X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=236bccfb59dee09d7869f8e61504f0f4873a4260;hb=8e45ad740239d950f7ceb8b322bf30ee307f4e98;hp=021e6e2cfb63d928755823bb3759a15230b2c92c;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 021e6e2..236bccf 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,32 +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;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public class ConservationThread extends AlignCalcWorker implements
         AlignCalcWorkerI
 {
@@ -71,6 +74,7 @@ public class ConservationThread extends AlignCalcWorker implements
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
       AlignmentI alignment = alignViewport.getAlignment();
@@ -79,7 +83,7 @@ public class ConservationThread extends AlignCalcWorker implements
       ourAnnot.add(conservation);
       ourAnnot.add(quality);
       ourAnnots = ourAnnot;
-
+      ConsPercGaps = alignViewport.getConsPercGaps();
       // AlignViewport.UPDATING_CONSERVATION = true;
 
       if (alignment == null || (alWidth = alignment.getWidth()) < 0)
@@ -124,7 +128,10 @@ 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