From cf4f0796ccc2d70bad2675e2feda184e5bef7a79 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 29 Jun 2010 15:21:16 +0000
Subject: [PATCH] patch for npe that occurs for importing Jalview projects
 where group conservation is displayed but no conservation
 for alignment is displayed - (observed during Jmol
 patching)

---
 src/jalview/analysis/AAFrequency.java |    5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index bc178df..46264d6 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -204,6 +204,11 @@ public class AAFrequency
           boolean includeAllConsSymbols, char[] alphabet)
   {
     float tval, value;
+    if (consensus==null || consensus.annotations==null || consensus.annotations.length<width)
+    {
+      // called with a bad alignment annotation row - wait for it to be initialised properly
+      return;
+    }
     for (int i = iStart; i < width; i++)
     {
       value = 0;
-- 
1.7.10.2