview/gui/FeatureSettings.java
index
e636455
..
572ada6
100644
(file)
--- a/
src/jalview/gui/FeatureSettings.java
+++ b/
src/jalview/gui/FeatureSettings.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
@@
-1529,7
+1531,7
@@
public class FeatureSettings extends JPanel
String text = MessageManager.formatMessage("label.show_linked_features",
nucleotide
? MessageManager.getString("label.protein")
String text = MessageManager.formatMessage("label.show_linked_features",
nucleotide
? MessageManager.getString("label.protein")
- .toLowerCase()
+ .toLowerCase(Locale.ROOT)
: "CDS");
showComplement = new JCheckBox(text);
showComplement.addActionListener(new ActionListener()
: "CDS");
showComplement = new JCheckBox(text);
showComplement.addActionListener(new ActionListener()
diff --git
a/src/jalview/gui/Finder.java
b/src/jalview/gui/Finder.java
index
df56986
..
93dcadf
100755
(executable)
--- a/
src/jalview/gui/Finder.java
+++ b/
src/jalview/gui/Finder.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.FocusAdapter;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.FocusAdapter;
@@
-335,7
+337,7
@@
public class Finder extends GFinder
if (idMatch.size() > 0 && searchResults.getCount() > 0)
{
message.append(" ").append(
if (idMatch.size() > 0 && searchResults.getCount() > 0)
{
message.append(" ").append(
- MessageManager.getString("label.and").toLowerCase())
+ MessageManager.getString("label.and").toLowerCase(Locale.ROOT))
.append(" ");
}
message.append(MessageManager.formatMessage(
.append(" ");
}
message.append(MessageManager.formatMessage(
diff --git
a/src/jalview/gui/JDatabaseTree.java
b/src/jalview/gui/JDatabaseTree.java
index
8d62433
..
7bdcb2e
100644
(file)
--- a/
src/jalview/gui/JDatabaseTree.java
+++ b/
src/jalview/gui/JDatabaseTree.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.util.MessageManager;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.util.MessageManager;
import jalview.ws.seqfetcher.DbSourceProxy;
@@
-227,11
+229,11
@@
public class JDatabaseTree extends JalviewDialog implements KeyListener
if (child.getUserObject() instanceof DbSourceProxy)
{
names[i] = ((DbSourceProxy) child.getUserObject()).getDbName()
if (child.getUserObject() instanceof DbSourceProxy)
{
names[i] = ((DbSourceProxy) child.getUserObject()).getDbName()
- .toLowerCase();
+ .toLowerCase(Locale.ROOT);
}
else
{
}
else
{
- names[i] = ((String) child.getUserObject()).toLowerCase();
+ names[i] = ((String) child.getUserObject()).toLowerCase(Locale.ROOT);
sortTreeNodes(child);
}
}
sortTreeNodes(child);
}
}
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
2a7fb9f
..
6b32efa
100644
(file)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
@@
-1125,7
+1127,7
@@
public class PopupMenu extends JPopupMenu implements ColourChangeListener
for (int d = 0; d < nd; d++)
{
DBRefEntry e = dbr.get(d);
for (int d = 0; d < nd; d++)
{
DBRefEntry e = dbr.get(d);
- String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
Object[] sarray = commonDbrefs.get(src);
if (sarray == null)
{
Object[] sarray = commonDbrefs.get(src);
if (sarray == null)
{
@@
-1171,7
+1173,7
@@
public class PopupMenu extends JPopupMenu implements ColourChangeListener
boolean usingNames = false;
// Now see which parts of the group apply for this URL
String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
boolean usingNames = false;
// Now see which parts of the group apply for this URL
String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
- Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
+ Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
String[] seqstr, ids; // input to makeUrl
if (idset != null)
{
String[] seqstr, ids; // input to makeUrl
if (idset != null)
{
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
849c278
..
9f9de6e
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-21,6
+21,8
@@
package jalview.gui;
package jalview.gui;
+import java.util.Locale;
+
import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.Collection;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.Collection;
@@
-1019,7
+1021,7
@@
public class StructureChooser extends GStructureChooser
if (pdbIdStr.split(":").length > 1)
{
pdbEntry.setId(pdbIdStr.split(":")[0]);
if (pdbIdStr.split(":").length > 1)
{
pdbEntry.setId(pdbIdStr.split(":")[0]);
- pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
}
else
{
}
else
{
@@
-1246,7
+1248,7
@@
public class StructureChooser extends GStructureChooser
// TODO move this pdb id search into the PDB specific
// FTSSearchEngine
// for moment, it will work fine as is because it is self-contained
// TODO move this pdb id search into the PDB specific
// FTSSearchEngine
// for moment, it will work fine as is because it is self-contained
- String searchTerm = text.toLowerCase();
+ String searchTerm = text.toLowerCase(Locale.ROOT);
searchTerm = searchTerm.split(":")[0];
// System.out.println(">>>>> search term : " + searchTerm);
List<FTSDataColumnI> wantedFields = new ArrayList<>();
searchTerm = searchTerm.split(":")[0];
// System.out.println(">>>>> search term : " + searchTerm);
List<FTSDataColumnI> wantedFields = new ArrayList<>();
diff --git
a/src/jalview/gui/TreePanel.java
b/src/jalview/gui/TreePanel.java
index
2d8e729
..
b730df4
100755
(executable)
--- a/
src/jalview/gui/TreePanel.java
+++ b/
src/jalview/gui/TreePanel.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
@@
-693,7
+695,7
@@
public class TreePanel extends GTreePanel
String tree = MessageManager.getString("label.tree");
ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
tree);
String tree = MessageManager.getString("label.tree");
ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
tree);
- exporter.doExport(null, this, width, height, tree.toLowerCase());
+ exporter.doExport(null, this, width, height, tree.toLowerCase(Locale.ROOT));
}
/**
}
/**
@@
-723,7
+725,7
@@
public class TreePanel extends GTreePanel
// search dbrefs, features and annotation
List<DBRefEntry> refs = jalview.util.DBRefUtils
.selectRefs(sq.getDBRefs(), new String[]
// search dbrefs, features and annotation
List<DBRefEntry> refs = jalview.util.DBRefUtils
.selectRefs(sq.getDBRefs(), new String[]
- { labelClass.toUpperCase() });
+ { labelClass.toUpperCase(Locale.ROOT) });
if (refs != null)
{
for (int i = 0, ni = refs.size(); i < ni; i++)
if (refs != null)
{
for (int i = 0, ni = refs.size(); i < ni; i++)
@@
-786,7
+788,7
@@
public class TreePanel extends GTreePanel
* i18n description of Neighbour Joining or Average Distance method
*/
String treecalcnm = MessageManager
* i18n description of Neighbour Joining or Average Distance method
*/
String treecalcnm = MessageManager
- .getString("label.tree_calc_" + treeType.toLowerCase());
+ .getString("label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
/*
* short score model name (long description can be too long)
/*
* short score model name (long description can be too long)
diff --git
a/src/jalview/gui/UserDefinedColours.java
b/src/jalview/gui/UserDefinedColours.java
index
4846049
..
c3f132b
100755
(executable)
--- a/
src/jalview/gui/UserDefinedColours.java
+++ b/
src/jalview/gui/UserDefinedColours.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.bin.Cache;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
@@
-205,8
+207,8
@@
public class UserDefinedColours extends GUserDefinedColours
{
int row = i / cols + 1;
int index = (row * cols) + i;
{
int row = i / cols + 1;
int index = (row * cols) + i;
- JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(),
- ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
+ JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(Locale.ROOT),
+ ResidueProperties.aa[i].toLowerCase(Locale.ROOT), lowerCaseButtons, i);
buttonPanel.add(button, index);
}
buttonPanel.add(button, index);
}
diff --git
a/src/jalview/gui/WebserviceInfo.java
b/src/jalview/gui/WebserviceInfo.java
index
0773a7b
..
ee1b473
100644
(file)
--- a/
src/jalview/gui/WebserviceInfo.java
+++ b/
src/jalview/gui/WebserviceInfo.java
@@
-20,6
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
@@
-545,7
+547,7
@@
public class WebserviceInfo extends GWebserviceInfo
{
return null;
}
{
return null;
}
- String lowertxt = text.toLowerCase();
+ String lowertxt = text.toLowerCase(Locale.ROOT);
int htmlpos = leaveFirst ? -1 : lowertxt.indexOf("<body");
int htmlend = leaveLast ? -1 : lowertxt.indexOf("</body");
int htmlpos = leaveFirst ? -1 : lowertxt.indexOf("<body");
int htmlend = leaveLast ? -1 : lowertxt.indexOf("</body");
@@
-574,7
+576,7
@@
public class WebserviceInfo extends GWebserviceInfo
{
return "";
}
{
return "";
}
- String lowertxt = text.toLowerCase();
+ String lowertxt = text.toLowerCase(Locale.ROOT);
int htmlpos = lowertxt.indexOf("<body");
int htmlend = lowertxt.indexOf("</body");
int doctype = lowertxt.indexOf("<!doctype");
int htmlpos = lowertxt.indexOf("<body");
int htmlend = lowertxt.indexOf("</body");
int doctype = lowertxt.indexOf("<!doctype");
diff --git
a/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
b/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
index
6651272
..
727d8e0
100644
(file)
--- a/
src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
+++ b/
src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
@@
-1,5
+1,7
@@
package jalview.gui.structurechooser;
package jalview.gui.structurechooser;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
@@
-78,7
+80,7
@@
public class PDBStructureChooserQuerySource
{
if (isValidSeqName(entry.getId()))
{
{
if (isValidSeqName(entry.getId()))
{
- String id = entry.getId().toLowerCase();
+ String id = entry.getId().toLowerCase(Locale.ROOT);
queryBuilder.append("pdb_id:").append(id).append(" OR ");
isPDBRefsFound = true;
pdbids.add(id);
queryBuilder.append("pdb_id:").append(id).append(" OR ");
isPDBRefsFound = true;
pdbids.add(id);
@@
-106,7
+108,7
@@
public class PDBStructureChooserQuerySource
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- String id = getDBRefId(dbRef).toLowerCase();
+ String id = getDBRefId(dbRef).toLowerCase(Locale.ROOT);
if (!pdbids.contains(id))
{
queryBuilder.append("pdb_id:").append(id).append(" OR ");
if (!pdbids.contains(id))
{
queryBuilder.append("pdb_id:").append(id).append(" OR ");
@@
-126,7
+128,7
@@
public class PDBStructureChooserQuerySource
{
String seqName = seq.getName();
seqName = sanitizeSeqName(seqName);
{
String seqName = seq.getName();
seqName = sanitizeSeqName(seqName);
- String[] names = seqName.toLowerCase().split("\\|");
+ String[] names = seqName.toLowerCase(Locale.ROOT).split("\\|");
for (String name : names)
{
// System.out.println("Found name : " + name);
for (String name : names)
{
// System.out.println("Found name : " + name);
@@
-185,7
+187,7
@@
public class PDBStructureChooserQuerySource
{
return false;
}
{
return false;
}
- seqName = seqName.toLowerCase();
+ seqName = seqName.toLowerCase(Locale.ROOT);
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
diff --git
a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
index
a4ae2c8
..
1aad2e0
100644
(file)
--- a/
src/jalview/gui/structurechooser/StructureChooserQuerySource.java
+++ b/
src/jalview/gui/structurechooser/StructureChooserQuerySource.java
@@
-1,5
+1,7
@@
package jalview.gui.structurechooser;
package jalview.gui.structurechooser;
+import java.util.Locale;
+
import java.util.Collection;
import java.util.List;
import java.util.Objects;
import java.util.Collection;
import java.util.List;
import java.util.Objects;
@@
-108,7
+110,7
@@
public abstract class StructureChooserQuerySource
{
return false;
}
{
return false;
}
- seqName = seqName.toLowerCase();
+ seqName = seqName.toLowerCase(Locale.ROOT);
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
diff --git
a/src/jalview/gui/structurechooser/TDBResultAnalyser.java
b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
index
9f57100
..
d3896a5
100644
(file)
--- a/
src/jalview/gui/structurechooser/TDBResultAnalyser.java
+++ b/
src/jalview/gui/structurechooser/TDBResultAnalyser.java
@@
-1,5
+1,7
@@
package jalview.gui.structurechooser;
package jalview.gui.structurechooser;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
@@
-85,7
+87,7
@@
public class TDBResultAnalyser
{
return 0;
}
{
return 0;
}
- String upper_cat = cat.toUpperCase();
+ String upper_cat = cat.toUpperCase(Locale.ROOT);
int idx = EXP_CATEGORIES.indexOf(upper_cat);
if (idx == -1)
{
int idx = EXP_CATEGORIES.indexOf(upper_cat);
if (idx == -1)
{
@@
-136,11
+138,11
@@
public class TDBResultAnalyser
int o1_s = (Integer) o1data[idx_ups];
int o1_e = (Integer) o1data[idx_upe];
int o1_cat = scoreCategory((String) o1data[idx_mcat]);
int o1_s = (Integer) o1data[idx_ups];
int o1_e = (Integer) o1data[idx_upe];
int o1_cat = scoreCategory((String) o1data[idx_mcat]);
- String o1_prov= ((String) o1data[idx_mprov]).toUpperCase();
+ String o1_prov= ((String) o1data[idx_mprov]).toUpperCase(Locale.ROOT);
int o2_s = (Integer) o2data[idx_ups];
int o2_e = (Integer) o2data[idx_upe];
int o2_cat = scoreCategory((String) o2data[idx_mcat]);
int o2_s = (Integer) o2data[idx_ups];
int o2_e = (Integer) o2data[idx_upe];
int o2_cat = scoreCategory((String) o2data[idx_mcat]);
- String o2_prov= ((String) o2data[idx_mprov]).toUpperCase();
+ String o2_prov= ((String) o2data[idx_mprov]).toUpperCase(Locale.ROOT);
if (o1_cat == o2_cat)
if (o1_cat == o2_cat)
diff --git
a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index
9b6d8e8
..
7a311f8
100644
(file)
--- a/
src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/
src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@
-138,7
+138,7
@@
public class ThreeDBStructureChooserQuerySource
{
return false;
}
{
return false;
}
- seqName = seqName.toLowerCase();
+ seqName = seqName.toLowerCase(Locale.ROOT);
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
4916bb3
..
e9c9ce2
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
@@
-443,7
+445,7
@@
public class AppletFormatAdapter
String data = dataObject.toString();
DataSourceType protocol = DataSourceType.PASTE;
String data = dataObject.toString();
DataSourceType protocol = DataSourceType.PASTE;
- String ft = data.toLowerCase().trim();
+ String ft = data.toLowerCase(Locale.ROOT).trim();
if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
|| ft.indexOf("file:") == 0)
{
if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
|| ft.indexOf("file:") == 0)
{
diff --git
a/src/jalview/io/FeaturesFile.java
b/src/jalview/io/FeaturesFile.java
index
c08c84e
..
dda59a7
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
@@
-234,7
+236,7
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
// skip comments/process pragmas
if (line.length() == 0 || line.startsWith("#"))
{
// skip comments/process pragmas
if (line.length() == 0 || line.startsWith("#"))
{
- if (line.toLowerCase().startsWith("##"))
+ if (line.toLowerCase(Locale.ROOT).startsWith("##"))
{
processGffPragma(line, gffProps, align, newseqs);
}
{
processGffPragma(line, gffProps, align, newseqs);
}
@@
-346,7
+348,7
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
String line;
while ((line = nextLine()) != null)
{
String line;
while ((line = nextLine()) != null)
{
- if (line.toUpperCase().startsWith(ENDFILTERS))
+ if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS))
{
return;
}
{
return;
}
diff --git
a/src/jalview/io/FileFormats.java
b/src/jalview/io/FileFormats.java
index
aadcdb9
..
9e0a7f7
100644
(file)
--- a/
src/jalview/io/FileFormats.java
+++ b/
src/jalview/io/FileFormats.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedHashMap;
@@
-102,7
+104,7
@@
public class FileFormats
protected void registerFileFormat(FileFormatI format,
boolean isIdentifiable)
{
protected void registerFileFormat(FileFormatI format,
boolean isIdentifiable)
{
- String name = format.getName().toUpperCase();
+ String name = format.getName().toUpperCase(Locale.ROOT);
if (formats.containsKey(name))
{
System.err.println("Overwriting file format: " + format.getName());
if (formats.containsKey(name))
{
System.err.println("Overwriting file format: " + format.getName());
@@
-121,7
+123,7
@@
public class FileFormats
*/
public void deregisterFileFormat(String name)
{
*/
public void deregisterFileFormat(String name)
{
- FileFormatI ff = formats.remove(name.toUpperCase());
+ FileFormatI ff = formats.remove(name.toUpperCase(Locale.ROOT));
identifiable.remove(ff);
}
identifiable.remove(ff);
}
@@
-174,7
+176,7
@@
public class FileFormats
*/
public FileFormatI forName(String format)
{
*/
public FileFormatI forName(String format)
{
- return format == null ? null : formats.get(format.toUpperCase());
+ return format == null ? null : formats.get(format.toUpperCase(Locale.ROOT));
}
/**
}
/**
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
85cf48a
..
31751f5
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
@@
-162,7
+164,7
@@
public class FormatAdapter extends AppletFormatAdapter
public boolean getCacheSuffixDefault(FileFormatI format)
{
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+ return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
true);
}
true);
}
diff --git
a/src/jalview/io/IdentifyFile.java
b/src/jalview/io/IdentifyFile.java
index
e7ee711
..
5a3d700
100755
(executable)
--- a/
src/jalview/io/IdentifyFile.java
+++ b/
src/jalview/io/IdentifyFile.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import java.io.File;
import java.io.IOException;
import java.io.File;
import java.io.IOException;
@@
-178,7
+180,7
@@
public class IdentifyFile
break;
}
}
break;
}
}
- data = data.toUpperCase();
+ data = data.toUpperCase(Locale.ROOT);
if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
@@
-332,7
+334,7
@@
public class IdentifyFile
if ((lessThan > -1)) // possible Markup Language data i.e HTML,
// RNAML, XML
{
if ((lessThan > -1)) // possible Markup Language data i.e HTML,
// RNAML, XML
{
- String upper = data.toUpperCase();
+ String upper = data.toUpperCase(Locale.ROOT);
if (upper.substring(lessThan).startsWith("<HTML"))
{
reply = FileFormat.Html;
if (upper.substring(lessThan).startsWith("<HTML"))
{
reply = FileFormat.Html;
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
6af92b7
..
ab2c00a
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-25,6
+25,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
@@
-409,7
+411,7
@@
public class JPredFile extends AlignFile
// check that no stray annotations have been added at the end.
{
SequenceI sq = seqs.elementAt(j - 1);
// check that no stray annotations have been added at the end.
{
SequenceI sq = seqs.elementAt(j - 1);
- if (sq.getName().toUpperCase().startsWith("JPRED"))
+ if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
{
annotSeqs.addElement(sq);
seqs.removeElementAt(--j);
{
annotSeqs.addElement(sq);
seqs.removeElementAt(--j);
diff --git
a/src/jalview/io/JalviewFileFilter.java
b/src/jalview/io/JalviewFileFilter.java
index
bc20342
..
28dd2eb
100755
(executable)
--- a/
src/jalview/io/JalviewFileFilter.java
+++ b/
src/jalview/io/JalviewFileFilter.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import java.io.File;
import java.util.Hashtable;
import java.util.Iterator;
import java.io.File;
import java.util.Hashtable;
import java.util.Iterator;
@@
-134,7
+136,7
@@
public class JalviewFileFilter extends FileFilter
if ((i > 0) && (i < (filename.length() - 1)))
{
if ((i > 0) && (i < (filename.length() - 1)))
{
- return filename.substring(i + 1).toLowerCase();
+ return filename.substring(i + 1).toLowerCase(Locale.ROOT);
}
;
}
;
@@
-150,7
+152,7
@@
public class JalviewFileFilter extends FileFilter
filters = new LinkedHashMap<>(5);
}
filters = new LinkedHashMap<>(5);
}
- filters.put(extension.toLowerCase(), this);
+ filters.put(extension.toLowerCase(Locale.ROOT), this);
fullDescription = null;
}
fullDescription = null;
}
diff --git
a/src/jalview/io/JalviewFileView.java
b/src/jalview/io/JalviewFileView.java
index
52d130c
..
b90bd7a
100755
(executable)
--- a/
src/jalview/io/JalviewFileView.java
+++ b/
src/jalview/io/JalviewFileView.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.util.MessageManager;
import java.io.File;
import jalview.util.MessageManager;
import java.io.File;
@@
-47,7
+49,7
@@
public class JalviewFileView extends FileView
String exts = ff.getExtensions();
for (String ext : exts.split(","))
{
String exts = ff.getExtensions();
for (String ext : exts.split(","))
{
- ext = ext.trim().toLowerCase();
+ ext = ext.trim().toLowerCase(Locale.ROOT);
extensions.put(ext,
desc + ("jar".equals(ext) ? " (old)" : ""));
}
extensions.put(ext,
desc + ("jar".equals(ext) ? " (old)" : ""));
}
@@
-136,7
+138,7
@@
public class JalviewFileView extends FileView
if ((i > 0) && (i < (s.length() - 1)))
{
if ((i > 0) && (i < (s.length() - 1)))
{
- ext = s.substring(i + 1).toLowerCase();
+ ext = s.substring(i + 1).toLowerCase(Locale.ROOT);
}
return ext;
}
return ext;
diff --git
a/src/jalview/io/JnetAnnotationMaker.java
b/src/jalview/io/JnetAnnotationMaker.java
index
6828202
..
27fc869
100755
(executable)
--- a/
src/jalview/io/JnetAnnotationMaker.java
+++ b/
src/jalview/io/JnetAnnotationMaker.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
@@
-88,7
+90,7
@@
public class JnetAnnotationMaker
while (i < preds.length)
{
while (i < preds.length)
{
- String id = preds[i].getName().toUpperCase();
+ String id = preds[i].getName().toUpperCase(Locale.ROOT);
if (id.startsWith("LUPAS") || id.startsWith("JNET")
|| id.startsWith("JPRED"))
if (id.startsWith("LUPAS") || id.startsWith("JNET")
|| id.startsWith("JPRED"))
diff --git
a/src/jalview/io/MSFfile.java
b/src/jalview/io/MSFfile.java
index
df2bed2
..
e954703
100755
(executable)
--- a/
src/jalview/io/MSFfile.java
+++ b/
src/jalview/io/MSFfile.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
@@
-184,7
+186,7
@@
public class MSFfile extends AlignFile
public int checkSum(String seq)
{
int check = 0;
public int checkSum(String seq)
{
int check = 0;
- String sequence = seq.toUpperCase();
+ String sequence = seq.toUpperCase(Locale.ROOT);
for (int i = 0; i < sequence.length(); i++)
{
for (int i = 0; i < sequence.length(); i++)
{
diff --git
a/src/jalview/io/NewickFile.java
b/src/jalview/io/NewickFile.java
index
f3eaa45
..
ec5d267
100755
(executable)
--- a/
src/jalview/io/NewickFile.java
+++ b/
src/jalview/io/NewickFile.java
@@
-26,6
+26,8
@@
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.SequenceNode;
import jalview.util.MessageManager;
import jalview.datamodel.SequenceNode;
import jalview.util.MessageManager;
@@
-656,7
+658,7
@@
public class NewickFile extends FileParse
try
{
// parse out code/value pairs
try
{
// parse out code/value pairs
- if (code.toLowerCase().equals("b"))
+ if (code.toLowerCase(Locale.ROOT).equals("b"))
{
int v = -1;
Float iv = Float.valueOf(value);
{
int v = -1;
Float iv = Float.valueOf(value);
diff --git
a/src/jalview/io/SequenceAnnotationReport.java
b/src/jalview/io/SequenceAnnotationReport.java
index
8e4e783
..
62b723d
100644
(file)
--- a/
src/jalview/io/SequenceAnnotationReport.java
+++ b/
src/jalview/io/SequenceAnnotationReport.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import java.util.Collection;
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.Collection;
import java.util.Comparator;
import java.util.LinkedHashMap;
@@
-273,7
+275,7
@@
public class SequenceAnnotationReport
* truncate overlong descriptions unless they contain an href
* before the truncation point (as truncation could leave corrupted html)
*/
* truncate overlong descriptions unless they contain an href
* before the truncation point (as truncation could leave corrupted html)
*/
- int linkindex = description.toLowerCase().indexOf("<a ");
+ int linkindex = description.toLowerCase(Locale.ROOT).indexOf("<a ");
boolean hasLink = linkindex > -1
&& linkindex < MAX_DESCRIPTION_LENGTH;
if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
boolean hasLink = linkindex > -1
&& linkindex < MAX_DESCRIPTION_LENGTH;
if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
@@
-400,8
+402,8
@@
public class SequenceAnnotationReport
+ "\" target=\""
+ urllink.get(0)
+ "\">"
+ "\" target=\""
+ urllink.get(0)
+ "\">"
- + (urllink.get(0).toLowerCase()
- .equals(urllink.get(1).toLowerCase()) ? urllink
+ + (urllink.get(0).toLowerCase(Locale.ROOT)
+ .equals(urllink.get(1).toLowerCase(Locale.ROOT)) ? urllink
.get(0) : (urllink.get(0) + ":" + urllink
.get(1)))
+ "</a><br/>");
.get(0) : (urllink.get(0) + ":" + urllink
.get(1)))
+ "</a><br/>");
diff --git
a/src/jalview/io/StockholmFile.java
b/src/jalview/io/StockholmFile.java
index
8b26757
..
c8c9c8a
100644
(file)
--- a/
src/jalview/io/StockholmFile.java
+++ b/
src/jalview/io/StockholmFile.java
@@
-23,6
+23,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
@@
-1110,7
+1112,7
@@
public class StockholmFile extends AlignFile
}
else
{
}
else
{
- key = type2id(aa.label.toLowerCase());
+ key = type2id(aa.label.toLowerCase(Locale.ROOT));
if (key == null)
{
label = aa.label;
if (key == null)
{
label = aa.label;
diff --git
a/src/jalview/io/gff/ExonerateHelper.java
b/src/jalview/io/gff/ExonerateHelper.java
index
da0c245
..
9ce4cc6
100644
(file)
--- a/
src/jalview/io/gff/ExonerateHelper.java
+++ b/
src/jalview/io/gff/ExonerateHelper.java
@@
-20,6
+20,8
@@
*/
package jalview.io.gff;
*/
package jalview.io.gff;
+import java.util.Locale;
+
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.MappingType;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.MappingType;
@@
-341,7
+343,7
@@
public class ExonerateHelper extends Gff2Helper
// e.g. exonerate:protein2genome:local
if (model != null)
{
// e.g. exonerate:protein2genome:local
if (model != null)
{
- String mdl = model.toLowerCase();
+ String mdl = model.toLowerCase(Locale.ROOT);
if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
|| mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
|| mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
|| mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
|| mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
diff --git
a/src/jalview/io/packed/ParsePackedSet.java
b/src/jalview/io/packed/ParsePackedSet.java
index
d40446d
..
37dd66b
100644
(file)
--- a/
src/jalview/io/packed/ParsePackedSet.java
+++ b/
src/jalview/io/packed/ParsePackedSet.java
@@
-20,6
+20,8
@@
*/
package jalview.io.packed;
*/
package jalview.io.packed;
+import java.util.Locale;
+
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
@@
-235,7
+237,7
@@
public class ParsePackedSet
String type = args[i++];
final String file = args[i++];
final JvDataType jtype = DataProvider.JvDataType
String type = args[i++];
final String file = args[i++];
final JvDataType jtype = DataProvider.JvDataType
- .valueOf(type.toUpperCase());
+ .valueOf(type.toUpperCase(Locale.ROOT));
if (jtype != null)
{
final FileParse fp;
if (jtype != null)
{
final FileParse fp;
@@
-254,7
+256,7
@@
public class ParsePackedSet
else
{
System.out.println("Couldn't parse source type token '"
else
{
System.out.println("Couldn't parse source type token '"
- + type.toUpperCase() + "'");
+ + type.toUpperCase(Locale.ROOT) + "'");
}
}
if (i < args.length)
}
}
if (i < args.length)
diff --git
a/src/jalview/io/vcf/VCFLoader.java
b/src/jalview/io/vcf/VCFLoader.java
index
f965c4e
..
dadb532
100644
(file)
--- a/
src/jalview/io/vcf/VCFLoader.java
+++ b/
src/jalview/io/vcf/VCFLoader.java
@@
-20,6
+20,8
@@
*/
package jalview.io.vcf;
*/
package jalview.io.vcf;
+import java.util.Locale;
+
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
@@
-431,7
+433,7
@@
public class VCFLoader
+ DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
}
+ DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
}
- reference = reference.toLowerCase();
+ reference = reference.toLowerCase(Locale.ROOT);
/*
* for a non-human species, or other assembly identifier,
/*
* for a non-human species, or other assembly identifier,
@@
-446,7
+448,7
@@
public class VCFLoader
String[] tokens = token.split("=");
if (tokens.length == 2)
{
String[] tokens = token.split("=");
if (tokens.length == 2)
{
- if (reference.contains(tokens[0].trim().toLowerCase()))
+ if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
{
vcfAssembly = tokens[1].trim();
break;
{
vcfAssembly = tokens[1].trim();
break;
@@
-463,7
+465,7
@@
public class VCFLoader
String[] tokens = token.split("=");
if (tokens.length == 2)
{
String[] tokens = token.split("=");
if (tokens.length == 2)
{
- if (reference.contains(tokens[0].trim().toLowerCase()))
+ if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
{
vcfSpecies = tokens[1].trim();
break;
{
vcfSpecies = tokens[1].trim();
break;
@@
-568,7
+570,7
@@
public class VCFLoader
{
for (Pattern p : filters)
{
{
for (Pattern p : filters)
{
- if (p.matcher(id.toUpperCase()).matches())
+ if (p.matcher(id.toUpperCase(Locale.ROOT)).matches())
{
return true;
}
{
return true;
}
@@
-662,7
+664,7
@@
public class VCFLoader
{
try
{
{
try
{
- patterns.add(Pattern.compile(token.toUpperCase()));
+ patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
} catch (PatternSyntaxException e)
{
System.err.println("Invalid pattern ignored: " + token);
} catch (PatternSyntaxException e)
{
System.err.println("Invalid pattern ignored: " + token);
@@
-1033,7
+1035,7
@@
public class VCFLoader
*/
String consequence = getConsequenceForAlleleAndFeature(variant, CSQ_FIELD,
altAlleleIndex, csqAlleleFieldIndex,
*/
String consequence = getConsequenceForAlleleAndFeature(variant, CSQ_FIELD,
altAlleleIndex, csqAlleleFieldIndex,
- csqAlleleNumberFieldIndex, seq.getName().toLowerCase(),
+ csqAlleleNumberFieldIndex, seq.getName().toLowerCase(Locale.ROOT),
csqFeatureFieldIndex);
/*
csqFeatureFieldIndex);
/*
@@
-1226,7
+1228,7
@@
public class VCFLoader
{
String featureIdentifier = csqFields[featureFieldIndex];
if (featureIdentifier.length() > 4
{
String featureIdentifier = csqFields[featureFieldIndex];
if (featureIdentifier.length() > 4
- && seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
+ && seqName.indexOf(featureIdentifier.toLowerCase(Locale.ROOT)) > -1)
{
/*
* feature (transcript) matched - now check for allele match
{
/*
* feature (transcript) matched - now check for allele match
diff --git
a/src/jalview/javascript/log4j/Level.java
b/src/jalview/javascript/log4j/Level.java
index
5691a47
..
582f2de
100644
(file)
--- a/
src/jalview/javascript/log4j/Level.java
+++ b/
src/jalview/javascript/log4j/Level.java
@@
-1,5
+1,7
@@
package jalview.javascript.log4j;
package jalview.javascript.log4j;
+import java.util.Locale;
+
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
@@
-162,7
+164,7
@@
public class Level extends Priority implements Serializable
{
return defaultLevel;
}
{
return defaultLevel;
}
- String s = sArg.toUpperCase();
+ String s = sArg.toUpperCase(Locale.ROOT);
if (s.equals(ALL_NAME))
{
if (s.equals(ALL_NAME))
{
diff --git
a/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
b/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
index
b3422ab
..
6b877bf
100644
(file)
--- a/
src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
+++ b/
src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
@@
-20,6
+20,8
@@
*/
package jalview.json.binding.biojson.v1;
*/
package jalview.json.binding.biojson.v1;
+import java.util.Locale;
+
import jalview.datamodel.AnnotatedCollectionI;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
@@
-62,7
+64,7
@@
public class ColourSchemeMapper
public static ColourSchemeI getJalviewColourScheme(
String colourSchemeName, AnnotatedCollectionI annotCol)
{
public static ColourSchemeI getJalviewColourScheme(
String colourSchemeName, AnnotatedCollectionI annotCol)
{
- switch (colourSchemeName.toUpperCase())
+ switch (colourSchemeName.toUpperCase(Locale.ROOT))
{
case "ZAPPO":
return csZappo;
{
case "ZAPPO":
return csZappo;
diff --git
a/src/jalview/project/Jalview2XML.java
b/src/jalview/project/Jalview2XML.java
index
ffd942f
..
9b6741b
100644
(file)
--- a/
src/jalview/project/Jalview2XML.java
+++ b/
src/jalview/project/Jalview2XML.java
@@
-20,6
+20,8
@@
*/
package jalview.project;
*/
package jalview.project;
+import java.util.Locale;
+
import static jalview.math.RotatableMatrix.Axis.X;
import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
import static jalview.math.RotatableMatrix.Axis.X;
import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
@@
-2076,8
+2078,8
@@
public class Jalview2XML
final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
final String pdbId = pdbentry.getId();
if (!pdbId.equals(entry.getId())
final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
final String pdbId = pdbentry.getId();
if (!pdbId.equals(entry.getId())
- && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
- .startsWith(pdbId.toLowerCase())))
+ && !(entry.getId().length() > 4 && entry.getId().toLowerCase(Locale.ROOT)
+ .startsWith(pdbId.toLowerCase(Locale.ROOT))))
{
/*
* not interested in a binding to a different PDB entry here
{
/*
* not interested in a binding to a different PDB entry here
@@
-2645,7
+2647,7
@@
public class Jalview2XML
for (int i = 0; i < colours.length; i++)
{
Colour col = new Colour();
for (int i = 0; i < colours.length; i++)
{
Colour col = new Colour();
- col.setName(ResidueProperties.aa[i].toLowerCase());
+ col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
col.setRGB(jalview.util.Format.getHexString(colours[i]));
// jbucs.addColour(col);
jbucs.getColour().add(col);
col.setRGB(jalview.util.Format.getHexString(colours[i]));
// jbucs.addColour(col);
jbucs.getColour().add(col);
diff --git
a/src/jalview/schemes/ColourSchemeLoader.java
b/src/jalview/schemes/ColourSchemeLoader.java
index
141ef10
..
061ccd4
100644
(file)
--- a/
src/jalview/schemes/ColourSchemeLoader.java
+++ b/
src/jalview/schemes/ColourSchemeLoader.java
@@
-20,6
+20,8
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.xml.binding.jalview.JalviewUserColours;
import java.awt.Color;
import jalview.xml.binding.jalview.JalviewUserColours;
import java.awt.Color;
@@
-92,7
+94,7
@@
public class ColourSchemeLoader
Color color = new Color(
Integer.parseInt(jucs.getColour().get(i).getRGB(), 16));
Color color = new Color(
Integer.parseInt(jucs.getColour().get(i).getRGB(), 16));
- if (name.toLowerCase().equals(name))
+ if (name.toLowerCase(Locale.ROOT).equals(name))
{
caseSensitive = true;
lowerCase[index] = color;
{
caseSensitive = true;
lowerCase[index] = color;
diff --git
a/src/jalview/schemes/ColourSchemes.java
b/src/jalview/schemes/ColourSchemes.java
index
d31fbba
..
faada0e
100644
(file)
--- a/
src/jalview/schemes/ColourSchemes.java
+++ b/
src/jalview/schemes/ColourSchemes.java
@@
-20,6
+20,8
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
@@
-104,7
+106,7
@@
public class ColourSchemes
* name is lower-case for non-case-sensitive lookup
* (name in the colour keeps its true case)
*/
* name is lower-case for non-case-sensitive lookup
* (name in the colour keeps its true case)
*/
- String lower = name.toLowerCase();
+ String lower = name.toLowerCase(Locale.ROOT);
if (schemes.containsKey(lower))
{
System.err
if (schemes.containsKey(lower))
{
System.err
@@
-122,7
+124,7
@@
public class ColourSchemes
{
if (name != null)
{
{
if (name != null)
{
- schemes.remove(name.toLowerCase());
+ schemes.remove(name.toLowerCase(Locale.ROOT));
}
}
}
}
@@
-148,7
+150,7
@@
public class ColourSchemes
{
return null;
}
{
return null;
}
- ColourSchemeI cs = schemes.get(name.toLowerCase());
+ ColourSchemeI cs = schemes.get(name.toLowerCase(Locale.ROOT));
return cs == null ? null
: cs.getInstance(viewport, forData);
}
return cs == null ? null
: cs.getInstance(viewport, forData);
}
@@
-193,6
+195,6
@@
public class ColourSchemes
{
return false;
}
{
return false;
}
- return schemes.containsKey(name.toLowerCase());
+ return schemes.containsKey(name.toLowerCase(Locale.ROOT));
}
}
}
}
diff --git
a/src/jalview/schemes/FeatureColour.java
b/src/jalview/schemes/FeatureColour.java
index
0d36f4f
..
e5bda58
100644
(file)
--- a/
src/jalview/schemes/FeatureColour.java
+++ b/
src/jalview/schemes/FeatureColour.java
@@
-20,6
+20,8
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.features.FeatureMatcher;
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.features.FeatureMatcher;
@@
-194,19
+196,19
@@
public class FeatureColour implements FeatureColourI
"Expected either 'label' or a colour specification in the line: "
+ descriptor);
}
"Expected either 'label' or a colour specification in the line: "
+ descriptor);
}
- if (nextToken.toLowerCase().startsWith(LABEL))
+ if (nextToken.toLowerCase(Locale.ROOT).startsWith(LABEL))
{
byLabel = true;
// get the token after the next delimiter:
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
}
{
byLabel = true;
// get the token after the next delimiter:
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
}
- else if (nextToken.toLowerCase().startsWith(SCORE))
+ else if (nextToken.toLowerCase(Locale.ROOT).startsWith(SCORE))
{
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
}
{
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
}
- else if (nextToken.toLowerCase().startsWith(ATTRIBUTE))
+ else if (nextToken.toLowerCase(Locale.ROOT).startsWith(ATTRIBUTE))
{
byAttribute = true;
attName = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
{
byAttribute = true;
attName = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
@@
-304,7
+306,7
@@
public class FeatureColour implements FeatureColourI
}
gcol.nextToken(); // skip next '|'
}
gcol.nextToken(); // skip next '|'
- if (tok.toLowerCase().startsWith(ABSOLUTE))
+ if (tok.toLowerCase(Locale.ROOT).startsWith(ABSOLUTE))
{
minval = gcol.nextToken();
gcol.nextToken(); // skip next '|'
{
minval = gcol.nextToken();
gcol.nextToken(); // skip next '|'
@@
-380,17
+382,17
@@
public class FeatureColour implements FeatureColourI
{
// threshold type and possibly a threshold value
ttype = gcol.nextToken();
{
// threshold type and possibly a threshold value
ttype = gcol.nextToken();
- if (ttype.toLowerCase().startsWith(BELOW))
+ if (ttype.toLowerCase(Locale.ROOT).startsWith(BELOW))
{
featureColour.setBelowThreshold(true);
}
{
featureColour.setBelowThreshold(true);
}
- else if (ttype.toLowerCase().startsWith(ABOVE))
+ else if (ttype.toLowerCase(Locale.ROOT).startsWith(ABOVE))
{
featureColour.setAboveThreshold(true);
}
else
{
{
featureColour.setAboveThreshold(true);
}
else
{
- if (!ttype.toLowerCase().startsWith("no"))
+ if (!ttype.toLowerCase(Locale.ROOT).startsWith("no"))
{
System.err.println(
"Ignoring unrecognised threshold type : " + ttype);
{
System.err.println(
"Ignoring unrecognised threshold type : " + ttype);
diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
5f84ca0
..
2eb303d
100755
(executable)
--- a/
src/jalview/schemes/ResidueProperties.java
+++ b/
src/jalview/schemes/ResidueProperties.java
@@
-20,6
+20,8
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.analysis.GeneticCodes;
import java.awt.Color;
import jalview.analysis.GeneticCodes;
import java.awt.Color;
@@
-2347,7
+2349,7
@@
public class ResidueProperties
{
continue;
}
{
continue;
}
- nuc = nuc.toUpperCase();
+ nuc = nuc.toUpperCase(Locale.ROOT);
if (!result.contains(nuc))
{
result.add(nuc);
if (!result.contains(nuc))
{
result.add(nuc);
@@
-2366,7
+2368,7
@@
public class ResidueProperties
{
continue;
}
{
continue;
}
- res = res.toUpperCase();
+ res = res.toUpperCase(Locale.ROOT);
if (!result.contains(res))
{
result.add(res);
if (!result.contains(res))
{
result.add(res);
@@
-2391,7
+2393,7
@@
public class ResidueProperties
return '0';
}
Integer index = ResidueProperties.aa3Hash
return '0';
}
Integer index = ResidueProperties.aa3Hash
- .get(threeLetterCode.toUpperCase());
+ .get(threeLetterCode.toUpperCase(Locale.ROOT));
return index == null ? '0' : aa[index].charAt(0);
}
}
return index == null ? '0' : aa[index].charAt(0);
}
}
diff --git
a/src/jalview/schemes/UserColourScheme.java
b/src/jalview/schemes/UserColourScheme.java
index
d77f2f5
..
d55ffbf
100755
(executable)
--- a/
src/jalview/schemes/UserColourScheme.java
+++ b/
src/jalview/schemes/UserColourScheme.java
@@
-20,6
+20,8
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import java.util.Locale;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.util.ColorUtils;
import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.util.ColorUtils;
@@
-215,7
+217,7
@@
public class UserColourScheme extends ResidueColourScheme
continue;
}
continue;
}
- if (residue.equals(residue.toLowerCase()))
+ if (residue.equals(residue.toLowerCase(Locale.ROOT)))
{
if (lowerCaseColours == null)
{
{
if (lowerCaseColours == null)
{
@@
-306,7
+308,7
@@
public class UserColourScheme extends ResidueColourScheme
c = lowerCaseColours[index];
if (c != null && !c.equals(Color.white))
{
c = lowerCaseColours[index];
if (c != null && !c.equals(Color.white))
{
- residue = residue.toLowerCase();
+ residue = residue.toLowerCase(Locale.ROOT);
if (colours.get(c) == null)
{
colours.put(c, new ArrayList<String>());
if (colours.get(c) == null)
{
colours.put(c, new ArrayList<String>());
diff --git
a/src/jalview/structure/StructureImportSettings.java
b/src/jalview/structure/StructureImportSettings.java
index
9662fee
..
cbd59b1
100644
(file)
--- a/
src/jalview/structure/StructureImportSettings.java
+++ b/
src/jalview/structure/StructureImportSettings.java
@@
-20,6
+20,8
@@
*/
package jalview.structure;
*/
package jalview.structure;
+import java.util.Locale;
+
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
@@
-130,7
+132,7
@@
public class StructureImportSettings
String defaultStructureFileFormat)
{
StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
String defaultStructureFileFormat)
{
StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
- .valueOf(defaultStructureFileFormat.toUpperCase());
+ .valueOf(defaultStructureFileFormat.toUpperCase(Locale.ROOT));
}
public static String getDefaultPDBFileParser()
}
public static String getDefaultPDBFileParser()
@@
-147,7
+149,7
@@
public class StructureImportSettings
public static void setDefaultPDBFileParser(String defaultPDBFileParser)
{
StructureImportSettings.defaultPDBFileParser = StructureParser
public static void setDefaultPDBFileParser(String defaultPDBFileParser)
{
StructureImportSettings.defaultPDBFileParser = StructureParser
- .valueOf(defaultPDBFileParser.toUpperCase());
+ .valueOf(defaultPDBFileParser.toUpperCase(Locale.ROOT));
}
}
}
}
diff --git
a/src/jalview/structures/models/AAStructureBindingModel.java
b/src/jalview/structures/models/AAStructureBindingModel.java
index
44773e9
..
748381f
100644
(file)
--- a/
src/jalview/structures/models/AAStructureBindingModel.java
+++ b/
src/jalview/structures/models/AAStructureBindingModel.java
@@
-20,6
+20,8
@@
*/
package jalview.structures.models;
*/
package jalview.structures.models;
+import java.util.Locale;
+
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
@@
-931,7
+933,7
@@
public abstract class AAStructureBindingModel
for (String reply : replies)
{
// return this error (Chimera only) to the user
for (String reply : replies)
{
// return this error (Chimera only) to the user
- if (reply.toLowerCase().contains("unequal numbers of atoms"))
+ if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
{
error += "; " + reply;
}
{
error += "; " + reply;
}
diff --git
a/src/jalview/util/CaseInsensitiveString.java
b/src/jalview/util/CaseInsensitiveString.java
index
a01c035
..
536671d
100644
(file)
--- a/
src/jalview/util/CaseInsensitiveString.java
+++ b/
src/jalview/util/CaseInsensitiveString.java
@@
-25,6
+25,8
@@
package jalview.util;
* want to preserve case, but do not want to duplicate upper and lower case
* variants
*/
* want to preserve case, but do not want to duplicate upper and lower case
* variants
*/
+import java.util.Locale;
+
public final class CaseInsensitiveString
{
String value;
public final class CaseInsensitiveString
{
String value;
@@
-72,6
+74,6
@@
public final class CaseInsensitiveString
public int hashCode()
{
return value == null ? super.hashCode()
public int hashCode()
{
return value == null ? super.hashCode()
- : value.toUpperCase().hashCode();
+ : value.toUpperCase(Locale.ROOT).hashCode();
}
}
}
}
diff --git
a/src/jalview/util/ColorUtils.java
b/src/jalview/util/ColorUtils.java
index
60129fb
..
5db333f
100644
(file)
--- a/
src/jalview/util/ColorUtils.java
+++ b/
src/jalview/util/ColorUtils.java
@@
-24,6
+24,8
@@
package jalview.util;
package jalview.util;
+import java.util.Locale;
+
import java.awt.Color;
import java.util.HashMap;
import java.util.Map;
import java.awt.Color;
import java.util.HashMap;
import java.util.Map;
@@
-324,7
+326,7
@@
public class ColorUtils
return null;
}
Color col = null;
return null;
}
Color col = null;
- name = name.toLowerCase();
+ name = name.toLowerCase(Locale.ROOT);
// or make a static map; or use reflection on the field name
switch (name)
// or make a static map; or use reflection on the field name
switch (name)
diff --git
a/src/jalview/util/DBRefUtils.java
b/src/jalview/util/DBRefUtils.java
index
ae0243e
..
bcb0bd3
100755
(executable)
--- a/
src/jalview/util/DBRefUtils.java
+++ b/
src/jalview/util/DBRefUtils.java
@@
-20,6
+20,8
@@
*/
package jalview.util;
*/
package jalview.util;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
@@
-73,7
+75,7
@@
public class DBRefUtils
// guarantee we always have lowercase entries for canonical string lookups
for (String k : canonicalSourceNameLookup.keySet())
{
// guarantee we always have lowercase entries for canonical string lookups
for (String k : canonicalSourceNameLookup.keySet())
{
- canonicalSourceNameLookup.put(k.toLowerCase(),
+ canonicalSourceNameLookup.put(k.toLowerCase(Locale.ROOT),
canonicalSourceNameLookup.get(k));
}
}
canonicalSourceNameLookup.get(k));
}
}
@@
-98,7
+100,7
@@
public class DBRefUtils
HashSet<String> srcs = new HashSet<String>();
for (String src : sources)
{
HashSet<String> srcs = new HashSet<String>();
for (String src : sources)
{
- srcs.add(src.toUpperCase());
+ srcs.add(src.toUpperCase(Locale.ROOT));
}
int nrefs = dbrefs.size();
}
int nrefs = dbrefs.size();
@@
-107,7
+109,7
@@
public class DBRefUtils
{
DBRefEntry dbr = dbrefs.get(ib);
String source = getCanonicalName(dbr.getSource());
{
DBRefEntry dbr = dbrefs.get(ib);
String source = getCanonicalName(dbr.getSource());
- if (srcs.contains(source.toUpperCase()))
+ if (srcs.contains(source.toUpperCase(Locale.ROOT)))
{
res.add(dbr);
}
{
res.add(dbr);
}
@@
-181,7
+183,7
@@
public class DBRefUtils
{
return null;
}
{
return null;
}
- String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
+ String canonical = canonicalSourceNameLookup.get(source.toLowerCase(Locale.ROOT));
return canonical == null ? source : canonical;
}
return canonical == null ? source : canonical;
}
diff --git
a/src/jalview/util/MessageManager.java
b/src/jalview/util/MessageManager.java
index
bb94566
..
ba7da10
100644
(file)
--- a/
src/jalview/util/MessageManager.java
+++ b/
src/jalview/util/MessageManager.java
@@
-162,7
+162,7
@@
public class MessageManager
*/
public static String getStringOrReturn(String keyroot, String name)
{
*/
public static String getStringOrReturn(String keyroot, String name)
{
- String smkey = keyroot + name.toLowerCase().replaceAll(" ", "");
+ String smkey = keyroot + name.toLowerCase(Locale.ROOT).replaceAll(" ", "");
try
{
name = rb.getString(smkey);
try
{
name = rb.getString(smkey);
diff --git
a/src/jalview/util/ParseHtmlBodyAndLinks.java
b/src/jalview/util/ParseHtmlBodyAndLinks.java
index
6713bbc
..
0f2d01d
100644
(file)
--- a/
src/jalview/util/ParseHtmlBodyAndLinks.java
+++ b/
src/jalview/util/ParseHtmlBodyAndLinks.java
@@
-20,6
+20,8
@@
*/
package jalview.util;
*/
package jalview.util;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.List;
import java.util.StringTokenizer;
import java.util.ArrayList;
import java.util.List;
import java.util.StringTokenizer;
@@
-103,7
+105,7
@@
public class ParseHtmlBodyAndLinks
return;
}
StringBuilder sb = new StringBuilder(description.length());
return;
}
StringBuilder sb = new StringBuilder(description.length());
- if (description.toUpperCase().indexOf("<HTML>") == -1)
+ if (description.toUpperCase(Locale.ROOT).indexOf("<HTML>") == -1)
{
htmlContent = false;
}
{
htmlContent = false;
}
@@
-129,7
+131,7
@@
public class ParseHtmlBodyAndLinks
token = token.substring(0, startTag);
}
token = token.substring(0, startTag);
}
- if (tag != null && tag.toUpperCase().startsWith("A HREF="))
+ if (tag != null && tag.toUpperCase(Locale.ROOT).startsWith("A HREF="))
{
if (token.length() > 0)
{
{
if (token.length() > 0)
{
diff --git
a/src/jalview/util/StringUtils.java
b/src/jalview/util/StringUtils.java
index
1f114a8
..
bf5b87a
100644
(file)
--- a/
src/jalview/util/StringUtils.java
+++ b/
src/jalview/util/StringUtils.java
@@
-20,6
+20,8
@@
*/
package jalview.util;
*/
package jalview.util;
+import java.util.Locale;
+
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
@@
-409,9
+411,9
@@
public class StringUtils
}
if (s.length() <= 1)
{
}
if (s.length() <= 1)
{
- return s.toUpperCase();
+ return s.toUpperCase(Locale.ROOT);
}
}
- return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
+ return s.substring(0, 1).toUpperCase(Locale.ROOT) + s.substring(1).toLowerCase(Locale.ROOT);
}
/**
}
/**
@@
-427,7
+429,7
@@
public class StringUtils
{
return null;
}
{
return null;
}
- String tmp2up = text.toUpperCase();
+ String tmp2up = text.toUpperCase(Locale.ROOT);
int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
{
int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
{
diff --git
a/src/jalview/util/matcher/Matcher.java
b/src/jalview/util/matcher/Matcher.java
index
51e1828
..
e43ead2
100644
(file)
--- a/
src/jalview/util/matcher/Matcher.java
+++ b/
src/jalview/util/matcher/Matcher.java
@@
-20,6
+20,8
@@
*/
package jalview.util.matcher;
*/
package jalview.util.matcher;
+import java.util.Locale;
+
import java.util.Objects;
/**
import java.util.Objects;
/**
@@
-102,7
+104,7
@@
public class Matcher implements MatcherI
patternType = PatternType.String;
}
patternType = PatternType.String;
}
- uppercasePattern = pattern == null ? null : pattern.toUpperCase();
+ uppercasePattern = pattern == null ? null : pattern.toUpperCase(Locale.ROOT);
// if we add regex conditions (e.g. matchesPattern), then
// pattern should hold the raw regex, and
// if we add regex conditions (e.g. matchesPattern), then
// pattern should hold the raw regex, and
@@
-172,7
+174,7
@@
public class Matcher implements MatcherI
boolean matchesString(String compareTo)
{
boolean matched = false;
boolean matchesString(String compareTo)
{
boolean matched = false;
- String upper = compareTo.toUpperCase().trim();
+ String upper = compareTo.toUpperCase(Locale.ROOT).trim();
switch(condition) {
case Matches:
matched = upper.equals(uppercasePattern);
switch(condition) {
case Matches:
matched = upper.equals(uppercasePattern);
diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
7daa7b4
..
9420465
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-20,6
+20,8
@@
*/
package jalview.ws;
*/
package jalview.ws;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Enumeration;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Enumeration;
@@
-243,7
+245,7
@@
public class DBRefFetcher implements Runnable
*/
void addSeqId(SequenceI seq, String key)
{
*/
void addSeqId(SequenceI seq, String key)
{
- key = key.toUpperCase();
+ key = key.toUpperCase(Locale.ROOT);
Vector<SequenceI> seqs;
if (seqRefs.containsKey(key))
Vector<SequenceI> seqs;
if (seqRefs.containsKey(key))
@@
-397,7
+399,7
@@
public class DBRefFetcher implements Runnable
DBRefEntry upref = uprefs.get(j);
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
DBRefEntry upref = uprefs.get(j);
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
- upref.getAccessionId().toUpperCase());
+ upref.getAccessionId().toUpperCase(Locale.ROOT));
}
}
else
}
}
else
@@
-436,7
+438,7
@@
public class DBRefFetcher implements Runnable
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ queries.addElement(token.toUpperCase(Locale.ROOT));
}
else
{
}
else
{
@@
-444,7
+446,7
@@
public class DBRefFetcher implements Runnable
// System.out.println("Not querying source with
// token="+token+"\n");
addSeqId(sequence, token);
// System.out.println("Not querying source with
// token="+token+"\n");
addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ queries.addElement(token.toUpperCase(Locale.ROOT));
}
}
}
}
}
}
@@
-540,7
+542,7
@@
public class DBRefFetcher implements Runnable
DBRefEntry ref = entryRefs.get(j);
String accessionId = ref.getAccessionId();
// match up on accessionId
DBRefEntry ref = entryRefs.get(j);
String accessionId = ref.getAccessionId();
// match up on accessionId
- if (seqRefs.containsKey(accessionId.toUpperCase()))
+ if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
{
Vector<SequenceI> seqs = seqRefs.get(accessionId);
for (int jj = 0; jj < seqs.size(); jj++)
{
Vector<SequenceI> seqs = seqRefs.get(accessionId);
for (int jj = 0; jj < seqs.size(); jj++)
@@
-592,7
+594,7
@@
public class DBRefFetcher implements Runnable
// sequenceMatches now contains the set of all sequences associated with
// the returned db record
final String retrievedSeqString = retrievedSeq.getSequenceAsString();
// sequenceMatches now contains the set of all sequences associated with
// the returned db record
final String retrievedSeqString = retrievedSeq.getSequenceAsString();
- String entrySeq = retrievedSeqString.toUpperCase();
+ String entrySeq = retrievedSeqString.toUpperCase(Locale.ROOT);
for (int m = 0; m < sequenceMatches.size(); m++)
{
sequence = sequenceMatches.elementAt(m);
for (int m = 0; m < sequenceMatches.size(); m++)
{
sequence = sequenceMatches.elementAt(m);
@@
-611,7
+613,7
@@
public class DBRefFetcher implements Runnable
boolean remoteEnclosesLocal = false;
String nonGapped = AlignSeq
.extractGaps("-. ", sequence.getSequenceAsString())
boolean remoteEnclosesLocal = false;
String nonGapped = AlignSeq
.extractGaps("-. ", sequence.getSequenceAsString())
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
int absStart = entrySeq.indexOf(nonGapped);
if (absStart == -1)
{
int absStart = entrySeq.indexOf(nonGapped);
if (absStart == -1)
{
@@
-731,10
+733,10
@@
public class DBRefFetcher implements Runnable
String ngAlsq = AlignSeq
.extractGaps("-. ",
alseqs[alsq].getSequenceAsString())
String ngAlsq = AlignSeq
.extractGaps("-. ",
alseqs[alsq].getSequenceAsString())
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
- .toUpperCase().indexOf(ngAlsq) + sequence.getStart());
+ .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart());
if (oldstrt != alseqs[alsq].getStart())
{
alseqs[alsq].setEnd(
if (oldstrt != alseqs[alsq].getStart())
{
alseqs[alsq].setEnd(
diff --git
a/src/jalview/ws/dbsources/EmblFlatfileSource.java
b/src/jalview/ws/dbsources/EmblFlatfileSource.java
index
6536958
..
7d3c6dd
100644
(file)
--- a/
src/jalview/ws/dbsources/EmblFlatfileSource.java
+++ b/
src/jalview/ws/dbsources/EmblFlatfileSource.java
@@
-1,5
+1,7
@@
package jalview.ws.dbsources;
package jalview.ws.dbsources;
+import java.util.Locale;
+
import java.io.File;
import java.io.IOException;
import java.io.File;
import java.io.IOException;
@@
-73,13
+75,13
@@
public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
try
{
reply = dbFetch.fetchDataAsFile(
try
{
reply = dbFetch.fetchDataAsFile(
- dbName.toLowerCase() + ":" + query.trim(), null, "gz");
+ dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null, "gz");
} catch (Exception e)
{
stopQuery();
throw new Exception(
String.format("EBI EMBL retrieval failed for %s:%s",
} catch (Exception e)
{
stopQuery();
throw new Exception(
String.format("EBI EMBL retrieval failed for %s:%s",
- dbName.toLowerCase(), query.trim()),
+ dbName.toLowerCase(Locale.ROOT), query.trim()),
e);
}
return getEmblSequenceRecords(dbName, query, reply);
e);
}
return getEmblSequenceRecords(dbName, query, reply);
diff --git
a/src/jalview/ws/dbsources/EmblXmlSource.java
b/src/jalview/ws/dbsources/EmblXmlSource.java
index
97d7c9f
..
c2d661b
100644
(file)
--- a/
src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/
src/jalview/ws/dbsources/EmblXmlSource.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
+import java.util.Locale;
+
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
@@
-102,14
+104,14
@@
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
try
{
reply = dbFetch.fetchDataAsFile(
try
{
reply = dbFetch.fetchDataAsFile(
- emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
+ emprefx.toLowerCase(Locale.ROOT) + ":" + query.trim(), "display=xml",
"xml");
} catch (Exception e)
{
stopQuery();
throw new Exception(
String.format("EBI EMBL XML retrieval failed for %s:%s",
"xml");
} catch (Exception e)
{
stopQuery();
throw new Exception(
String.format("EBI EMBL XML retrieval failed for %s:%s",
- emprefx.toLowerCase(), query.trim()),
+ emprefx.toLowerCase(Locale.ROOT), query.trim()),
e);
}
return getEmblSequenceRecords(emprefx, query, reply);
e);
}
return getEmblSequenceRecords(emprefx, query, reply);
diff --git
a/src/jalview/ws/dbsources/TDBeacons.java
b/src/jalview/ws/dbsources/TDBeacons.java
index
b2fbc17
..
345e217
100644
(file)
--- a/
src/jalview/ws/dbsources/TDBeacons.java
+++ b/
src/jalview/ws/dbsources/TDBeacons.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
@@
-142,7
+144,7
@@
public class TDBeacons extends DbSourceProxyImpl
startQuery();
try
{
startQuery();
try
{
- queries = queries.toUpperCase().replaceAll(
+ queries = queries.toUpperCase(Locale.ROOT).replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
diff --git
a/src/jalview/ws/dbsources/Uniprot.java
b/src/jalview/ws/dbsources/Uniprot.java
index
2fc5893
..
a80a530
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
@@
-139,7
+141,7
@@
public class Uniprot extends DbSourceProxyImpl
startQuery();
try
{
startQuery();
try
{
- queries = queries.toUpperCase().replaceAll(
+ queries = queries.toUpperCase(Locale.ROOT).replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
diff --git
a/src/jalview/ws/dbsources/Xfam.java
b/src/jalview/ws/dbsources/Xfam.java
index
f0cb14b
..
9340f65
100644
(file)
--- a/
src/jalview/ws/dbsources/Xfam.java
+++ b/
src/jalview/ws/dbsources/Xfam.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
@@
-75,11
+77,11
@@
public abstract class Xfam extends DbSourceProxyImpl
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
// getDbSource(),
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
// getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
if (!getDbSource().equals(getXfamSource()))
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
if (!getDbSource().equals(getXfamSource()))
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
}
}
stopQuery();
}
}
stopQuery();
@@
-88,7
+90,7
@@
public abstract class Xfam extends DbSourceProxyImpl
String getURL(String queries)
{
String getURL(String queries)
{
- return getURLPrefix() + "/family/" + queries.trim().toUpperCase()
+ return getURLPrefix() + "/family/" + queries.trim().toUpperCase(Locale.ROOT)
+ getURLSuffix();
}
+ getURLSuffix();
}
diff --git
a/src/jalview/ws/ebi/EBIFetchClient.java
b/src/jalview/ws/ebi/EBIFetchClient.java
index
b773d4e
..
1d04351
100644
(file)
--- a/
src/jalview/ws/ebi/EBIFetchClient.java
+++ b/
src/jalview/ws/ebi/EBIFetchClient.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.ebi;
*/
package jalview.ws.ebi;
+import java.util.Locale;
+
import jalview.datamodel.DBRefSource;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.datamodel.DBRefSource;
import jalview.util.MessageManager;
import jalview.util.Platform;
@@
-280,12
+282,12
@@
public class EBIFetchClient
|| database.equalsIgnoreCase(DBRefSource.EMBLCDS))
{
url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
|| database.equalsIgnoreCase(DBRefSource.EMBLCDS))
{
url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
- + ids.toLowerCase() + "?download=true&gzip=true";
+ + ids.toLowerCase(Locale.ROOT) + "?download=true&gzip=true";
}
else
{
url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
}
else
{
url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
- + database.toLowerCase() + "/" + ids.toLowerCase()
+ + database.toLowerCase(Locale.ROOT) + "/" + ids.toLowerCase(Locale.ROOT)
+ (format != null ? "/" + format : "");
}
return url;
+ (format != null ? "/" + format : "");
}
return url;
diff --git
a/src/jalview/ws/io/mime/MimeTypes.java
b/src/jalview/ws/io/mime/MimeTypes.java
index
83252d8
..
7e6e660
100644
(file)
--- a/
src/jalview/ws/io/mime/MimeTypes.java
+++ b/
src/jalview/ws/io/mime/MimeTypes.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.io.mime;
*/
package jalview.ws.io.mime;
+import java.util.Locale;
+
import jalview.io.packed.DataProvider.JvDataType;
/**
import jalview.io.packed.DataProvider.JvDataType;
/**
@@
-53,7
+55,7
@@
public class MimeTypes
*/
public static JvDataType getTypeOf(String mimeType)
{
*/
public static JvDataType getTypeOf(String mimeType)
{
- String mt = mimeType.toLowerCase();
+ String mt = mimeType.toLowerCase(Locale.ROOT);
for (int i = 0; i < typemap.length; i += 2)
{
if (typemap[i].equals(mt))
for (int i = 0; i < typemap.length; i += 2)
{
if (typemap[i].equals(mt))
diff --git
a/src/jalview/ws/jws1/JPredClient.java
b/src/jalview/ws/jws1/JPredClient.java
index
3b7bdb6
..
e9c2aea
100644
(file)
--- a/
src/jalview/ws/jws1/JPredClient.java
+++ b/
src/jalview/ws/jws1/JPredClient.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.jws1;
*/
package jalview.ws.jws1;
+import java.util.Locale;
+
import jalview.analysis.AlignSeq;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.analysis.AlignSeq;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
@@
-183,7
+185,7
@@
public class JPredClient extends WS1Client
private String getPredictionName(String webServiceName)
{
private String getPredictionName(String webServiceName)
{
- if (webServiceName.toLowerCase()
+ if (webServiceName.toLowerCase(Locale.ROOT)
.indexOf("secondary structure prediction") > -1)
{
return webServiceName;
.indexOf("secondary structure prediction") > -1)
{
return webServiceName;
diff --git
a/src/jalview/ws/jws1/MsaWSClient.java
b/src/jalview/ws/jws1/MsaWSClient.java
index
4a09625
..
dad314b
100644
(file)
--- a/
src/jalview/ws/jws1/MsaWSClient.java
+++ b/
src/jalview/ws/jws1/MsaWSClient.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.jws1;
*/
package jalview.ws.jws1;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
@@
-119,7
+121,7
@@
public class MsaWSClient extends WS1Client
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
- String jobtitle = WebServiceName.toLowerCase();
+ String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
if (jobtitle.endsWith("alignment"))
{
if (submitGaps && (!jobtitle.endsWith("realignment")
if (jobtitle.endsWith("alignment"))
{
if (submitGaps && (!jobtitle.endsWith("realignment")
diff --git
a/src/jalview/ws/jws2/MsaWSClient.java
b/src/jalview/ws/jws2/MsaWSClient.java
index
e33b4bd
..
8ed4a36
100644
(file)
--- a/
src/jalview/ws/jws2/MsaWSClient.java
+++ b/
src/jalview/ws/jws2/MsaWSClient.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.jws2;
*/
package jalview.ws.jws2;
+import java.util.Locale;
+
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
@@
-148,7
+150,7
@@
public class MsaWSClient extends Jws2Client
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
- String jobtitle = WebServiceName.toLowerCase();
+ String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
if (jobtitle.endsWith("alignment"))
{
if (submitGaps && (!jobtitle.endsWith("realignment")
if (jobtitle.endsWith("alignment"))
{
if (submitGaps && (!jobtitle.endsWith("realignment")
diff --git
a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index
45bddac
..
a30a09c
100644
(file)
--- a/
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.jws2;
*/
package jalview.ws.jws2;
+import java.util.Locale;
+
import jalview.api.AlignCalcWorkerI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.api.AlignCalcWorkerI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
@@
-128,7
+130,7
@@
public class SequenceAnnotationWSClient extends Jws2Client
worker.updateParameters(this.preset, paramset);
}
}
worker.updateParameters(this.preset, paramset);
}
}
- if (sh.action.toLowerCase().contains("disorder"))
+ if (sh.action.toLowerCase(Locale.ROOT).contains("disorder"))
{
// build IUPred style client. take sequences, returns annotation per
// sequence.
{
// build IUPred style client. take sequences, returns annotation per
// sequence.
diff --git
a/src/jalview/ws/rest/InputType.java
b/src/jalview/ws/rest/InputType.java
index
88431a6
..
a96b6d9
100644
(file)
--- a/
src/jalview/ws/rest/InputType.java
+++ b/
src/jalview/ws/rest/InputType.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.rest;
*/
package jalview.ws.rest;
+import java.util.Locale;
+
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.OptionI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.OptionI;
@@
-232,7
+234,7
@@
public abstract class InputType
{
valid = false;
warnings.append("Invalid value for parameter "
{
valid = false;
warnings.append("Invalid value for parameter "
- + mtch.group(1).toLowerCase() + " '" + mtch.group(2)
+ + mtch.group(1).toLowerCase(Locale.ROOT) + " '" + mtch.group(2)
+ "' (expected an integer)\n");
}
+ "' (expected an integer)\n");
}
diff --git
a/src/jalview/ws/rest/RestJobThread.java
b/src/jalview/ws/rest/RestJobThread.java
index
acb7904
..
20b517b
100644
(file)
--- a/
src/jalview/ws/rest/RestJobThread.java
+++ b/
src/jalview/ws/rest/RestJobThread.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.rest;
*/
package jalview.ws.rest;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
@@
-401,7
+403,7
@@
public class RestJobThread extends AWSThread
*/
String f;
StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
*/
String f;
StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
- f = f.toLowerCase();
+ f = f.toLowerCase(Locale.ROOT);
int body = f.indexOf("<body");
if (body > -1)
{
int body = f.indexOf("<body");
if (body > -1)
{
diff --git
a/src/jalview/ws/sifts/SiftsClient.java
b/src/jalview/ws/sifts/SiftsClient.java
index
ae58082
..
5a03aea
100644
(file)
--- a/
src/jalview/ws/sifts/SiftsClient.java
+++ b/
src/jalview/ws/sifts/SiftsClient.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.sifts;
*/
package jalview.ws.sifts;
+import java.util.Locale;
+
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
@@
-219,7
+221,7
@@
public class SiftsClient implements SiftsClientI
}
String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
}
String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase() + ".xml.gz";
+ + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz";
File siftsFile = new File(siftsFileName);
if (siftsFile.exists())
{
File siftsFile = new File(siftsFileName);
if (siftsFile.exists())
{
@@
-233,7
+235,7
@@
public class SiftsClient implements SiftsClientI
BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
try
{
BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
try
{
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
oldSiftsFile.delete();
return siftsFile;
} catch (IOException e)
oldSiftsFile.delete();
return siftsFile;
} catch (IOException e)
@@
-250,7
+252,7
@@
public class SiftsClient implements SiftsClientI
}
try
{
}
try
{
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
} catch (IOException e)
{
throw new SiftsException(e.getMessage());
} catch (IOException e)
{
throw new SiftsException(e.getMessage());
@@
-356,7
+358,7
@@
public class SiftsClient implements SiftsClientI
public static boolean deleteSiftsFileByPDBId(String pdbId)
{
File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
public static boolean deleteSiftsFileByPDBId(String pdbId)
{
File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase() + ".xml.gz");
+ + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz");
if (siftsFile.exists())
{
return siftsFile.delete();
if (siftsFile.exists())
{
return siftsFile.delete();
@@
-431,7
+433,7
@@
public class SiftsClient implements SiftsClientI
for (MapRegion mapRegion : mapRegions)
{
accessions
for (MapRegion mapRegion : mapRegions)
{
accessions
- .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
+ .add(mapRegion.getDb().getDbAccessionId().toLowerCase(Locale.ROOT));
}
}
}
}
}
}
@@
-501,9
+503,9
@@
public class SiftsClient implements SiftsClientI
HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
for (DBRefEntry dbref : seq.getDBRefs())
{
HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
for (DBRefEntry dbref : seq.getDBRefs())
{
- dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
+ dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase(Locale.ROOT));
}
}
- dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase());
+ dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase(Locale.ROOT));
curDBRefAccessionIdsString = dbRefAccessionIdsString;
curSourceDBRef = sourceDBRef.getAccessionId();
curDBRefAccessionIdsString = dbRefAccessionIdsString;
curSourceDBRef = sourceDBRef.getAccessionId();
@@
-891,14
+893,14
@@
public class SiftsClient implements SiftsClientI
{
boolean isStrictMatch = true;
return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
{
boolean isStrictMatch = true;
return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
- : curDBRefAccessionIdsString.contains(accession.toLowerCase());
+ : curDBRefAccessionIdsString.contains(accession.toLowerCase(Locale.ROOT));
}
private boolean isFoundInSiftsEntry(String accessionId)
{
Set<String> siftsDBRefs = getAllMappingAccession();
return accessionId != null
}
private boolean isFoundInSiftsEntry(String accessionId)
{
Set<String> siftsDBRefs = getAllMappingAccession();
return accessionId != null
- && siftsDBRefs.contains(accessionId.toLowerCase());
+ && siftsDBRefs.contains(accessionId.toLowerCase(Locale.ROOT));
}
/**
}
/**
diff --git
a/test/jalview/analysis/AlignmentGenerator.java
b/test/jalview/analysis/AlignmentGenerator.java
index
9d3877c
..
d01b23e
100644
(file)
--- a/
test/jalview/analysis/AlignmentGenerator.java
+++ b/
test/jalview/analysis/AlignmentGenerator.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
@@
-91,7
+93,7
@@
public class AlignmentGenerator
ps = new PrintStream(new File(args[6]));
}
ps = new PrintStream(new File(args[6]));
}
- boolean nucleotide = args[0].toLowerCase().startsWith("n");
+ boolean nucleotide = args[0].toLowerCase(Locale.ROOT).startsWith("n");
int width = Integer.parseInt(args[1]);
int height = Integer.parseInt(args[2]);
long randomSeed = Long.valueOf(args[3]);
int width = Integer.parseInt(args[1]);
int height = Integer.parseInt(args[2]);
long randomSeed = Long.valueOf(args[3]);
diff --git
a/test/jalview/analysis/RnaTest.java
b/test/jalview/analysis/RnaTest.java
index
1faf3f2
..
cc35976
100644
(file)
--- a/
test/jalview/analysis/RnaTest.java
+++ b/
test/jalview/analysis/RnaTest.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
@@
-182,7
+184,7
@@
public class RnaTest
char second = bases.charAt(j);
boolean result = Rna.isCanonicalOrWobblePair(first, second);
String pair = new String(new char[] { first, second })
char second = bases.charAt(j);
boolean result = Rna.isCanonicalOrWobblePair(first, second);
String pair = new String(new char[] { first, second })
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
|| pair.equals("UA") || pair.equals("GC")
|| pair.equals("CG") || pair.equals("GT")
if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
|| pair.equals("UA") || pair.equals("GC")
|| pair.equals("CG") || pair.equals("GT")
@@
-211,7
+213,7
@@
public class RnaTest
char second = bases.charAt(j);
boolean result = Rna.isCanonicalPair(first, second);
String pair = new String(new char[] { first, second })
char second = bases.charAt(j);
boolean result = Rna.isCanonicalPair(first, second);
String pair = new String(new char[] { first, second })
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
|| pair.equals("UA") || pair.equals("GC")
|| pair.equals("CG"))
if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
|| pair.equals("UA") || pair.equals("GC")
|| pair.equals("CG"))
diff --git
a/test/jalview/commands/EditCommandTest.java
b/test/jalview/commands/EditCommandTest.java
index
348d871
..
91f844e
100644
(file)
--- a/
test/jalview/commands/EditCommandTest.java
+++ b/
test/jalview/commands/EditCommandTest.java
@@
-20,6
+20,8
@@
*/
package jalview.commands;
*/
package jalview.commands;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
@@
-286,7
+288,7
@@
public class EditCommandTest
assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
assertEquals("fghjZ-xYopq", seqs[1].getSequenceAsString());
// Dataset Sequence should always be uppercase
assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
assertEquals("fghjZ-xYopq", seqs[1].getSequenceAsString());
// Dataset Sequence should always be uppercase
- assertEquals("fghjZxYopq".toUpperCase(),
+ assertEquals("fghjZxYopq".toUpperCase(Locale.ROOT),
seqs[1].getDatasetSequence().getSequenceAsString());
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
assertEquals("1234567890", seqs[3].getSequenceAsString());
seqs[1].getDatasetSequence().getSequenceAsString());
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
assertEquals("1234567890", seqs[3].getSequenceAsString());
@@
-317,7
+319,7
@@
public class EditCommandTest
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
// Dataset sequence always uppercase
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
// Dataset sequence always uppercase
- assertEquals("ABxyZDEF".toUpperCase(),
+ assertEquals("ABxyZDEF".toUpperCase(Locale.ROOT),
seq.getDatasetSequence().getSequenceAsString());
assertEquals(8, seq.getDatasetSequence().getEnd());
seq.getDatasetSequence().getSequenceAsString());
assertEquals(8, seq.getDatasetSequence().getEnd());
@@
-343,7
+345,7
@@
public class EditCommandTest
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
// dataset sequence should be Uppercase
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
// dataset sequence should be Uppercase
- assertEquals("ABxyZDEF".toUpperCase(),
+ assertEquals("ABxyZDEF".toUpperCase(Locale.ROOT),
seq.getDatasetSequence().getSequenceAsString());
assertEquals(8, seq.getDatasetSequence().getEnd());
seq.getDatasetSequence().getSequenceAsString());
assertEquals(8, seq.getDatasetSequence().getEnd());
@@
-367,7
+369,7
@@
public class EditCommandTest
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged and UPPERCASE !
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged and UPPERCASE !
- assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString());
+ assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
@@
-394,7
+396,7
@@
public class EditCommandTest
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged AND UPPERCASE !
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged AND UPPERCASE !
- assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString());
+ assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
diff --git
a/test/jalview/datamodel/ResidueCountTest.java
b/test/jalview/datamodel/ResidueCountTest.java
index
e90e1a9
..
a6e7429
100644
(file)
--- a/
test/jalview/datamodel/ResidueCountTest.java
+++ b/
test/jalview/datamodel/ResidueCountTest.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import java.util.Locale;
+
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;
@@
-181,7
+183,7
@@
public class ResidueCountTest
ResidueCount rc = new ResidueCount(false);
// expected characters (upper or lower case):
String aas = "ACDEFGHIKLMNPQRSTVWXY";
ResidueCount rc = new ResidueCount(false);
// expected characters (upper or lower case):
String aas = "ACDEFGHIKLMNPQRSTVWXY";
- String lower = aas.toLowerCase();
+ String lower = aas.toLowerCase(Locale.ROOT);
for (int i = 0; i < aas.length(); i++)
{
rc.put(aas.charAt(i), i);
for (int i = 0; i < aas.length(); i++)
{
rc.put(aas.charAt(i), i);
@@
-206,7
+208,7
@@
public class ResidueCountTest
ResidueCount rc = new ResidueCount(true);
// expected characters (upper or lower case):
String nucs = "ACGTUN";
ResidueCount rc = new ResidueCount(true);
// expected characters (upper or lower case):
String nucs = "ACGTUN";
- String lower = nucs.toLowerCase();
+ String lower = nucs.toLowerCase(Locale.ROOT);
for (int i = 0; i < nucs.length(); i++)
{
rc.put(nucs.charAt(i), i);
for (int i = 0; i < nucs.length(); i++)
{
rc.put(nucs.charAt(i), i);
diff --git
a/test/jalview/datamodel/SequenceTest.java
b/test/jalview/datamodel/SequenceTest.java
index
5069759
..
2b44261
100644
(file)
--- a/
test/jalview/datamodel/SequenceTest.java
+++ b/
test/jalview/datamodel/SequenceTest.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
@@
-812,7
+814,7
@@
public class SequenceTest
} catch (IllegalArgumentException e)
{
// TODO Jalview error/exception class for raising implementation errors
} catch (IllegalArgumentException e)
{
// TODO Jalview error/exception class for raising implementation errors
- assertTrue(e.getMessage().toLowerCase()
+ assertTrue(e.getMessage().toLowerCase(Locale.ROOT)
.contains("implementation error"));
}
assertTrue(sq.getSequenceFeatures().isEmpty());
.contains("implementation error"));
}
assertTrue(sq.getSequenceFeatures().isEmpty());
diff --git
a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index
9e9d9a4
..
c927f04
100644
(file)
--- a/
test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/
test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@
-20,6
+20,8
@@
*/
package jalview.ext.ensembl;
*/
package jalview.ext.ensembl;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
@@
-230,7
+232,7
@@
public class EnsemblCdnaTest
assertTrue(testee.retainFeature(sf, accId));
// test is not case-sensitive
assertTrue(testee.retainFeature(sf, accId));
// test is not case-sensitive
- assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
+ assertTrue(testee.retainFeature(sf, accId.toLowerCase(Locale.ROOT)));
// feature with wrong parent is not retained
sf.setValue("Parent", "XYZ");
// feature with wrong parent is not retained
sf.setValue("Parent", "XYZ");
diff --git
a/test/jalview/ext/ensembl/EnsemblGeneTest.java
b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index
ef12ed4
..
e16197a
100644
(file)
--- a/
test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/
test/jalview/ext/ensembl/EnsemblGeneTest.java
@@
-20,6
+20,8
@@
*/
package jalview.ext.ensembl;
*/
package jalview.ext.ensembl;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
@@
-161,7
+163,7
@@
public class EnsemblGeneTest
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
22000, 22500, 0f, null);
// id matching should not be case-sensitive
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
22000, 22500, 0f, null);
// id matching should not be case-sensitive
- sf3.setValue("Parent", geneId.toLowerCase());
+ sf3.setValue("Parent", geneId.toLowerCase(Locale.ROOT));
sf3.setValue("id", "transcript3");
genomic.addSequenceFeature(sf3);
sf3.setValue("id", "transcript3");
genomic.addSequenceFeature(sf3);
diff --git
a/test/jalview/ext/paradise/TestAnnotate3D.java
b/test/jalview/ext/paradise/TestAnnotate3D.java
index
7d0916b
..
80fffff
100644
(file)
--- a/
test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/
test/jalview/ext/paradise/TestAnnotate3D.java
@@
-20,6
+20,8
@@
*/
package jalview.ext.paradise;
*/
package jalview.ext.paradise;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignmentI;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignmentI;
@@
-151,11
+153,11
@@
public class TestAnnotate3D
{
{
SequenceI struseq = null;
{
{
SequenceI struseq = null;
- String sq_ = sq.getSequenceAsString().toLowerCase();
+ String sq_ = sq.getSequenceAsString().toLowerCase(Locale.ROOT);
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
final String lowerCase = _struseq.getSequenceAsString()
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
final String lowerCase = _struseq.getSequenceAsString()
- .toLowerCase();
+ .toLowerCase(Locale.ROOT);
if (lowerCase.equals(sq_))
{
struseq = _struseq;
if (lowerCase.equals(sq_))
{
struseq = _struseq;
diff --git
a/test/jalview/io/FileFormatsTest.java
b/test/jalview/io/FileFormatsTest.java
index
bf01fb7
..
3d25bf1
100644
(file)
--- a/
test/jalview/io/FileFormatsTest.java
+++ b/
test/jalview/io/FileFormatsTest.java
@@
-1,5
+1,7
@@
package jalview.io;
package jalview.io;
+import java.util.Locale;
+
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotEquals;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotEquals;
@@
-103,8
+105,8
@@
public class FileFormatsTest
for (FileFormatI ff : FileFormat.values())
{
assertSame(ff, formats.forName(ff.getName()));
for (FileFormatI ff : FileFormat.values())
{
assertSame(ff, formats.forName(ff.getName()));
- assertSame(ff, formats.forName(ff.getName().toUpperCase()));
- assertSame(ff, formats.forName(ff.getName().toLowerCase()));
+ assertSame(ff, formats.forName(ff.getName().toUpperCase(Locale.ROOT)));
+ assertSame(ff, formats.forName(ff.getName().toLowerCase(Locale.ROOT)));
}
assertNull(formats.forName(null));
assertNull(formats.forName("rubbish"));
}
assertNull(formats.forName(null));
assertNull(formats.forName("rubbish"));
diff --git
a/test/jalview/ws/gui/Jws2ParamView.java
b/test/jalview/ws/gui/Jws2ParamView.java
index
80b48c3
..
2318971
100644
(file)
--- a/
test/jalview/ws/gui/Jws2ParamView.java
+++ b/
test/jalview/ws/gui/Jws2ParamView.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.gui;
*/
package jalview.ws.gui;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.gui.JvOptionPane;
import jalview.gui.WsJobParameters;
import jalview.bin.Cache;
import jalview.gui.JvOptionPane;
import jalview.gui.WsJobParameters;
@@
-66,7
+68,7
@@
public class Jws2ParamView
public static List<String> presetTests = new ArrayList<String>();
static
{
public static List<String> presetTests = new ArrayList<String>();
static
{
- serviceTests.add("AAConWS".toLowerCase());
+ serviceTests.add("AAConWS".toLowerCase(Locale.ROOT));
}
public static Jws2Discoverer disc = null;
}
public static Jws2Discoverer disc = null;
@@
-91,7
+93,7
@@
public class Jws2ParamView
for (Jws2Instance service : disc.getServices())
{
if (serviceTests.size() == 0
for (Jws2Instance service : disc.getServices())
{
if (serviceTests.size() == 0
- || serviceTests.contains(service.serviceType.toLowerCase()))
+ || serviceTests.contains(service.serviceType.toLowerCase(Locale.ROOT)))
{
List<Preset> prl = null;
Preset pr = null;
{
List<Preset> prl = null;
Preset pr = null;
diff --git
a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index
e8b6c2b
..
d13dc0f
100644
(file)
--- a/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.jabaws;
*/
package jalview.ws.jabaws;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
@@
-85,7
+87,7
@@
public class DisorderAnnotExportImport
iupreds = new ArrayList<Jws2Instance>();
for (Jws2Instance svc : disc.getServices())
{
iupreds = new ArrayList<Jws2Instance>();
for (Jws2Instance svc : disc.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
+ if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("iupredws"))
{
iupreds.add(svc);
}
{
iupreds.add(svc);
}
diff --git
a/test/jalview/ws/jabaws/RNAStructExportImport.java
b/test/jalview/ws/jabaws/RNAStructExportImport.java
index
889c003
..
cc9aba0
100644
(file)
--- a/
test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/
test/jalview/ws/jabaws/RNAStructExportImport.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.jabaws;
*/
package jalview.ws.jabaws;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
@@
-98,7
+100,7
@@
public class RNAStructExportImport
for (Jws2Instance svc : disc.getServices())
{
for (Jws2Instance svc : disc.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+ if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("rnaalifoldws"))
{
rnaalifoldws = svc;
}
{
rnaalifoldws = svc;
}
diff --git
a/test/jalview/ws/jws2/ParameterUtilsTest.java
b/test/jalview/ws/jws2/ParameterUtilsTest.java
index
c0aa2ee
..
51ff19c
100644
(file)
--- a/
test/jalview/ws/jws2/ParameterUtilsTest.java
+++ b/
test/jalview/ws/jws2/ParameterUtilsTest.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.jws2;
*/
package jalview.ws.jws2;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
@@
-68,7
+70,7
@@
public class ParameterUtilsTest
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- serviceTests.add("AAConWS".toLowerCase());
+ serviceTests.add("AAConWS".toLowerCase(Locale.ROOT));
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
@@
-131,7
+133,7
@@
public class ParameterUtilsTest
public boolean isForTesting(Jws2Instance service)
{
return serviceTests.size() == 0
public boolean isForTesting(Jws2Instance service)
{
return serviceTests.size() == 0
- || serviceTests.contains(service.serviceType.toLowerCase());
+ || serviceTests.contains(service.serviceType.toLowerCase(Locale.ROOT));
}
@Test(groups = { "Network" })
}
@Test(groups = { "Network" })
diff --git
a/test/junit/extensions/PrivilegedAccessor.java
b/test/junit/extensions/PrivilegedAccessor.java
index
23f1c6e
..
c5c0f04
100644
(file)
--- a/
test/junit/extensions/PrivilegedAccessor.java
+++ b/
test/junit/extensions/PrivilegedAccessor.java
@@
-15,6
+15,8
@@
*/
package junit.extensions;
*/
package junit.extensions;
+import java.util.Locale;
+
import java.lang.reflect.Array;
import java.lang.reflect.Constructor;
import java.lang.reflect.Field;
import java.lang.reflect.Array;
import java.lang.reflect.Constructor;
import java.lang.reflect.Field;
@@
-432,7
+434,7
@@
final class PrivilegedAccessor
{
return false;
}
{
return false;
}
- if (className.startsWith(className.substring(0, 1).toUpperCase()))
+ if (className.startsWith(className.substring(0, 1).toUpperCase(Locale.ROOT)))
{
return true;
}
{
return true;
}