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 ea7b30e..8700ec0 100644 (file)
--- 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 <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.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<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);
   }
 
   /**
@@ -46,14 +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.
@@ -119,6 +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
    *