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JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations
author
Jim Procter
<jprocter@issues.jalview.org>
Mon, 10 Aug 2020 14:10:35 +0000
(15:10 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Mon, 10 Aug 2020 14:10:35 +0000
(15:10 +0100)
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/JnetAnnotationMaker.java
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src/jalview/io/MSFfile.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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diff --git
a/src/jalview/io/FeaturesFile.java
b/src/jalview/io/FeaturesFile.java
index
92473ec
..
7e62f6b
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-28,6
+28,7
@@
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.TreeMap;
import java.util.Map;
import java.util.Map.Entry;
import java.util.TreeMap;
@@
-346,7
+347,8
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
String line;
while ((line = nextLine()) != null)
{
String line;
while ((line = nextLine()) != null)
{
- if (line.toUpperCase().startsWith(ENDFILTERS))
+ // TODO: use .trim().equalsIgnoreCase here instead ?
+ 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
..
de83e9b
100644
(file)
--- a/
src/jalview/io/FileFormats.java
+++ b/
src/jalview/io/FileFormats.java
@@
-24,6
+24,7
@@
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Set;
import java.util.Map;
import java.util.Set;
@@
-102,7
+103,7
@@
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
+122,7
@@
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
+175,7
@@
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
6d3c18a
..
4d8794f
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-33,6
+33,7
@@
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.io.IOException;
import jalview.util.Comparison;
import java.io.IOException;
+import java.util.Locale;
/**
* Additional formatting methods used by the application in a number of places.
/**
* Additional formatting methods used by the application in a number of places.
@@
-161,7
+162,7
@@
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
ff959b0
..
ed1c29f
100755
(executable)
--- a/
src/jalview/io/IdentifyFile.java
+++ b/
src/jalview/io/IdentifyFile.java
@@
-21,6
+21,7
@@
package jalview.io;
import java.io.IOException;
package jalview.io;
import java.io.IOException;
+import java.util.Locale;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-143,7
+144,7
@@
public class IdentifyFile
break;
}
}
break;
}
}
- data = data.toUpperCase();
+ data = data.toUpperCase(Locale.ROOT);
if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
@@
-284,7
+285,7
@@
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
6732e82
..
8f93b48
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-33,6
+33,7
@@
import jalview.util.MessageManager;
import java.io.IOException;
import java.util.Hashtable;
import java.io.IOException;
import java.util.Hashtable;
+import java.util.Locale;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.StringTokenizer;
import java.util.Vector;
@@
-408,7
+409,7
@@
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/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
..
db29848
100755
(executable)
--- a/
src/jalview/io/MSFfile.java
+++ b/
src/jalview/io/MSFfile.java
@@
-29,6
+29,7
@@
import java.io.IOException;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.Locale;
import java.util.StringTokenizer;
/**
import java.util.StringTokenizer;
/**
@@
-184,7
+185,7
@@
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/packed/ParsePackedSet.java
b/src/jalview/io/packed/ParsePackedSet.java
index
1635682
..
91575bf
100644
(file)
--- a/
src/jalview/io/packed/ParsePackedSet.java
+++ b/
src/jalview/io/packed/ParsePackedSet.java
@@
-34,6
+34,7
@@
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
public class ParsePackedSet
{
public class ParsePackedSet
{
@@
-234,7
+235,7
@@
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;
@@
-253,7
+254,7
@@
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
13d7ae8
..
d6a530b
100644
(file)
--- a/
src/jalview/io/vcf/VCFLoader.java
+++ b/
src/jalview/io/vcf/VCFLoader.java
@@
-48,6
+48,7
@@
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
@@
-569,7
+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;
}
@@
-663,7
+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);