if ((sg != null) && (sg.getSize() >= 1))
{
- originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+ originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
start = sg.getStartRes();
end = sg.getEndRes();
}
else
{
- originalSequences = ap.av.alignment.getSequencesArray();
+ originalSequences = ap.av.getAlignment().getSequencesArray();
start = 0;
- end = ap.av.alignment.getWidth();
+ end = ap.av.getAlignment().getWidth();
}
height = originalSequences.length;
redundancy[i] = 0f;
}
- if (ap.av.hasHiddenColumns)
+ if (ap.av.hasHiddenColumns())
{
omitHidden = ap.av.getViewAsString(sg != null);
}
}
EditCommand cut = new EditCommand("Remove Redundancy",
- EditCommand.CUT, deleted, 0, width, ap.av.alignment);
+ EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
for (int i = 0; i < del.size(); i++)
{
- ap.av.alignment.deleteSequence(deleted[i]);
+ ap.av.getAlignment().deleteSequence(deleted[i]);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
if (sg != null)
{