- * A helper method that deletes any HMM consensus sequence from the given
- * collection, and from the parent alignment if <code>ac</code> is a subgroup
- *
- * @param ac
- */
- void deleteHmmSequences(AnnotatedCollectionI ac)
- {
- List<SequenceI> hmmSeqs = ac.getHmmSequences();
- for (SequenceI hmmSeq : hmmSeqs)
- {
- if (ac instanceof SequenceGroup)
- {
- ((SequenceGroup) ac).deleteSequence(hmmSeq, false);
- AnnotatedCollectionI context = ac.getContext();
- if (context != null && context instanceof AlignmentI)
- {
- ((AlignmentI) context).deleteSequence(hmmSeq);
- }
- }
- else
- {
- ((AlignmentI) ac).deleteSequence(hmmSeq);
- }
- }
- }
-
- /**