import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+ ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
}