X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=e9d418e84f03d697b9b7c1cc726d5eddab8beb22;hb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;hp=99084ba1c7c519c50e50b2ae231feaa4aec89174;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 99084ba..e9d418e 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -919,7 +919,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     // remove old automatic annotation
     // add any new annotation
 
-    Vector gr = av.getAlignment().getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+    ; // OrderedBy(av.alignment.getSequencesArray());
     // intersect alignment annotation with alignment groups
 
     AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
@@ -936,13 +936,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
         }
       }
     }
-    SequenceGroup sg;
-    if (gr != null)
+    if (av.getAlignment().getGroups()!= null)
     {
-      for (int g = 0; g < gr.size(); g++)
+      for (SequenceGroup sg:av.getAlignment().getGroups())
       {
         updateCalcs = false;
-        sg = (SequenceGroup) gr.elementAt(g);
         if (applyGlobalSettings || !oldrfs.containsKey(sg))
         {
           // set defaults for this group's conservation/consensus