private final ScoreMatrix PAM250;
+ private final ScoreMatrix DNA;
+
private static ScoreModels instance = new ScoreModels();
private Map<String, ScoreModelI> models;
* <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/dna.scm");
- loadScoreMatrix("scoreModel/seqspace.scm");
- registerScoreModel(new FeatureScoreModel());
- registerScoreModel(new PIDScoreModel());
+ registerScoreModel(new PIDModel());
+ DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new FeatureDistanceModel());
}
/**
* @param forPeptide
* @return
*/
- public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
+ public ScoreMatrix getDefaultModel(boolean forPeptide)
{
- return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
- : forName("DNA"));
+ return forPeptide ? BLOSUM62 : DNA;
}
public ScoreMatrix getBlosum62()