+ /**
+ *
+ * Similar to AlignedCodonFrame.getMappingBetween
+ *
+ * @param sequenceRef
+ * - a reference sequence mappable to this contactMatrix - may be
+ * null
+ * @return null or the MapList mapping to the coordinates of the reference
+ * sequence (or if hasReferenceSeq() is false, and sequenceRef is
+ * null, any mapping present)
+ *
+ */
+ MapList getMapFor(SequenceI sequenceRef);
+
+ /**
+ * Locate a position in the mapped sequence for a single column in the matrix.
+ * this to resolve positions corresponding to column clusters
+ *
+ * @param localFrame
+ * - sequence derivced from reference sequence
+ * @param column
+ * - matrix row/column
+ * @return sequence position(s) corresponding to column in contact matrix
+ */
+ int[] getMappedPositionsFor(SequenceI localFrame, int column);
+
+ /**
+ * Locate a position in the mapped sequence for a contiguous range of columns
+ * in the matrix use this to resolve positions corresponding to column
+ * clusters
+ *
+ * @param localFrame
+ * - sequence derivced from reference sequence
+ * @param column
+ * - matrix row/column
+ * @return sequence position(s) corresponding to column in contact matrix
+ */
+ int[] getMappedPositionsFor(SequenceI localFrame, int from, int to);
+
+ ContactMatrixI getMappedMatrix();