* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
- sg.setColourScheme(cs);
+ sg.setColourScheme(cs.getInstance(sg, hiddenRepSequences));
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
for (int seqNo = ranges
- .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))