From 574045b24991af25bbb25526fbb9abd3b92c3fac Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 24 Sep 2008 13:30:52 +0000
Subject: [PATCH] fixed sequence associated annotation reading bug where only
 first annotation is associated with sequence when more than
 one follow a SEQUENCE_REF

---
 src/jalview/io/AnnotationFile.java |    8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 1bc5eff..d9fd871 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -554,15 +554,17 @@ public class AnnotationFile
         if (refSeq != null)
         {
           annotation.belowAlignment = false;
+          // make a copy of refSeq so we can find other matches in the alignment
+          SequenceI referedSeq = refSeq;
           do
           {
             // copy before we do any mapping business.
             // TODO: verify that undo/redo with 1:many sequence associated
             // annotations can be undone correctly
             AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
-            annotation.createSequenceMapping(refSeq, refSeqIndex, false);
+            annotation.createSequenceMapping(referedSeq, refSeqIndex, false);
             annotation.adjustForAlignment();
-            refSeq.addAlignmentAnnotation(annotation);
+            referedSeq.addAlignmentAnnotation(annotation);
             al.addAnnotation(annotation);
             al.setAnnotationIndex(annotation,
                     al.getAlignmentAnnotation().length
@@ -571,7 +573,7 @@ public class AnnotationFile
             annotation = ann;
 
           } while (refSeqId != null
-                  && (refSeq = al.findName(refSeq, refSeqId, true)) != null);
+                  && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
         }
         else
         {
-- 
1.7.10.2