- seq.insertCharAt(0, sg.getStartRes(), '-');
- seq.insertCharAt(sg.getEndRes(),
- alignment.getWidth() - sg.getEndRes(), '-');
- SequenceI topSeq = sg.getSequencesInOrder(alignment)[0];
- int topIndex = alignment.findIndex(topSeq);
- alignment.getSequences().add(topIndex, seq);
- sg.setSeqrep(seq);
- viewport.getSelectionGroup().addSequence(seq, false);
+ /*
+ * fudge: move HMM consensus sequence from last to first
+ */
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+ alignment.insertSequenceAt(0, seq);