package jalview.analysis.scoremodels;
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.DistanceModelI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
*/
public class ScoreModels
{
+ private final ScoreMatrix BLOSUM62;
+
+ private final ScoreMatrix PAM250;
+
+ private final ScoreMatrix DNA;
+
private static ScoreModels instance = new ScoreModels();
- private Map<String, ScoreModelI> models;
+ private Map<String, DistanceModelI> models;
public static ScoreModels getInstance()
{
/*
* using LinkedHashMap keeps models ordered as added
*/
- models = new LinkedHashMap<String, ScoreModelI>();
- loadScoreMatrix("scoreModel/blosum62.scm");
- loadScoreMatrix("scoreModel/pam250.scm");
+ models = new LinkedHashMap<String, DistanceModelI>();
+ BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
+ PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
loadScoreMatrix("scoreModel/seqspace.scm");
- loadScoreMatrix("scoreModel/dna.scm");
- registerScoreModel(new FeatureScoreModel());
- registerScoreModel(new PIDScoreModel());
+ // drop seqspace.scm for IdentityScoreModel once JAL-2379 merged in?
+ // registerScoreModel(new IdentityScoreModel());
+ DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new FeatureDistanceModel());
+ registerScoreModel(new PIDDistanceModel());
}
/**
- * Try to load a score matrix from the given resource file, and if successful,
- * register it. Answers true if successful, else false.
+ * Tries to load a score matrix from the given resource file, and if
+ * successful, registers it.
*
* @param string
+ * @return
*/
- boolean loadScoreMatrix(String resourcePath)
+ ScoreMatrix loadScoreMatrix(String resourcePath)
{
try
{
FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
registerScoreModel(sm);
- return true;
+ return sm;
} catch (IOException e)
{
System.err.println("Error reading " + resourcePath + ": "
+ e.getMessage());
}
- return false;
+ return null;
+ }
+
+ /**
+ * Registers a pairwise score model
+ *
+ * @param sm
+ */
+ public void registerScoreModel(PairwiseScoreModelI sm)
+ {
+ registerScoreModel(new PairwiseDistanceModel(sm));
}
/**
*
* @return
*/
- public Iterable<ScoreModelI> getModels()
+ public Iterable<DistanceModelI> getModels()
{
return models.values();
}
- public ScoreModelI forName(String s)
+ public DistanceModelI forName(String s)
{
return models.get(s);
}
- public void registerScoreModel(ScoreModelI sm)
+ public void registerScoreModel(DistanceModelI sm)
{
- ScoreModelI sm2 = models.get(sm.getName());
+ DistanceModelI sm2 = models.get(sm.getName());
if (sm2 != null)
{
System.err.println("Warning: replacing score model " + sm2.getName());
}
models.put(sm.getName(), sm);
}
+
+ /**
+ * Returns the default peptide or nucleotide score model, currently BLOSUM62
+ * or DNA
+ *
+ * @param forPeptide
+ * @return
+ */
+ public ScoreMatrix getDefaultModel(boolean forPeptide)
+ {
+ return forPeptide ? BLOSUM62 : DNA;
+ }
+
+ public ScoreMatrix getBlosum62()
+ {
+ return BLOSUM62;
+ }
+
+ public ScoreMatrix getPam250()
+ {
+ return PAM250;
+ }
}