JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...

[jalview.git] / src / jalview / workers / ConservationThread.java

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 1075e4d..54b0191 100644 (file)
--- 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();
@@ -95,7 +96,6 @@ public class ConservationThread extends AlignCalcWorker
       try
       {
         cons = Conservation.calculateConservation("All",
-                jalview.schemes.ResidueProperties.propHash, 3,
                 alignment.getSequences(), 0, alWidth - 1, false,
                 ConsPercGaps, quality != null);
       } catch (IndexOutOfBoundsException x)
@@ -108,16 +108,22 @@ public class ConservationThread extends AlignCalcWorker
     } catch (OutOfMemoryError error)
     {
       ap.raiseOOMWarning("calculating conservation", error);
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
       // alignViewport.conservation = null;
       // this.alignViewport.quality = null;
 
     }
     calcMan.workerComplete(this);
 
+    if ((alignViewport == null) || (calcMan == null)
+            || (alignViewport.isClosed()))
+    {
+      abortAndDestroy();
+      return;
+    }
     if (ap != null)
     {
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
 
   }