gps = jalview.analysis.Grouping.makeGroupsFromCols(
(sg == null) ? viewport.getAlignment().getSequencesArray()
: sg.getSequences().toArray(new SequenceI[0]),
- cs, viewport.getAlignment().getGroups());
+ cs, viewport.getAlignment().getGroups(),
+ viewport.getAlignment().getHiddenColumns());
}
}
if (gps != null)