X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=86c140f0a8071566edb454d883f52c1e3b0caa0b;hb=12aa3352bd2981b8aa86d9d28e4c405fa56a2c29;hp=c839271a27809dd78e6dd4224c76824fb1fe3e5f;hpb=64eb36a729257a5b03ec3b663ff74797f55e728c;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index c839271..86c140f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -394,7 +394,8 @@ public class Alignment implements AlignmentI
 
         while (i < sequences.size())
         {
-            SequenceI s = getSequenceAt(i);
+            Sequence s = (Sequence)getSequenceAt(i);
+            s.hiddenSequences = null;
             s.setColor(java.awt.Color.white);
             i++;
         }
@@ -405,6 +406,9 @@ public class Alignment implements AlignmentI
     {
         if (groups.contains(g))
         {
+          //remove any hidden representatives
+        //  for(int i=0; i<g.getsiz
+         //   g.getSequences()
             groups.removeElement(g);
         }
     }