From 6a66abccec20d56e2923634fa9bf9a5fa58a62bf Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 18 Apr 2007 12:01:56 +0000
Subject: [PATCH] adjustForAlignment on new seq ref

---
 src/jalview/io/AnnotationFile.java |    2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 1b7b72a..2053fef 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -367,6 +367,7 @@ public class AnnotationFile
           catch (Exception ex)
           {
             refSeqIndex = 1;
+            refSeq=null;
           }
 
           continue ;
@@ -433,6 +434,7 @@ public class AnnotationFile
         if (refSeq != null)
         {
           annotation.createSequenceMapping(refSeq, refSeqIndex, false);
+          annotation.adjustForAlignment();
           refSeq.addAlignmentAnnotation(annotation);
         }
 
-- 
1.7.10.2