AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
/**
- * Set the hidden columns collection on the alignment
+ * Set the hidden columns collection on the alignment. Answers true if the
+ * hidden column selection changed, else false.
*
* @param cols
+ * @return
*/
- public void setHiddenColumns(HiddenColumns cols);
+ public boolean setHiddenColumns(HiddenColumns cols);
/**
* Set the first sequence as representative and hide its insertions. Typically
public HiddenColumns propagateInsertions(SequenceI profileseq,
AlignmentView input);
+ /**
+ * 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);
}