From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 18 Apr 2007 13:35:07 +0000 (+0000)
Subject: dont set seqref null if index incorrect
X-Git-Tag: Release_2_3~218
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=ac5e49397d04c63fd42c5e2b32174052657950ff

dont set seqref null if index incorrect
---

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);