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.
+ * set the reference or representative sequence for this collection. Reference
+ * is assumed to be present within the collection.
+ *
* @return
*/
void setSeqrep(SequenceI refseq);