From 38a8b402c703cb7481a367cdbf26781244af2aa5 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 24 Jun 2011 16:55:15 +0100
Subject: [PATCH] fix to preserve sequence numbering in MSF (JAL-847)

---
 src/jalview/io/MSFfile.java |    2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 28f1f97..71510cc 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -228,7 +228,7 @@ public class MSFfile extends AlignFile
     {
       // Replace all internal gaps with . and external spaces with ~
       s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
-              .replace('-', '.'));
+              .replace('-', '.'), seqs[i].getStart(),seqs[i].getEnd());
 
       StringBuffer sb = new StringBuffer();
       sb.append(s[i].getSequence());
-- 
1.7.10.2