JAL-3878 Add getCalcName to AlignCalcWorkerI.

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

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 990f724..a78037c 100644 (file)
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,7 +21,6 @@
 package jalview.workers;
 
 import jalview.analysis.Conservation;
-import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
@@ -30,8 +29,7 @@ import jalview.datamodel.AlignmentI;
 import java.util.ArrayList;
 import java.util.List;
 
-public class ConservationThread extends AlignCalcWorker implements
-        AlignCalcWorkerI
+public class ConservationThread extends AlignCalcWorker
 {
 
   private int ConsPercGaps = 25; // JBPNote : This should be a configurable
@@ -51,75 +49,57 @@ public class ConservationThread extends AlignCalcWorker implements
   int alWidth;
 
   @Override
+  public String getCalcName()
+  {
+    return "Conservation";
+  }
+
+  @Override
   public void run()
   {
+    if ((alignViewport == null) || (calcMan == null)
+            || (alignViewport.isClosed()))
+    {
+      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;
+
+    if (alignment == null || (alWidth = alignment.getWidth()) < 0)
+    {
+      // .updatingConservation = false;
+      // AlignViewport.UPDATING_CONSERVATION = false;
+      return;
+    }
     try
     {
-      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;
-
-        return;
-      }
-      try
-      {
-        cons = Conservation.calculateConservation("All",
-                jalview.schemes.ResidueProperties.propHash, 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)
+      cons = Conservation.calculateConservation("All",
+              alignment.getSequences(), 0, alWidth - 1, false,
+              ConsPercGaps, quality != null);
+    } catch (IndexOutOfBoundsException x)
     {
-      ap.raiseOOMWarning("calculating conservation", error);
-      calcMan.workerCannotRun(this);
-      // alignViewport.conservation = null;
-      // this.alignViewport.quality = null;
-
+      // probable race condition. just finish and return without any fuss.
+      return;
     }
-    calcMan.workerComplete(this);
+    updateResultAnnotation(true);
 
+    if ((alignViewport == null) || (calcMan == null)
+            || (alignViewport.isClosed()))
+    {
+      abortAndDestroy();
+      return;
+    }
     if (ap != null)
     {
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
 
   }