package jalview.api.analysis;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentView;
import jalview.math.MatrixI;
* @param options
* @return
*/
- MatrixI findSimilarities(AlignmentView seqData, SimilarityParamsI options);
+ MatrixI findSimilarities(AlignmentView seqData,
+ SimilarityParamsI options);
+
+ /**
+ * Returns a score model object configured for the given alignment view.
+ * Depending on the score model, this may just be a singleton instance, or a
+ * new instance configured with data from the view.
+ *
+ * @param avp
+ * @return
+ */
+ ScoreModelI getInstance(AlignmentViewPanel avp);
}