JAL-1264 exclude score-only from 'Add Reference Annotations'

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 89066cb..3f74327 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -139,9 +139,9 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -3903,35 +3903,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     if (viewport.getAlignment().getAlignmentAnnotation()
-            .hashCode() != _annotationScoreVectorHash)
+            .hashCode() == _annotationScoreVectorHash)
     {
-      sortByAnnotScore.removeAll();
-      // almost certainly a quicker way to do this - but we keep it simple
-      Hashtable scoreSorts = new Hashtable();
-      AlignmentAnnotation aann[];
-      for (SequenceI sqa : viewport.getAlignment().getSequences())
+      return;
+    }
+
+    sortByAnnotScore.removeAll();
+    Set<String> scoreSorts = new HashSet<>();
+    for (SequenceI sqa : viewport.getAlignment().getSequences())
+    {
+      AlignmentAnnotation[] anns = sqa.getAnnotation();
+      for (int i = 0; anns != null && i < anns.length; i++)
       {
-        aann = sqa.getAnnotation();
-        for (int i = 0; aann != null && i < aann.length; i++)
+        AlignmentAnnotation aa = anns[i];
+        if (aa != null && aa.hasScore() && aa.sequenceRef != null)
         {
-          if (aann[i].hasScore() && aann[i].sequenceRef != null)
-          {
-            scoreSorts.put(aann[i].label, aann[i].label);
-          }
+          scoreSorts.add(aa.label);
         }
       }
-      Enumeration labels = scoreSorts.keys();
-      while (labels.hasMoreElements())
-      {
-        addSortByAnnotScoreMenuItem(sortByAnnotScore,
-                (String) labels.nextElement());
-      }
-      sortByAnnotScore.setVisible(scoreSorts.size() > 0);
-      scoreSorts.clear();
-
-      _annotationScoreVectorHash = viewport.getAlignment()
-              .getAlignmentAnnotation().hashCode();
     }
+    for (String label : scoreSorts)
+    {
+      addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
+    }
+    sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
+
+    _annotationScoreVectorHash = viewport.getAlignment()
+            .getAlignmentAnnotation().hashCode();
   }
 
   /**