X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;fp=src%2Fjalview%2Fworkers%2FConservationThread.java;h=571234cb749388a0fe8f2a875301e25aae5918b7;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=11ec5212593d67803a905de96e98e479f5c34c23;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 11ec521..571234c 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;
@@ -94,7 +95,7 @@ public class ConservationThread extends AlignCalcWorker
       }
       try
       {
-        cons = Conservation.calculateConservation("All", 3,
+        cons = Conservation.calculateConservation("All",
                 alignment.getSequences(), 0, alWidth - 1, false,
                 ConsPercGaps, quality != null);
       } catch (IndexOutOfBoundsException x)
@@ -114,6 +115,12 @@ public class ConservationThread extends AlignCalcWorker
     }
     calcMan.workerComplete(this);
 
+    if ((alignViewport == null) || (calcMan == null)
+            || (alignViewport.isClosed()))
+    {
+      abortAndDestroy();
+      return;
+    }
     if (ap != null)
     {
       ap.paintAlignment(true);