X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=137ca1462889764105d36885e9b7eef5659900dc;hb=301ee338cd1b31b9d50cfd983e00513861940c27;hp=40c51cb7e5ad3466feab09fb819560df068d7ce7;hpb=a4685bdf439ef8c5b61593c9dbb574e884385a2b;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 40c51cb..137ca14 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -172,7 +172,7 @@ public class PopupMenu extends JPopupMenu
                 noColourmenuItem.setSelected(true);
             }
 
-            if (sg.cs instanceof ConservationColourScheme)
+            if (sg.cs!=null && sg.cs.conservationApplied())
             {
                 conservationMenuItem.setSelected(true);
             }
@@ -615,22 +615,13 @@ public class PopupMenu extends JPopupMenu
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
 
-            if (sg.cs instanceof ResidueColourScheme)
-            {
-                ((ResidueColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
-            }
-            else if (sg.cs instanceof ScoreColourScheme)
-            {
-                ((ScoreColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
-            }
+           sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
             SliderPanel.showPIDSlider();
         }
         else // remove PIDColouring
         {
-            ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-            rcs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
-            sg.cs = rcs;
+            sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
         }
 
         refresh();
@@ -715,17 +706,14 @@ public class PopupMenu extends JPopupMenu
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
 
-            ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-            sg.cs = ccs;
+            sg.cs.setConservation(c);
 
-            SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+            SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
             SliderPanel.showConservationSlider();
         }
         else // remove ConservationColouring
         {
-            ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
-            sg.cs = ccs.cs;
+            sg.cs.setConservation(null);
         }
 
         refresh();