From 8c6e707d6d9b1b8ad6385eb7eeef0bc78cb46f6e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 6 Jul 2005 12:21:25 +0000
Subject: [PATCH] Remove group if sequences are null

---
 src/jalview/datamodel/Alignment.java |    9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 28849b6..61735ee 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -334,9 +334,16 @@ public class Alignment implements AlignmentI
     {
         Vector temp = new Vector();
 
-        for (int i = 0; i < this.groups.size(); i++)
+        int gSize = groups.size();
+        for (int i = 0; i < gSize; i++)
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+            if(sg==null || sg.sequences==null)
+            {
+              this.deleteGroup(sg);
+              gSize--;
+              continue;
+            }
 
             if (sg.sequences.contains(s))
             {
-- 
1.7.10.2