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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...
[jalview.git]
/
src
/
jalview
/
io
/
vcf
/
VCFLoader.java
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