X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=0c470feab378bf66a66a74f739837f24eeccdadc;hb=18fb9dd58b1f0c4277b269c5e8bc2d3ed98394a5;hp=abb8f63b221914066c563f5c809ae53e1007ad64;hpb=4f094851cd2247ea2d982e7829a6f5b663042573;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index abb8f63..0c470fe 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -626,9 +626,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (cs != null)
     {
-      // if (getConservationSelected() || getAbovePIDThreshold()
-      // || cs instanceof PIDColourScheme
-      // || cs instanceof Blosum62ColourScheme)
       if (getConservationSelected())
       {
         residueShading.setConservation(hconservation);
@@ -1076,7 +1073,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
-   * Set the selection group for this window.
+   * Set the selection group for this window. Also sets the current alignment as
+   * the context for the group, if it does not already have one.
    * 
    * @param sg
    *          - group holding references to sequences in this alignment view
@@ -1086,6 +1084,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setSelectionGroup(SequenceGroup sg)
   {
     selectionGroup = sg;
+    if (sg != null && sg.getContext() == null)
+    {
+      sg.setContext(alignment);
+    }
   }
 
   public void setHiddenColumns(ColumnSelection colsel)
@@ -2428,6 +2430,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setViewStyle(ViewStyleI settingsForView)
   {
     viewStyle = new ViewStyle(settingsForView);
+    if (residueShading != null)
+    {
+      residueShading.setConservationApplied(settingsForView
+              .isConservationColourSelected());
+    }
   }
 
   @Override