package jalview.analysis.scoremodels;
+import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.ScoreModelI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
* <ul>
* <li>BLOSUM62</li>
* <li>PAM250</li>
- * <li>SeqSpace (identity matrix)</li>
+ * <li>PID</li>
* <li>DNA</li>
* <li>Sequence Feature Similarity</li>
- * <li>Percentage Identity</li>
* </ul>
*/
private ScoreModels()
models = new LinkedHashMap<String, ScoreModelI>();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- loadScoreMatrix("scoreModel/seqspace.scm");
- // drop seqspace.scm for IdentityScoreModel once JAL-2379 merged in?
- // registerScoreModel(new IdentityScoreModel());
+ registerScoreModel(new PIDModel());
DNA = loadScoreMatrix("scoreModel/dna.scm");
registerScoreModel(new FeatureDistanceModel());
- registerScoreModel(new PIDDistanceModel());
}
/**
return models.values();
}
- public ScoreModelI forName(String s)
+ /**
+ * Returns an instance of a score model for the given name. If the model is of
+ * 'view dependent' type (e.g. feature similarity), instantiates a new
+ * instance configured for the given view. Otherwise returns a cached instance
+ * of the score model.
+ *
+ * @param name
+ * @param avp
+ * @return
+ */
+ public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)
{
- return models.get(s);
+ ScoreModelI model = models.get(name);
+ return model == null ? null : model.getInstance(avp);
}
public void registerScoreModel(ScoreModelI sm)