int scalestartx = (startx / 10) * 10;
SequenceI refSeq = av.getAlignment().getSeqrep();
- int refSp = 0, refEp = -1;
+ int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
if (refSeq != null)
{
// find bounds and set origin appopriately
refSp = refbounds[0];
refEp = refbounds[1];
+ refStart = refbounds[2];
+ refEnd = refbounds[3];
+ refStartI = refbounds[4];
+ refEndI = refbounds[5];
scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
}
// TODO show bounds if position is a gap
// - ie L--R -> "1L|2R" for
// marker
- if (iadj < refSp)
+ if (iadj < refStartI)
{
- string = String.valueOf(iadj - refSp);
+ string = String.valueOf(iadj - refStartI);
}
- else if (iadj > refEp)
+ else if (iadj > refEndI)
{
- string = "+" + String.valueOf(iadj - refEp);
+ string = "+" + String.valueOf(iadj - refEndI);
}
else
{