*/
package jalview.datamodel;
+import java.util.Locale;
+
import jalview.analysis.Rna;
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.analysis.WUSSParseException;
seqPos = i + startRes;
}
- sequenceMapping.put(new Integer(seqPos), annotations[i]);
+ sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
}
}
{
for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
{
- index = new Integer(a);
+ index = Integer.valueOf(a);
Annotation annot = sequenceMapping.get(index);
if (annot != null)
{
{
if (seqname && this.sequenceRef != null)
{
- int i = description.toLowerCase().indexOf("<html>");
+ int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
if (i > -1)
{
// move the html tag to before the sequence reference.