1 package jalview.analysis.scoremodels;
3 import jalview.api.analysis.ScoreModelI;
4 import jalview.io.DataSourceType;
5 import jalview.io.FileParse;
6 import jalview.io.ScoreMatrixFile;
8 import java.io.IOException;
9 import java.util.LinkedHashMap;
13 * A class that can register and serve instances of ScoreModelI
15 public class ScoreModels
17 private final ScoreMatrix BLOSUM62;
19 private final ScoreMatrix PAM250;
21 private static ScoreModels instance = new ScoreModels();
23 private Map<String, ScoreModelI> models;
25 public static ScoreModels getInstance()
31 * Private constructor to enforce use of singleton. Registers Jalview's
32 * "built-in" score models:
36 * <li>SeqSpace (identity matrix)</li>
38 * <li>Sequence Feature Similarity</li>
39 * <li>Percentage Identity</li>
45 * using LinkedHashMap keeps models ordered as added
47 models = new LinkedHashMap<String, ScoreModelI>();
48 BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
49 PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
50 loadScoreMatrix("scoreModel/dna.scm");
51 loadScoreMatrix("scoreModel/seqspace.scm");
52 registerScoreModel(new FeatureScoreModel());
53 registerScoreModel(new PIDScoreModel());
57 * Tries to load a score matrix from the given resource file, and if
58 * successful, registers it.
63 ScoreMatrix loadScoreMatrix(String resourcePath)
68 * delegate parsing to ScoreMatrixFile
70 FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
71 ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
72 registerScoreModel(sm);
74 } catch (IOException e)
76 System.err.println("Error reading " + resourcePath + ": "
83 * Answers an iterable set of the registered score models. Currently these are
84 * returned in the order in which they were registered.
88 public Iterable<ScoreModelI> getModels()
90 return models.values();
93 public ScoreModelI forName(String s)
98 public void registerScoreModel(ScoreModelI sm)
100 ScoreModelI sm2 = models.get(sm.getName());
103 System.err.println("Warning: replacing score model " + sm2.getName());
105 models.put(sm.getName(), sm);
109 * Returns the default peptide or nucleotide score model, currently BLOSUM62
115 public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
117 return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
121 public ScoreMatrix getBlosum62()
126 public ScoreMatrix getPam250()