From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 28 Feb 2017 12:25:11 +0000 (+0000)
Subject: JAL-2426 Checks on conservation thread in case we are shutting down
X-Git-Tag: Release_2_10_2~3^2~92^2~62
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5ae21c312e4dcc80389bc4f5c534db9428db2217;p=jalview.git

JAL-2426 Checks on conservation thread in case we are shutting down
---

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index e71c4f5..b2a67b7 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -55,7 +55,7 @@ public class ConservationThread extends AlignCalcWorker
     {
       calcMan.notifyStart(this); // updatingConservation = true;
 
-      while (!calcMan.notifyWorking(this))
+      while ((calcMan != null) && (!calcMan.notifyWorking(this)))
       {
         try
         {
@@ -69,7 +69,8 @@ public class ConservationThread extends AlignCalcWorker
           ex.printStackTrace();
         }
       }
-      if (alignViewport.isClosed())
+      if ((alignViewport == null) || (calcMan == null)
+              || (alignViewport.isClosed()))
       {
         abortAndDestroy();
         return;