From 390461d621255f960721a8370ee8fb06ba20aec9 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 1 May 2007 16:33:27 +0000
Subject: [PATCH] Make sure annots are alignment width

---
 src/jalview/io/AMSAFile.java |    6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 1f3fca0..e7e6d97 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -45,9 +45,12 @@ public class AMSAFile
     AlignmentAnnotation aa;
     if (al.getAlignmentAnnotation() != null)
     {
+
       for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
         aa = al.getAlignmentAnnotation()[i];
+
+
         if (aa.autoCalculated || !aa.visible)
         {
           continue;
@@ -61,7 +64,8 @@ public class AMSAFile
 
         out.append("\n");
 
-        int nochunks = (aa.annotations.length / len) + 1;
+        int nochunks = Math.min(aa.annotations.length, al.getWidth())
+                        / len + 1;
 
         for (int j = 0; j < nochunks; j++)
         {
-- 
1.7.10.2