- // this should largely be a method in Alignment
- hiddenRow = false;
- if (hasHiddenRows)
- {
- // look for sequence in hidden rows
- seq = av.getAlignment().getHiddenSequences()
- .getHiddenSequence(lastrow);
- if (seq == null)
- {
- // didn't find in hidden rows, adjust the index and retrieve from
- // full row set
- int index = av.getAlignment().getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = av.getAlignment().getSequenceAt(index);
- }
- else
- {
- // found in hidden rows, ergo this row is hidden
- hiddenRow = true;
- }
- }
- else
- {
- seq = av.getAlignment().getSequenceAt(lastrow);
- }
- // end of Alignment method
+ // get the sequence which would be at alignment index 'lastrow' if no
+ // columns were hidden, and determine whether it is hidden or not
+ hiddenRow = av.getAlignment().isHidden(lastrow);
+ seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);