From 6c87693cd4f9dcf81b01983a3dbebc5dec6fde06 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 14 Jun 2012 11:32:08 +0100
Subject: [PATCH] JAL-1115 trap exception arising from race condition when
 alignment edited during calculation

---
 src/jalview/workers/ConservationThread.java |    8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 23d1773..194c389 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -83,10 +83,16 @@ public class ConservationThread extends AlignCalcWorker implements AlignCalcWork
 
         return;
       }
-
+      try {
       cons = Conservation.calculateConservation("All",
               jalview.schemes.ResidueProperties.propHash, 3,
               alignment.getSequences(), 0, alWidth - 1, false, ConsPercGaps, quality!=null);
+      } catch (IndexOutOfBoundsException x)
+      {
+        // probable race condition. just finish and return without any fuss.
+        calcMan.workerComplete(this);
+        return;
+      }
       updateResultAnnotation(true);
     } catch (OutOfMemoryError error)
     {
-- 
1.7.10.2