* @param results
* @return -1 or index of sequence in alignment
*/
- int findIndex(SearchResults results);
+ int findIndex(SearchResultsI results);
/**
* append sequences and annotation from another alignment object to this one.
* @return
*/
public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+
+ /**
+ * resolve a contact list instance (if any) associated with the annotation row
+ * and column position
+ *
+ * @param _aa
+ * @param column
+ * @return
+ */
+ ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
+
+ AlignmentAnnotation addContactList(ContactMatrixI cm);
}