/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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
*/
int getStartRes();