JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index c440c0f..11ec521 100644 (file)
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,35 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
  * 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
@@ -72,6 +72,7 @@ public class ConservationThread extends AlignCalcWorker implements
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
       AlignmentI alignment = alignViewport.getAlignment();
@@ -93,8 +94,7 @@ public class ConservationThread extends AlignCalcWorker implements
       }
       try
       {
-        cons = Conservation.calculateConservation("All",
-                jalview.schemes.ResidueProperties.propHash, 3,
+        cons = Conservation.calculateConservation("All", 3,
                 alignment.getSequences(), 0, alWidth - 1, false,
                 ConsPercGaps, quality != null);
       } catch (IndexOutOfBoundsException x)
@@ -107,7 +107,7 @@ 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;