List<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps);
-
int getWidth();
+ /**
+ *
+ * @return true if getSeqrep doesn't return null
+ */
+ boolean hasSeqrep();
+ /**
+ * get the reference or representative sequence within this collection
+ * @return null or the current reference sequence
+ */
+ SequenceI getSeqrep();
+ /**
+ * set the reference or representative sequence for this collection.
+ * Reference is assumed to be present within the collection.
+ * @return
+ */
+ void setSeqrep(SequenceI refseq);
/**
* @return the first column included in this collection. Runs from 0<=i<N_cols