X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=b07dce8c38ad66fe6221a94952380c4b76cf0d75;hb=79f4b175e12f4c16d598b4cb56ffe62532b592a1;hp=8d747c2f02f29915c5fc1bd4e06cd51bc27e326d;hpb=34e7d17e5283f39efcbfdaa46de54f9d0aec1e91;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8d747c2..b07dce8 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -395,22 +395,28 @@ public class PopupMenu extends JPopupMenu
 
   protected void abovePIDColour_actionPerformed(ActionEvent e)
   {
-    if(abovePIDColour.isSelected())
-{
+    SequenceGroup sg = getGroup();
+    if (abovePIDColour.isSelected())
+    {
+      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                                               ap.av.alignment.getWidth()));
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
+      if (sg.cs instanceof ResidueColourScheme)
+        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
+      else if (sg.cs instanceof ScoreColourScheme)
+        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
 
-   Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());
-   refresh();
-}
-else // remove PIDColouring
-{
-    ColourSchemeI cs = getGroup().cs;
-      ResidueColourScheme rcs = (ResidueColourScheme)cs;
-      rcs.setThreshold(0);
-      getGroup().cs = rcs;
-      refresh();
-}
+      SliderPanel.showPIDSlider();
 
+    }
+    else // remove PIDColouring
+    {
+      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
+      rcs.setThreshold(0);
+      sg.cs = rcs;
+    }
 
+    refresh();
 
   }
 
@@ -434,7 +440,7 @@ else // remove PIDColouring
 
   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    getGroup().cs = new Blosum62ColourScheme(ap.av);
+    getGroup().cs = new Blosum62ColourScheme();
     refresh();
   }
 
@@ -458,13 +464,14 @@ else // remove PIDColouring
                                           ap.av.alignment.getWidth());
 
         c.calculate();
-        c.verdict(false, 100);
+        c.verdict(false, ap.av.ConsPercGaps);
         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
 
       sg.cs = ccs;
 
-      Desktop.setConservationSliderSource(ap, ccs, sg.getName());
+      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+      SliderPanel.showConservationSlider();
     }
     else // remove ConservationColouring
     {
@@ -539,7 +546,7 @@ else // remove PIDColouring
     if(s!=null)
     {
       sequence.setName(s);
-      ap.RefreshPanels();
+      ap.repaint();
     }
 
   }
@@ -549,7 +556,7 @@ else // remove PIDColouring
      SequenceGroup sg = ap.av.getSelectionGroup();
      ap.av.alignment.deleteGroup(sg);
      ap.av.setSelectionGroup(null);
-     ap.RefreshPanels();
+     ap.repaint();
   }
 
   void pdbMenuItem_actionPerformed(ActionEvent e)