X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5cc5111cecb79a31ba1423d084eb849e5bdd534a;hb=56308882b011c6c6ff96786490bbb1c937d3ade3;hp=5a0d13ea1391a358e02f345ca8e13010ca46b9ac;hpb=3e4598b8df2fdae8195148cf965a1e2c2d255b46;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5a0d13e..5cc5111 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3346,39 +3346,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (cs != null)
     {
       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
-      // Make sure viewport is up to date w.r.t. any sliders
-      // ? not needed as handled by SliderPanel.valueChanged?
-//       if (viewport.getAbovePIDThreshold())
-//       {
-      // int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-//       "Background");
-       //todo is threshold held in viewport style or in colour scheme?
-//       viewport.setThreshold(threshold);
-      // }
-      //
-      // if (viewport.getConservationSelected())
-      // {
-      // cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
-      // cs, "Background"));
-      // }
     }
 
     viewport.setGlobalColourScheme(cs);
-    if (viewport.getConservationSelected())
-    {
-      int conservationInc = SliderPanel.getConservationValue();
-      viewport.getViewportColourScheme()
-              .setConservationInc(conservationInc);
-    }
 
     alignPanel.paintAlignment(true);
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Show the PID threshold slider panel
    */
   @Override
   protected void modifyPID_actionPerformed()
@@ -3392,10 +3368,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Show the Conservation slider panel
    */
   @Override
   protected void modifyConservation_actionPerformed()
@@ -3418,6 +3391,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     boolean selected = conservationMenuItem.isSelected();
     modifyConservation.setEnabled(selected);
     viewport.setConservationSelected(selected);
+    viewport.getViewportColourScheme().setConservationApplied(selected);
 
     changeColour(viewport.getGlobalColourScheme());
     if (selected)