*/
package jalview.datamodel;
+import java.util.Locale;
+
import java.util.HashSet;
import java.util.List;
import java.util.Set;
* 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)
{
- allele = allele.trim().toUpperCase();
+ allele = allele.trim().toUpperCase(Locale.ROOT);
if (allele.length() > 1 || "-".equals(allele))
{
continue; // multi-locus variant
*/
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;
public int[] getMappedPositions(int begin, int end)
{
MapList map = mapping.getMap();
- return mapping.to == featureSequence ? map.locateInFrom(begin, end)
- : map.locateInTo(begin, end);
+ return mapping.to == featureSequence ? map.getOverlapsInFrom(begin, end)
+ : map.getOverlapsInTo(begin, end);
}
/**