X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=194c389cef1d8df1f043a2c13bc5a2a3b4a81f4a;hb=80916c21f32a24ec777b51c758df0cc2f57f6bb8;hp=23d17732072a735b59566259a30389046b86450b;hpb=f61b2748a32ef03e687abc37b97640873c2e44aa;p=jalview.git

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)
     {