- SequenceGroup sg = ap.av.getSelectionGroup();
- ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
- omitHidden = ap.av.getViewAsString(true);
- Alignment oal = new Alignment(ap.av.getSequenceSelection());
- AlignmentAnnotation[] nala = ap.av.getAlignment()
- .getAlignmentAnnotation();
- if (nala != null)
+
+ AlignmentView selvew = ap.av.getAlignmentView(true, false);
+ AlignmentI aselview = selvew.getVisibleAlignment(ap.av
+ .getGapCharacter());
+ List<AlignmentAnnotation> ala = (ap.av
+ .getVisibleAlignmentAnnotation(true));
+ if (ala != null)