From 6d5aff5f7ace98b6416c7e9dc2a8fdc6ad194902 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 15 Apr 2005 15:00:57 +0000
Subject: [PATCH] pid and conservation changes

---
 src/jalview/gui/PopupMenu.java |   37 ++++++++++++++++++++++---------------
 src/jalview/gui/SeqPanel.java  |   23 ++++++-----------------
 2 files changed, 28 insertions(+), 32 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8d505ea..b04530c 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();
   }
 
@@ -464,7 +470,8 @@ else // remove PIDColouring
 
       sg.cs = ccs;
 
-      Desktop.setConservationSliderSource(ap, ccs, sg.getName());
+      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+      SliderPanel.showConservationSlider();
     }
     else // remove ConservationColouring
     {
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3bfc7db..0fa6d17 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -420,14 +420,9 @@ public class SeqPanel extends JPanel
       stretchGroup = sg;
 
       if(av.getConservationSelected())
-        Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");
-      else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())
-      {
-        ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();
-        int threshold = rcs.getThreshold();
-        if (threshold > 0)
-          Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
-      }
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
+      if(av.getAbovePIDThreshold())
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
 
     }
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
@@ -472,13 +467,9 @@ public class SeqPanel extends JPanel
 
     else if(stretchGroup.cs instanceof ConservationColourScheme)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
-
-
+       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
        stretchGroup.cs = ccs;
-
-
-       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
+       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
 
        repaint();
     }
@@ -487,9 +478,7 @@ public class SeqPanel extends JPanel
       if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
       {
         ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;
-        int threshold = rcs.getThreshold();
-        if(threshold>0)
-          Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
       }
 
     }
-- 
1.7.10.2