*/
package jalview.analysis;
+import java.util.Locale;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
// 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(
- 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
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))
*/
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;