set sequence_ref alignment

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