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();
/**
+ * Retrieve a ContactListI corresponding to column in an annotation row in an
+ * alignment.
+ *
+ * @param _aa
+ * - annotation with associated matrix data
+ * @param column
+ * - column in alignment where _aa is associated
+ */
+ 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.
*
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
-
/**
* notify all concerned that the alignment data has changed and derived data
* needs to be recalculated
*/
public void notifyAlignmentChanged();
+
+ /**
+ * retrieve a matrix associated with the view's alignment's annotation
+ * @param alignmentAnnotation
+ * @return contact matrix or NULL
+ */
+ ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
}