From c793b702ed3c1ec890411db7156c63dfb3c40153 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 28 Feb 2017 14:50:10 +0000
Subject: [PATCH] JAL-2426 Removal of NPE in conservation thread when closing
 Jalview

---
 src/jalview/workers/ConservationThread.java |    6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index e71c4f5..4ada8ea 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -114,6 +114,12 @@ public class ConservationThread extends AlignCalcWorker
     }
     calcMan.workerComplete(this);
 
+    if ((alignViewport == null) || (calcMan == null)
+            || (alignViewport.isClosed()))
+    {
+      abortAndDestroy();
+      return;
+    }
     if (ap != null)
     {
       ap.paintAlignment(true);
-- 
1.7.10.2