+/*
+ * 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.AlignmentViewPanel;
import jalview.api.analysis.ScoreModelI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
+import jalview.util.Platform;
import java.io.IOException;
import java.util.LinkedHashMap;
private final ScoreMatrix PAM250;
- private static ScoreModels instance = new ScoreModels();
+ private final ScoreMatrix DNA;
- private Map<String, ScoreModelI> models;
+ private static ScoreModels instance;
+ /**
+ * Answers the singleton instance of this class, with lazy initialisation
+ * (built-in score models are loaded on the first call to this method)
+ *
+ * @return
+ */
public static ScoreModels getInstance()
{
- return instance;
+ ScoreModels m = instance;
+ @SuppressWarnings("unused")
+ ThreadGroup g = null;
+ if (Platform.isJS())
+ {
+ g = Thread.currentThread().getThreadGroup();
+ /**
+ * @j2sNative m = g._jalviewScoreModelsInstance;
+ *
+ */
+ }
+ if (m == null)
+ {
+ m = new ScoreModels();
+ if (Platform.isJS())
+ {
+ /**
+ * @j2sNative g._jalviewScoreModelsInstance = m;
+ *
+ */
+ }
+ else
+ {
+ instance = m;
+ }
+ }
+ return m;
}
+ private Map<String, ScoreModelI> models;
+
/**
* Private constructor to enforce use of singleton. Registers Jalview's
* "built-in" score models:
* <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, ScoreModelI>();
+ models = new LinkedHashMap<>();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- loadScoreMatrix("scoreModel/dna.scm");
- loadScoreMatrix("scoreModel/seqspace.scm");
- registerScoreModel(new FeatureScoreModel());
- registerScoreModel(new PIDScoreModel());
+ DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new PIDModel());
+ registerScoreModel(new FeatureDistanceModel());
}
/**
/*
* 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;
}
return models.values();
}
- public ScoreModelI 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(ScoreModelI sm)
}
/**
+ * Resets to just the built-in score models
+ */
+ public void reset()
+ {
+ instance = new ScoreModels();
+ }
+
+ /**
* Returns the default peptide or nucleotide score model, currently BLOSUM62
* or DNA
*
* @param forPeptide
* @return
*/
- public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
+ public ScoreMatrix getDefaultModel(boolean forPeptide)
{
- return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
- : forName("DNA"));
+ return forPeptide ? BLOSUM62 : DNA;
}
public ScoreMatrix getBlosum62()