2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis.scoremodels;
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.analysis.ScoreModelI;
25 import jalview.bin.ApplicationSingletonProvider;
26 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
27 import jalview.io.DataSourceType;
28 import jalview.io.FileParse;
29 import jalview.io.ScoreMatrixFile;
31 import java.io.IOException;
32 import java.util.LinkedHashMap;
36 * A class that can register and serve instances of ScoreModelI
38 public class ScoreModels implements ApplicationSingletonI
41 * Answers the singleton instance of this class, with lazy initialisation
42 * (built-in score models are loaded on the first call to this method)
46 public static ScoreModels getInstance()
48 return (ScoreModels) ApplicationSingletonProvider.getInstance(ScoreModels.class);
52 * Private constructor to enforce use of singleton. Registers Jalview's
53 * "built-in" score models:
59 * <li>Sequence Feature Similarity</li>
65 * using LinkedHashMap keeps models ordered as added
67 models = new LinkedHashMap<>();
68 BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
69 PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
70 DNA = loadScoreMatrix("scoreModel/dna.scm");
71 registerScoreModel(new PIDModel());
72 registerScoreModel(new FeatureDistanceModel());
75 private final ScoreMatrix BLOSUM62;
77 private final ScoreMatrix PAM250;
79 private final ScoreMatrix DNA;
81 private Map<String, ScoreModelI> models;
84 * Tries to load a score matrix from the given resource file, and if
85 * successful, registers it.
90 ScoreMatrix loadScoreMatrix(String resourcePath)
95 * delegate parsing to ScoreMatrixFile
97 FileParse fp = new FileParse(resourcePath,
98 DataSourceType.CLASSLOADER);
99 ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
100 registerScoreModel(sm);
102 } catch (IOException e)
105 "Error reading " + resourcePath + ": " + e.getMessage());
111 * Answers an iterable set of the registered score models. Currently these are
112 * returned in the order in which they were registered.
116 public Iterable<ScoreModelI> getModels()
118 return models.values();
122 * Returns an instance of a score model for the given name. If the model is of
123 * 'view dependent' type (e.g. feature similarity), instantiates a new
124 * instance configured for the given view. Otherwise returns a cached instance
125 * of the score model.
131 public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)
133 ScoreModelI model = models.get(name);
134 return model == null ? null : model.getInstance(avp);
137 public void registerScoreModel(ScoreModelI sm)
139 ScoreModelI sm2 = models.get(sm.getName());
142 System.err.println("Warning: replacing score model " + sm2.getName());
144 models.put(sm.getName(), sm);
148 * Resets to just the built-in score models
152 ApplicationSingletonProvider.removeInstance(this.getClass());
156 * Returns the default peptide or nucleotide score model, currently BLOSUM62
162 public ScoreMatrix getDefaultModel(boolean forPeptide)
164 return forPeptide ? BLOSUM62 : DNA;
167 public ScoreMatrix getBlosum62()
172 public ScoreMatrix getPam250()