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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...
[jalview.git]
/
src
/
jalview
/
datamodel
/
MappedFeatures.java
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;