- // locate first visible position for this sequence
- refSp = av.getAlignment().getHiddenColumns()
- .locateVisibleBoundsOfSequence(refSeq);
+ // locate first residue in sequence which is not hidden
+ Iterator<int[]> it = hc.iterator();
+ int index = refSeq.firstResidueOutsideIterator(it);
+ refSp = hc.absoluteToVisibleColumn(index);