- /*
- * copy over sequences, excluding hmm consensus sequences
- * hmm sequences are also deleted in preparation for
- * re-adding them when recalculated; Information annotation is not
- * deleted, it will be updated to reference the new hmm sequence
- * by InformationThread.findOrCreateAnnotation
- */
- Iterator<SequenceI> it = copy.iterator();
- while (it.hasNext())
+ deleteHmmSequences(ac);
+
+ List<SequenceI> copy = new ArrayList<>();
+ if (ac instanceof Alignment)
+ {
+ copy.addAll(ac.getSequences());
+ }
+ else