- hmmSeqs = alignment.getHMMConsensusSequences(true);
- HMMERCommands.exportData(alignment, true, false,
- new HiddenMarkovModel());
+ SequenceI[] array;
+ List<SequenceI> seqs = alignment
+ .getHMMConsensusSequences(true);
+ cmds.setHmmSeqs(seqs);
+ if (group != null)
+ {
+ array = group.getSelectionAsNewSequences(alignment);
+ }
+ else
+ {
+ if (!alignment.isAligned())
+ {
+ alignment.padGaps();
+ }
+ array = alignment.getSequencesArray();
+ }
+ SequenceI[] newArr = new SequenceI[array.length];
+ int index = 0;
+ for (SequenceI seq : array)
+ {
+ newArr[index] = new Sequence(seq);
+ index++;
+ }
+ cmds.uniquifySequences(newArr);
+ cmds.exportData(newArr, stoTemp, null, null);
+ jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
+