X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=37528411a561530081339094f1cb4127dd0aa076;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=11ec5212593d67803a905de96e98e479f5c34c23;hpb=2bd3c28fe234c6883bec5412db83a809ab8d1500;p=jalview.git

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 11ec521..3752841 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -51,72 +51,49 @@ public class ConservationThread extends AlignCalcWorker
   @Override
   public void run()
   {
-    try
+    if ((alignViewport == null) || (calcMan == null)
+            || (alignViewport.isClosed()))
     {
-      calcMan.notifyStart(this); // updatingConservation = true;
-
-      while (!calcMan.notifyWorking(this))
-      {
-        try
-        {
-          if (ap != null)
-          {
-            // ap.paintAlignment(false);
-          }
-          Thread.sleep(200);
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-      if (alignViewport.isClosed())
-      {
-        abortAndDestroy();
-        return;
-      }
-      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
-      AlignmentI alignment = alignViewport.getAlignment();
-      conservation = alignViewport.getAlignmentConservationAnnotation();
-      quality = alignViewport.getAlignmentQualityAnnot();
-      ourAnnot.add(conservation);
-      ourAnnot.add(quality);
-      ourAnnots = ourAnnot;
-      ConsPercGaps = alignViewport.getConsPercGaps();
-      // AlignViewport.UPDATING_CONSERVATION = true;
-
-      if (alignment == null || (alWidth = alignment.getWidth()) < 0)
-      {
-        calcMan.workerComplete(this);
-        // .updatingConservation = false;
-        // AlignViewport.UPDATING_CONSERVATION = false;
+      abortAndDestroy();
+      return;
+    }
+    List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
+    AlignmentI alignment = alignViewport.getAlignment();
+    conservation = alignViewport.getAlignmentConservationAnnotation();
+    quality = alignViewport.getAlignmentQualityAnnot();
+    ourAnnot.add(conservation);
+    ourAnnot.add(quality);
+    ourAnnots = ourAnnot;
+    ConsPercGaps = alignViewport.getConsPercGaps();
+    // AlignViewport.UPDATING_CONSERVATION = true;
 
-        return;
-      }
-      try
-      {
-        cons = Conservation.calculateConservation("All", 3,
-                alignment.getSequences(), 0, alWidth - 1, false,
-                ConsPercGaps, quality != null);
-      } catch (IndexOutOfBoundsException x)
-      {
-        // probable race condition. just finish and return without any fuss.
-        calcMan.workerComplete(this);
-        return;
-      }
-      updateResultAnnotation(true);
-    } catch (OutOfMemoryError error)
+    if (alignment == null || (alWidth = alignment.getWidth()) < 0)
     {
-      ap.raiseOOMWarning("calculating conservation", error);
-      calcMan.disableWorker(this);
-      // alignViewport.conservation = null;
-      // this.alignViewport.quality = null;
-
+      // .updatingConservation = false;
+      // AlignViewport.UPDATING_CONSERVATION = false;
+      return;
     }
-    calcMan.workerComplete(this);
+    try
+    {
+      cons = Conservation.calculateConservation("All",
+              alignment.getSequences(), 0, alWidth - 1, false,
+              ConsPercGaps, quality != null);
+    } catch (IndexOutOfBoundsException x)
+    {
+      // probable race condition. just finish and return without any fuss.
+      return;
+    }
+    updateResultAnnotation(true);
 
+    if ((alignViewport == null) || (calcMan == null)
+            || (alignViewport.isClosed()))
+    {
+      abortAndDestroy();
+      return;
+    }
     if (ap != null)
     {
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
 
   }