public interface SequenceCollectionI
{
+ /**
+ *
+ * @return (visible) sequences in this collection. This may be a direct
+ * reference to the collection so not thread safe
+ */
List<SequenceI> getSequences();
+ /**
+ * FIXME: AlignmentI.getSequences(hiddenReps) doesn't actually obey this
+ * contract!
+ *
+ * @param hiddenReps
+ * @return the full set of sequences in this collection, including any
+ * sequences represented by sequences in the collection.
+ */
List<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps);
boolean isNucleotide();
/**
- * Returns the HMM consensus sequence (if any) for the collection, or null
+ * Returns the (possibly empty) list of HMM consensus sequences in the
+ * collection
*
* @return
*/
- SequenceI getHmmConsensus();
-
- /**
- * Sets the HMM consensus sequence for the collection
- */
- void setHmmConsensus(SequenceI hmmSeq);
+ List<SequenceI> getHmmSequences();
}