From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 21 Feb 2017 10:53:40 +0000 (+0000)
Subject: Merge branch 'develop' into features/JAL-2388OverviewWindow
X-Git-Tag: Release_2_10_2~3^2~92^2~69
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=46b2ffc28aeef5800f35ce31a742a65095e01621;hp=-c;p=jalview.git

Merge branch 'develop' into features/JAL-2388OverviewWindow
---

46b2ffc28aeef5800f35ce31a742a65095e01621
diff --combined src/jalview/gui/AlignViewport.java
index 87ab946,e0efa7c..3d0eb21
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@@ -46,6 -46,7 +46,6 @@@ import jalview.schemes.ColourSchemeI
  import jalview.schemes.ColourSchemeProperty;
  import jalview.schemes.ResidueColourScheme;
  import jalview.schemes.UserColourScheme;
 -import jalview.structure.CommandListener;
  import jalview.structure.SelectionSource;
  import jalview.structure.StructureSelectionManager;
  import jalview.structure.VamsasSource;
@@@ -71,7 -72,7 +71,7 @@@ import javax.swing.JInternalFrame
   * @version $Revision: 1.141 $
   */
  public class AlignViewport extends AlignmentViewport implements
 -        SelectionSource, CommandListener
 +        SelectionSource
  {
    Font font;
  
@@@ -383,11 -384,6 +383,6 @@@
      super.setViewStyle(settingsForView);
      setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
              viewStyle.getFontSize()), false);
-     if (residueShading != null)
-     {
-       residueShading.setConservationApplied(settingsForView
-               .isConservationColourSelected());
-     }
    }
  
    /**
diff --combined src/jalview/viewmodel/AlignmentViewport.java
index e5ce3e9,0c470fe..fb2b4071
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@@ -2430,6 -2430,11 +2430,11 @@@ public abstract class AlignmentViewpor
    public void setViewStyle(ViewStyleI settingsForView)
    {
      viewStyle = new ViewStyle(settingsForView);
+     if (residueShading != null)
+     {
+       residueShading.setConservationApplied(settingsForView
+               .isConservationColourSelected());
+     }
    }
  
    @Override
@@@ -2640,7 -2645,6 +2645,7 @@@
      this.followHighlight = b;
    }
  
 +  @Override
    public int getStartRes()
    {
      return startRes;
@@@ -2652,7 -2656,6 +2657,7 @@@
      return endRes;
    }
  
 +  @Override
    public int getStartSeq()
    {
      return startSeq;
@@@ -2696,7 -2699,6 +2701,7 @@@
      this.endSeq = seq;
    }
  
 +  @Override
    public int getEndSeq()
    {
      return endSeq;