From ae687fbf5b5d6c34e8ccfbe27afdc0ff0eff747f Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 21 Aug 2006 12:51:46 +0000
Subject: [PATCH] fix for truncation of sequence associated annotation mapped
 onto alignment

---
 src/jalview/datamodel/AlignmentAnnotation.java |    9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 04689cd..2850eeb 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -285,13 +285,10 @@ public class AlignmentAnnotation
         for(int i = 0; i < annotations.length; i++)
         {
             seqPos = sequenceRef.findPosition(i + fileOffset);
-            if(seqPos<annotations.length)
+            if (annotations[i] != null)
             {
-              if (annotations[i] != null)
-              {
-                  sequenceMapping.put(new Integer(seqPos),
-                                      annotations[i]);
-              }
+              sequenceMapping.put(new Integer(seqPos),
+                  annotations[i]);
             }
          }
 
-- 
1.7.10.2