*/
package jalview.api.analysis;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentView;
+import jalview.math.MatrixI;
public interface ScoreModelI
{
-
- float[][] findDistances(AlignmentView seqData);
-
+ /**
+ * Answers a name for the score model, suitable for display in menus. Names
+ * should be unique across score models in use.
+ *
+ * @return
+ * @see jalview.analysis.scoremodels.ScoreModels#forName(String)
+ */
String getName();
+ /**
+ * Answers an informative description of the model, suitable for use in
+ * tooltips. Descriptions may be internationalised, and need not be unique
+ * (but should be).
+ *
+ * @return
+ */
+ String getDescription();
+
+ /**
+ * Answers true if this model is applicable for nucleotide data (so should be
+ * shown in menus in that context)
+ *
+ * @return
+ */
boolean isDNA();
+ /**
+ * Answers true if this model is applicable for peptide data (so should be
+ * shown in menus in that context)
+ *
+ * @return
+ */
boolean isProtein();
+ // TODO getName, isDNA, isProtein can be static methods in Java 8
+
+ default public boolean isSecondaryStructure()
+ {
+ return false;
+ }
+
+ /**
+ * Answers false by default Answers true if the data has secondary structure
+ * (so should be shown in menus in that context)
+ *
+ * @return
+ */
+
+ /**
+ * Returns a distance score for the given sequence regions, that is, a matrix
+ * whose value [i][j] is the distance of sequence i from sequence j by some
+ * measure. The options parameter provides configuration choices for how the
+ * similarity score is calculated.
+ *
+ * @param seqData
+ * @param options
+ * @return
+ */
+
+ MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
+
+ /**
+ * Returns a similarity score for the given sequence regions, that is, a
+ * matrix whose value [i][j] is the similarity of sequence i to sequence j by
+ * some measure. The options parameter provides configuration choices for how
+ * the similarity score is calculated.
+ *
+ * @param seqData
+ * @param options
+ * @return
+ */
+ 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);
}