From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 18 Apr 2007 12:01:56 +0000 (+0000)
Subject: adjustForAlignment on new seq ref
X-Git-Tag: Release_2_3~226
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=6a66abccec20d56e2923634fa9bf9a5fa58a62bf

adjustForAlignment on new seq ref
---

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);
         }