JAL-961 store result of conservation analysis worker on the alignment viewport

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 6f3a2af..7e383a9 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * 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.viewmodel;
 
@@ -298,7 +299,13 @@ public abstract class AlignmentViewport implements AlignViewportI
    * view
    */
   protected Hashtable[] hStrucConsensus = null;
-
+  
+  protected Conservation hconservation = null;
+  @Override
+  public void setConservation(Conservation cons)
+  {
+    hconservation = cons;
+  }
   /**
    * percentage gaps allowed in a column before all amino acid properties should
    * be considered unconserved
@@ -1504,8 +1511,7 @@ public abstract class AlignmentViewport implements AlignViewportI
         if (aan[an].autoCalculated && aan[an].groupRef != null)
         {
           oldrfs.add(aan[an].groupRef);
-          alignment.deleteAnnotation(aan[an]);
-          aan[an] = null;
+          alignment.deleteAnnotation(aan[an],false);
         }
       }
     }