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.io.DataSourceType;
26 import jalview.io.FileParse;
27 import jalview.io.ScoreMatrixFile;
29 import java.io.IOException;
30 import java.util.LinkedHashMap;
34 * A class that can register and serve instances of ScoreModelI
36 public class ScoreModels
38 private final ScoreMatrix BLOSUM62;
40 private final ScoreMatrix PAM250;
42 private final ScoreMatrix DNA;
44 private static ScoreModels instance;
46 private Map<String, ScoreModelI> models;
49 * Answers the singleton instance of this class, with lazy initialisation
50 * (built-in score models are loaded on the first call to this method)
54 public static ScoreModels getInstance()
58 instance = new ScoreModels();
64 * Private constructor to enforce use of singleton. Registers Jalview's
65 * "built-in" score models:
71 * <li>Sequence Feature Similarity</li> *
72 * <li>Secondary Structure Similarity</li>
78 * using LinkedHashMap keeps models ordered as added
80 models = new LinkedHashMap<>();
81 BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
82 PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
83 DNA = loadScoreMatrix("scoreModel/dna.scm");
84 registerScoreModel(new PIDModel());
85 registerScoreModel(new FeatureDistanceModel());
86 registerScoreModel(new SecondaryStructureDistanceModel());
90 * Tries to load a score matrix from the given resource file, and if
91 * successful, registers it.
96 ScoreMatrix loadScoreMatrix(String resourcePath)
101 * delegate parsing to ScoreMatrixFile
103 FileParse fp = new FileParse(resourcePath,
104 DataSourceType.CLASSLOADER);
105 ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
106 registerScoreModel(sm);
108 } catch (IOException e)
110 jalview.bin.Console.errPrintln(
111 "Error reading " + resourcePath + ": " + e.getMessage());
117 * Answers an iterable set of the registered score models. Currently these are
118 * returned in the order in which they were registered.
122 public Iterable<ScoreModelI> getModels()
124 return models.values();
128 * Returns an instance of a score model for the given name. If the model is of
129 * 'view dependent' type (e.g. feature similarity), instantiates a new
130 * instance configured for the given view. Otherwise returns a cached instance
131 * of the score model.
137 public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)
139 ScoreModelI model = models.get(name);
140 return model == null ? null : model.getInstance(avp);
143 public void registerScoreModel(ScoreModelI sm)
145 ScoreModelI sm2 = models.get(sm.getName());
148 jalview.bin.Console.errPrintln(
149 "Warning: replacing score model " + sm2.getName());
151 models.put(sm.getName(), sm);
155 * Resets to just the built-in score models
159 instance = new ScoreModels();
163 * Returns the default peptide or nucleotide score model, currently BLOSUM62
169 public ScoreMatrix getDefaultModel(boolean forPeptide)
171 return forPeptide ? BLOSUM62 : DNA;
174 public ScoreMatrix getBlosum62()
179 public ScoreMatrix getPam250()