X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=ebc9a26d0a0c9260f9f7b9ee16a2122aec2b886a;hb=daa1765ab2101480a724b92a3f3e7dee662ba943;hp=377fdef247d06381f4616ae3963a1eaa767656c1;hpb=ff8c06845590fd9fd423aa59809dcce9610ab295;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 377fdef..ebc9a26 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,5 +1,26 @@
+/*
+ * 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 .
+ * 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;
@@ -14,12 +35,28 @@ import java.util.Map;
*/
public class ScoreModels
{
- private static ScoreModels instance = new ScoreModels();
+ private final ScoreMatrix BLOSUM62;
+
+ private final ScoreMatrix PAM250;
+
+ private final ScoreMatrix DNA;
+
+ private static ScoreModels instance;
private Map models;
+ /**
+ * 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()
{
+ if (instance == null)
+ {
+ instance = new ScoreModels();
+ }
return instance;
}
@@ -29,10 +66,9 @@ public class ScoreModels
*
* - BLOSUM62
* - PAM250
- * - SeqSpace (identity matrix)
+ * - PID
* - DNA
* - Sequence Feature Similarity
- * - Percentage Identity
*
*/
private ScoreModels()
@@ -40,38 +76,39 @@ public class ScoreModels
/*
* using LinkedHashMap keeps models ordered as added
*/
- models = new LinkedHashMap();
- loadScoreMatrix("scoreModel/blosum62.scm");
- loadScoreMatrix("scoreModel/pam250.scm");
- loadScoreMatrix("scoreModel/seqspace.scm");
- loadScoreMatrix("scoreModel/dna.scm");
- registerScoreModel(new FeatureScoreModel());
- registerScoreModel(new PIDScoreModel());
+ models = new LinkedHashMap<>();
+ BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
+ PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
+ DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new PIDModel());
+ registerScoreModel(new FeatureDistanceModel());
}
/**
- * Try to load a score matrix from the given resource file, and if successful,
- * register it. Answers true if successful, else false.
+ * Tries to load a score matrix from the given resource file, and if
+ * successful, registers it.
*
* @param string
+ * @return
*/
- boolean loadScoreMatrix(String resourcePath)
+ ScoreMatrix loadScoreMatrix(String resourcePath)
{
try
{
/*
* 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 true;
+ return sm;
} catch (IOException e)
{
- System.err.println("Error reading " + resourcePath + ": "
- + e.getMessage());
+ System.err.println(
+ "Error reading " + resourcePath + ": " + e.getMessage());
}
- return false;
+ return null;
}
/**
@@ -85,9 +122,20 @@ public class ScoreModels
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)
@@ -99,4 +147,34 @@ public class ScoreModels
}
models.put(sm.getName(), 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 ScoreMatrix getDefaultModel(boolean forPeptide)
+ {
+ return forPeptide ? BLOSUM62 : DNA;
+ }
+
+ public ScoreMatrix getBlosum62()
+ {
+ return BLOSUM62;
+ }
+
+ public ScoreMatrix getPam250()
+ {
+ return PAM250;
+ }
}