JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

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

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 58510e5..3752841 100644 (file)
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,34 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.workers;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import jalview.analysis.Conservation;
-import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignmentViewPanel;
 import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 
-public class ConservationThread extends AlignCalcWorker implements
-        AlignCalcWorkerI
+import java.util.ArrayList;
+import java.util.List;
+
+public class ConservationThread extends AlignCalcWorker
 {
 
   private int ConsPercGaps = 25; // JBPNote : This should be a configurable
@@ -50,72 +51,49 @@ public class ConservationThread extends AlignCalcWorker implements
   @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();
-      }
-      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
-      AlignmentI alignment = alignViewport.getAlignment();
-      conservation = alignViewport.getAlignmentConservationAnnotation();
-      quality = alignViewport.getAlignmentQualityAnnot();
-      ourAnnot.add(conservation);
-      ourAnnot.add(quality);
-      ourAnnots = ourAnnot;
-
-      // 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",
-                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)
+    if (alignment == null || (alWidth = alignment.getWidth()) < 0)
     {
-      ap.raiseOOMWarning("calculating conservation", error);
-      calcMan.workerCannotRun(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);
     }
 
   }
@@ -124,7 +102,10 @@ public class ConservationThread extends AlignCalcWorker implements
   {
     if (b || !calcMan.isWorking(this) && cons != null
             && conservation != null && quality != null)
+    {
+      alignViewport.setConservation(cons);
       cons.completeAnnotations(conservation, quality, 0, alWidth);
+    }
   }
 
   @Override