- seq.setIsHMMConsensusSequence(true);
- alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
- alignment.insertSequenceAt(0, seq);
+ if (seq.hasHMMProfile())
+ {
+ /*
+ * fudge: move HMM consensus sequence from last to first
+ */
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+ alignment.insertSequenceAt(0, seq);
+ }