+ /**
+ * 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);