*/
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.renderer.ResidueShaderI;
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;
+import jalview.viewmodel.seqfeatures.IdColumns;
/**
* @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);
/**
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+ IdColumns getIdColumns();
+
ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
}