+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis.scoremodels;
-import jalview.api.analysis.DistanceModelI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.analysis.ScoreModelI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
private static ScoreModels instance = new ScoreModels();
- private Map<String, DistanceModelI> models;
+ private Map<String, ScoreModelI> models;
public static ScoreModels getInstance()
{
* <ul>
* <li>BLOSUM62</li>
* <li>PAM250</li>
- * <li>SeqSpace (identity matrix)</li>
+ * <li>PID</li>
* <li>DNA</li>
* <li>Sequence Feature Similarity</li>
- * <li>Percentage Identity</li>
* </ul>
*/
private ScoreModels()
/*
* using LinkedHashMap keeps models ordered as added
*/
- models = new LinkedHashMap<String, DistanceModelI>();
+ models = new LinkedHashMap<String, ScoreModelI>();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- loadScoreMatrix("scoreModel/seqspace.scm");
- // drop seqspace.scm for IdentityScoreModel once JAL-2379 merged in?
- // registerScoreModel(new IdentityScoreModel());
+ registerScoreModel(new PIDModel());
DNA = loadScoreMatrix("scoreModel/dna.scm");
registerScoreModel(new FeatureDistanceModel());
- registerScoreModel(new PIDDistanceModel());
}
/**
/*
* delegate parsing to ScoreMatrixFile
*/
- FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
+ FileParse fp = new FileParse(resourcePath,
+ DataSourceType.CLASSLOADER);
ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
registerScoreModel(sm);
return sm;
} catch (IOException e)
{
- System.err.println("Error reading " + resourcePath + ": "
- + e.getMessage());
+ System.err.println(
+ "Error reading " + resourcePath + ": " + e.getMessage());
}
return null;
}
/**
- * Registers a pairwise score model
- *
- * @param sm
- */
- public void registerScoreModel(PairwiseScoreModelI sm)
- {
- registerScoreModel(new PairwiseDistanceModel(sm));
- }
-
- /**
* Answers an iterable set of the registered score models. Currently these are
* returned in the order in which they were registered.
*
* @return
*/
- public Iterable<DistanceModelI> getModels()
+ public Iterable<ScoreModelI> getModels()
{
return models.values();
}
- public DistanceModelI forName(String s)
+ /**
+ * Returns an instance of a score model for the given name. If the model is of
+ * 'view dependent' type (e.g. feature similarity), instantiates a new
+ * instance configured for the given view. Otherwise returns a cached instance
+ * of the score model.
+ *
+ * @param name
+ * @param avp
+ * @return
+ */
+ public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)
{
- return models.get(s);
+ ScoreModelI model = models.get(name);
+ return model == null ? null : model.getInstance(avp);
}
- public void registerScoreModel(DistanceModelI sm)
+ public void registerScoreModel(ScoreModelI sm)
{
- DistanceModelI sm2 = models.get(sm.getName());
+ ScoreModelI sm2 = models.get(sm.getName());
if (sm2 != null)
{
System.err.println("Warning: replacing score model " + sm2.getName());