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 021e6e2..54b0191 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 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.
- *
- * 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
+ * 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.
+ *  
+ * 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
@@ -54,7 +55,7 @@ public class ConservationThread extends AlignCalcWorker implements
     {
       calcMan.notifyStart(this); // updatingConservation = true;
 
-      while (!calcMan.notifyWorking(this))
+      while ((calcMan != null) && (!calcMan.notifyWorking(this)))
       {
         try
         {
@@ -68,18 +69,20 @@ public class ConservationThread extends AlignCalcWorker implements
           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();
       ourAnnot.add(conservation);
       ourAnnot.add(quality);
       ourAnnots = ourAnnot;
-
+      ConsPercGaps = alignViewport.getConsPercGaps();
       // AlignViewport.UPDATING_CONSERVATION = true;
 
       if (alignment == null || (alWidth = alignment.getWidth()) < 0)
@@ -93,7 +96,6 @@ public class ConservationThread extends AlignCalcWorker implements
       try
       {
         cons = Conservation.calculateConservation("All",
-                jalview.schemes.ResidueProperties.propHash, 3,
                 alignment.getSequences(), 0, alWidth - 1, false,
                 ConsPercGaps, quality != null);
       } catch (IndexOutOfBoundsException x)
@@ -106,16 +108,22 @@ public class ConservationThread extends AlignCalcWorker implements
     } 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);
     }
 
   }
@@ -124,7 +132,10 @@ 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