From 9d31636d87ba5d3243625a1e1b77db45d4fc9584 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 2 Sep 2010 15:59:26 +0000
Subject: [PATCH] fix occasional arrayIndexOutOfBounds when sequences in
 subgroup are shorter than alignment width

---
 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 46264d6..8fd60c4 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -211,6 +211,11 @@ public class AAFrequency
     }
     for (int i = iStart; i < width; i++)
     {
+      if (i>=hconsensus.length) {
+        // happens if sequences calculated over were shorter than alignment width
+        consensus.annotations[i]=null;
+        continue;
+      }
       value = 0;
       if (ignoreGapsInConsensusCalculation)
       {
-- 
1.7.10.2