package jalview.analysis.scoremodels;
-import jalview.api.analysis.DistanceModelI;
+import jalview.api.analysis.ScoreModelI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
private static ScoreModels instance = new ScoreModels();
- private Map<String, DistanceModelI> models;
+ private Map<String, ScoreModelI> models;
public static ScoreModels getInstance()
{
* <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()
/*
* using LinkedHashMap keeps models ordered as added
*/
- models = new LinkedHashMap<String, DistanceModelI>();
+ 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());
}
/**
}
/**
- * Registers a pairwise score model
- *
- * @param sm
- */
- public void registerScoreModel(PairwiseScoreModelI sm)
- {
- registerScoreModel(new PairwiseDistanceModel(sm));
- }
-
- /**
* Answers an iterable set of the registered score models. Currently these are
* returned in the order in which they were registered.
*
* @return
*/
- public Iterable<DistanceModelI> getModels()
+ public Iterable<ScoreModelI> getModels()
{
return models.values();
}
- public DistanceModelI forName(String s)
+ public ScoreModelI forName(String s)
{
return models.get(s);
}
- public void registerScoreModel(DistanceModelI sm)
+ public void registerScoreModel(ScoreModelI sm)
{
- DistanceModelI sm2 = models.get(sm.getName());
+ ScoreModelI sm2 = models.get(sm.getName());
if (sm2 != null)
{
System.err.println("Warning: replacing score model " + sm2.getName());