Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch

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

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 021e6e2..cae430f 100644 (file)
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.1)
+ * Copyright (C) 2014 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
+ * 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
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.workers;
 
@@ -79,7 +80,7 @@ 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 +125,10 @@ 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