JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / jalview / analysis / scoremodels / ScoreModels.java

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 7262fb8..8700ec0 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -22,6 +22,8 @@ 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;
@@ -33,21 +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<String, ScoreModelI> 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);
   }
 
   /**
@@ -66,14 +64,22 @@ public class 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");
-    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<String, ScoreModelI> models;
+
   /**
    * Tries to load a score matrix from the given resource file, and if
    * successful, registers it.
@@ -139,6 +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
    *