intersect did not intersect (used in selection listener)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index abc6d45..c0d8f5e 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -824,15 +824,22 @@ public class SequenceGroup
   public SequenceGroup intersect(AlignmentI alignment, Hashtable hashtable)
   {
     SequenceGroup sgroup = new SequenceGroup(this);
-    Enumeration en = getSequences(hashtable).elements();
-    while (en.hasMoreElements())
-    {
-      SequenceI elem = (SequenceI) en.nextElement();
-      if (alignment.getSequences().contains(elem))
-      {
-        sgroup.addSequence(elem, false);
-      }
+    SequenceI[] insect=getSequencesInOrder(alignment);
+    sgroup.sequences = new Vector();
+    for (int s=0;insect!=null && s<insect.length;s++) { 
+      if (hashtable==null || hashtable.containsKey(insect[s]))
+              {
+      sgroup.sequences.addElement(insect[s]); }
     }
+    //Enumeration en =getSequences(hashtable).elements();
+    //while (en.hasMoreElements())
+   // {
+   //   SequenceI elem = (SequenceI) en.nextElement();
+   //   if (alignment.getSequences().contains(elem))
+   //   {
+   //     sgroup.addSequence(elem, false);
+   //   }
+   // }
     return sgroup;
   }