+ List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
+
+ /**
+ * Method to call to indicate that the sequence (characters or alignment/gaps)
+ * has been modified. Provided to allow any cursors on residue/column
+ * positions to be invalidated.
+ */
+ void sequenceChanged();
+
+ /**
+ *
+ * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+ * returns true.
+ */
+ BitSet getInsertionsAsBits();
+
+ /**
+ * Replaces every occurrence of c1 in the sequence with c2 and returns the
+ * number of characters changed
+ *
+ * @param c1
+ * @param c2
+ */
+ public int replace(char c1, char c2);