X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=54b0191169f79e21eebc431d55d75c3dbf5efc9c;hb=5143fe21d91fa16c40be42cc0923be0d6f2f6536;hp=4ada8eac5de5d04a584adc1009448935b66a9126;hpb=c793b702ed3c1ec890411db7156c63dfb3c40153;p=jalview.git

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 4ada8ea..54b0191 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
         {
@@ -69,12 +69,13 @@ public class ConservationThread extends AlignCalcWorker
           ex.printStackTrace();
         }
       }
-      if (alignViewport.isClosed())
+      if ((alignViewport == null) || (calcMan == null)
+              || (alignViewport.isClosed()))
       {
         abortAndDestroy();
         return;
       }
-      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+      List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
       AlignmentI alignment = alignViewport.getAlignment();
       conservation = alignViewport.getAlignmentConservationAnnotation();
       quality = alignViewport.getAlignmentQualityAnnot();
@@ -122,7 +123,7 @@ public class ConservationThread extends AlignCalcWorker
     }
     if (ap != null)
     {
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
 
   }