import jalview.datamodel.AlignmentI;
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;
*/
SearchResultsI getSearchResults();
+ ContactListI getContactList(AlignmentAnnotation _aa, int column);
+
/**
* Updates view settings with the given font. You may need to call
* AlignmentPanel.fontChanged to update the layout geometry.
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
IdColumns getIdColumns();
+
+ ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
}