From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 1 May 2014 13:32:45 +0000 (+0100)
Subject: JAL-961 store result of conservation analysis worker on the alignment viewport
X-Git-Tag: Jalview_2_9~190^2~19
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8f1b417b654a575bf7a368b4edeffee813042a5c;p=jalview.git

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 4f78145..44fef0e 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -22,6 +22,7 @@ import java.awt.Color;
 import java.util.Hashtable;
 import java.util.Map;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -186,5 +187,7 @@ public interface AlignViewportI
 
   void setColumnSelection(ColumnSelection cs);
 
+  void setConservation(Conservation cons);
+
 
 }
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d49572d..7e383a9 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -299,7 +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
diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index b6186d4..681007e 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -125,7 +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