X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=398294b7cd9874d59c3d78a31c2adb7de99d81ca;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=8d505ea3ab3dd0186a04ca8156775aff26a17d53;hpb=ac07859006686a2c62bcf57b24742eb610bc46f0;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8d505ea..398294b 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -395,22 +395,29 @@ 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 +441,13 @@ else // remove PIDColouring
 
   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    getGroup().cs = new Blosum62ColourScheme(ap.av);
+    SequenceGroup sg = getGroup();
+
+    sg.cs = new Blosum62ColourScheme();
+
+    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                                               ap.av.alignment.getWidth()));
+
     refresh();
   }
 
@@ -464,7 +477,8 @@ else // remove PIDColouring
 
       sg.cs = ccs;
 
-      Desktop.setConservationSliderSource(ap, ccs, sg.getName());
+      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+      SliderPanel.showConservationSlider();
     }
     else // remove ConservationColouring
     {
@@ -539,7 +553,7 @@ else // remove PIDColouring
     if(s!=null)
     {
       sequence.setName(s);
-      ap.RefreshPanels();
+      ap.repaint();
     }
 
   }
@@ -549,7 +563,7 @@ 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)