import jalview.io.ScoreMatrixFile;
import java.io.IOException;
+import java.util.LinkedHashMap;
import java.util.Map;
-import java.util.TreeMap;
/**
* A class that can register and serve instances of ScoreModelI
*/
public class ScoreModels
{
- private static ScoreModels instance = new ScoreModels();
+ /*
+ * constants for built-in score model names
+ * NB! these have to match names in loaded score matrix files
+ */
+ public static final String BLOSUM62 = "BLOSUM62";
+
+ public static final String PAM250 = "PAM250";
+ public static final String DNA = "DNA";
+
+ private static ScoreModels instance = new ScoreModels();
private Map<String, ScoreModelI> models;
public static ScoreModels getInstance()
* <ul>
* <li>BLOSUM62</li>
* <li>PAM250</li>
+ * <li>SeqSpace (identity matrix)</li>
* <li>DNA</li>
* <li>Sequence Feature Similarity</li>
* <li>Percentage Identity</li>
private ScoreModels()
{
/*
- * using TreeMap keeps models ordered alphabetically by name
+ * using LinkedHashMap keeps models ordered as added
*/
- models = new TreeMap<String, ScoreModelI>(String.CASE_INSENSITIVE_ORDER);
+ models = new LinkedHashMap<String, ScoreModelI>();
loadScoreMatrix("scoreModel/blosum62.scm");
loadScoreMatrix("scoreModel/pam250.scm");
+ loadScoreMatrix("scoreModel/seqspace.scm");
loadScoreMatrix("scoreModel/dna.scm");
registerScoreModel(new FeatureScoreModel());
registerScoreModel(new PIDScoreModel());
/**
* Answers an iterable set of the registered score models. Currently these are
- * ordered by name (not case sensitive).
+ * returned in the order in which they were registered.
*
* @return
*/
}
models.put(sm.getName(), sm);
}
+
+ /**
+ * Returns the default peptide or nucleotide score model, currently BLOSUM62
+ * or DNA
+ *
+ * @param forPeptide
+ * @return
+ */
+ public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
+ {
+ return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
+ : forName("DNA"));
+ }
}