+
+ /**
+ * @return the first column included in this collection. Runs from 0<=i<N_cols
+ */
+ int getStartRes();
+
+ /**
+ *
+ * @return the last column in this collection. Runs from 0<=i<N_cols
+ */
+ 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();