From 12aa3352bd2981b8aa86d9d28e4c405fa56a2c29 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 18 Aug 2006 13:57:14 +0000
Subject: [PATCH] remove all representative seqs on delete groups

---
 src/jalview/datamodel/Alignment.java |    6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

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);
         }
     }
-- 
1.7.10.2