From ac5e49397d04c63fd42c5e2b32174052657950ff Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 18 Apr 2007 13:35:07 +0000
Subject: [PATCH] dont set seqref null if index incorrect

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2053fef..2ce076a 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -367,7 +367,6 @@ public class AnnotationFile
           catch (Exception ex)
           {
             refSeqIndex = 1;
-            refSeq=null;
           }
 
           continue ;
@@ -433,6 +432,7 @@ public class AnnotationFile
 
         if (refSeq != null)
         {
+          System.out.println(refSeq.getName()+" "+refSeqIndex);
           annotation.createSequenceMapping(refSeq, refSeqIndex, false);
           annotation.adjustForAlignment();
           refSeq.addAlignmentAnnotation(annotation);
-- 
1.7.10.2