+
+ /**
+ * Locate the first position in this sequence which is not contained in an
+ * iterator region. If no such position exists, return 0
+ *
+ * @param it
+ * iterator over regions
+ * @return first residue not contained in regions
+ */
+ public int firstResidueOutsideIterator(Iterator<int[]> it);
+
+
+ /**
+ * Answers true if this sequence has an associated Hidden Markov Model
+ *
+ * @return
+ */
+ boolean hasHMMProfile();