From d7f018c09e7831fad82d6c3b268a45a3854658ef Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 11 Mar 2010 17:04:54 +0000
Subject: [PATCH] raise a warning if column annotation gets truncated.

---
 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 20cf745..1fcda43 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -86,7 +86,11 @@ public class AMSAFile extends jalview.io.FastaFile
             {
               ch = aa.annotations[k].displayCharacter;
             }
-
+            if (ch.length()>1)
+            {
+              this.warningMessage="Truncated column annotation to first letter.";
+              ch = ch.substring(0,1);
+            }
             out.append(ch);
 
           }
-- 
1.7.10.2