X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=8700ec04c12c7f1fa7a9b1edfafaedf896a72430;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=654136ac0cf498007a6bdc4ef9ef5e743ee78975;hpb=333d483bec66b894088e71902095a78e902a462f;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 654136a..8700ec0 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,7 +1,29 @@
+/*
+ * 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.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
@@ -13,21 +35,17 @@ import java.util.Map;
/**
* A class that can register and serve instances of ScoreModelI
*/
-public class ScoreModels
+public class ScoreModels implements ApplicationSingletonI
{
- private final ScoreMatrix BLOSUM62;
-
- private final ScoreMatrix PAM250;
-
- private final ScoreMatrix DNA;
-
- private static ScoreModels instance = new ScoreModels();
-
- 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()
{
- return instance;
+ return (ScoreModels) ApplicationSingletonProvider.getInstance(ScoreModels.class);
}
/**
@@ -46,14 +64,22 @@ public class ScoreModels
/*
* using LinkedHashMap keeps models ordered as added
*/
- models = new LinkedHashMap();
+ models = new LinkedHashMap<>();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- registerScoreModel(new PIDModel());
DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new PIDModel());
registerScoreModel(new FeatureDistanceModel());
}
+ private final ScoreMatrix BLOSUM62;
+
+ private final ScoreMatrix PAM250;
+
+ private final ScoreMatrix DNA;
+
+ private Map models;
+
/**
* Tries to load a score matrix from the given resource file, and if
* successful, registers it.
@@ -68,14 +94,15 @@ public class ScoreModels
/*
* 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;
}
@@ -118,6 +145,14 @@ public class ScoreModels
}
/**
+ * Resets to just the built-in score models
+ */
+ public void reset()
+ {
+ ApplicationSingletonProvider.removeInstance(this.getClass());
+ }
+
+ /**
* Returns the default peptide or nucleotide score model, currently BLOSUM62
* or DNA
*