From dad6e1eb4bd44e9f70e4bbb5f3a7da6e25a917bd Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 14 Dec 2006 19:37:53 +0000
Subject: [PATCH] set sequence_ref alignment

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index a211d1a..1f5a7ad 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -53,7 +53,12 @@ public class AnnotationFile
       color = null;
 
       if( row.sequenceRef == null)
+      {
+        if(seqref!=null)
+          text.append("\nSEQUENCE_REF\tALIGNMENT\n");
+
         seqref = null;
+      }
 
       else if (seqref == null || seqref != row.sequenceRef)
       {
-- 
1.7.10.2