int scalestartx = (startx / 10) * 10;
SequenceI refSeq = av.getAlignment().getSeqrep();
- int refSp = 0, refStartI = 0, refEndI = -1;
+ int refSp = 0;
+ int refStartI = 0;
+ int refEndI = -1;
if (refSeq != null)
{
- // find bounds and set origin appopriately
+ // find bounds and set origin appropriately
// locate first visible position for this sequence
- int[] refbounds = av.getAlignment().getHiddenColumns()
+ refSp = av.getAlignment().getHiddenColumns()
.locateVisibleBoundsOfSequence(refSeq);
- refSp = refbounds[0];
- refStartI = refbounds[1];
- refEndI = refbounds[2];
+ refStartI = refSeq.findIndex(refSeq.getStart()) - 1;
+
+ int seqlength = refSeq.getLength();
+ // get sequence position past the end of the sequence
+ int pastEndPos = refSeq.findPosition(seqlength + 1);
+ refEndI = refSeq.findIndex(pastEndPos - 1) - 1;
+
scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
}