From 13627d2cded75044b5e80c7c19aa2c789939bce9 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 10 May 2007 08:39:40 +0000
Subject: [PATCH] fixed array index out of bounds when not removing alignment
 annotation

---
 src/jalview/datamodel/Alignment.java |    4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 9c7f2fb..677f436 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -489,8 +489,8 @@ public class Alignment
         swap=true;
         continue;
       }
-
-      temp[tIndex++] = annotations[i];
+      if (tIndex<temp.length)
+        temp[tIndex++] = annotations[i];
     }
 
     if (swap)
-- 
1.7.10.2