From 04528015839067053e02cfc2f7a1ced70302bb1f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 19 Jul 2006 15:33:16 +0000
Subject: [PATCH] Make new seq[] when modifying hidden bits

---
 src/jalview/io/FormatAdapter.java |    5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 84940a8..2901969 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -36,10 +36,13 @@ public class FormatAdapter extends AppletFormatAdapter
     {
       if(omitHiddenColumns!=null)
       {
+        SequenceI [] tmp = new SequenceI[seqs.length];
         for(int i=0; i<seqs.length; i++)
-          seqs [i] = new Sequence(
+          tmp [i] = new Sequence(
               seqs[i].getName(), omitHiddenColumns[i],
               seqs[i].getStart(), seqs[i].getEnd());
+
+        seqs = tmp;
       }
 
       return formatSequences(format, seqs);
-- 
1.7.10.2