From: jprocter <Jim Procter>
Date: Thu, 2 Sep 2010 15:59:26 +0000 (+0000)
Subject: fix occasional arrayIndexOutOfBounds when sequences in subgroup are shorter than... 
X-Git-Tag: Release_2_6~73
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9d31636d87ba5d3243625a1e1b77db45d4fc9584;p=jalview.git

fix occasional arrayIndexOutOfBounds when sequences in subgroup are shorter than alignment width
---

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)
       {