JAL-3253 preliminary static fixes for JavaScript

[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..fd579dc 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -25,6 +25,7 @@ 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;
@@ -41,15 +42,47 @@ public class ScoreModels
 
   private final ScoreMatrix DNA;
 
-  private static ScoreModels instance = new ScoreModels();
-
-  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:
@@ -66,11 +99,11 @@ 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());
   }
 
@@ -139,6 +172,14 @@ public class ScoreModels
   }
 
   /**
+   * 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
    *