*/
package jalview.api;
+import java.awt.Color;
+import java.awt.Font;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
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;
import jalview.schemes.ColourSchemeI;
import jalview.viewmodel.ViewportRanges;
-import java.awt.Color;
-import java.awt.Font;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
/**
* @author jimp
*
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);
}