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

[jalview.git] / src / jalview / analysis / AlignmentSorter.java

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 427db84..8634db6 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -22,6 +22,8 @@ package jalview.analysis;
 
 import jalview.analysis.scoremodels.PIDModel;
 import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
@@ -29,7 +31,6 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
-import jalview.util.Platform;
 import jalview.util.QuickSort;
 
 import java.util.ArrayList;
@@ -52,9 +53,20 @@ import java.util.List;
  * from the first tobesorted position in the alignment. e.g. (a,tb2,b,tb1,c,tb3
  * becomes a,tb1,tb2,tb3,b,c)
  */
-public class AlignmentSorter
+public class AlignmentSorter implements ApplicationSingletonI
 {
 
+  private AlignmentSorter()
+  {
+    // private singleton
+  }
+
+  private static AlignmentSorter getInstance()
+  {
+    return (AlignmentSorter) ApplicationSingletonProvider
+            .getInstance(AlignmentSorter.class);
+  }
+
   /**
    * types of feature ordering: Sort by score : average score - or total score -
    * over all features in region Sort by feature label text: (or if null -
@@ -67,43 +79,6 @@ public class AlignmentSorter
 
   public static final String FEATURE_DENSITY = "density";
 
-  static AlignmentSorter instance;
-
-  public static AlignmentSorter getInstance()
-  {
-
-    // BH 2019.05.08 need to isolate static fields in JavaScript
-
-    AlignmentSorter i = instance;
-    @SuppressWarnings("unused")
-    ThreadGroup g = null;
-    if (Platform.isJS())
-    {
-      g = Thread.currentThread().getThreadGroup();
-      /**
-       * @j2sNative i = g._jalviewAlignmentSorterInstance;
-       * 
-       */
-    }
-    if (i == null)
-    {
-      i = new AlignmentSorter();
-
-      if (Platform.isJS())
-      {
-        /**
-         * @j2sNative g._jalviewAlignmentSorterInstance = i;
-         * 
-         */
-      }
-      else
-      {
-        instance = i;
-      }
-    }
-    return i;
-  }
-
   /*
    * todo: refactor searches to follow a basic pattern: (search property, last
    * search state, current sort direction)