X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=1f5a7add9e93b1ad24da1326b84fdef50f34d47e;hb=dad6e1eb4bd44e9f70e4bbb5f3a7da6e25a917bd;hp=a211d1aa415ab7ac9761286137a3a35a77ed6d88;hpb=a7bec763a3e4f17a549115f8f9f19ee4c742c26b;p=jalview.git

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)
       {