/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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();
*/
int getEndRes();
+ /**
+ * Answers true if sequence data is nucleotide (according to some heuristic)
+ *
+ * @return
+ */
+ boolean isNucleotide();
+
+ /**
+ * Returns the (possibly empty) list of HMM consensus sequences in the
+ * collection
+ *
+ * @return
+ */
+ List<SequenceI> getHmmSequences();
}