From b7c522b6eba60889fb1078f75e83e8e6c97ef7f8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 21 Jan 2005 18:30:06 +0000
Subject: [PATCH] Commented out code removed

---
 src/jalview/gui/PopupMenu.java |  218 +---------------------------------------
 1 file changed, 5 insertions(+), 213 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 19698b7..722bad1 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -332,6 +332,11 @@ public class PopupMenu extends JPopupMenu
 
   void refresh()
   {
+    SequenceGroup sg = getGroup();
+    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
+    if( superG !=null)
+      superG.setSuperGroupProperties( sg );
+
     ap.seqPanel.seqCanvas.paintFlag=true;
     ap.seqPanel.repaint();
   }
@@ -456,219 +461,6 @@ frame.setMaximizable(false);
      refresh();
   }
 
-/*
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( null );
-    changeColour();
-  }
-
-
-  public void clustalColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
-    conservationMenuItem.setSelected(false);
-    abovePIDThreshold.setSelected(false);
-    changeColour();
-  }
-
-  public void zappoColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new ZappoColourScheme() );
-    changeColour();
-  }
-
-  public void taylorColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new TaylorColourScheme() );
-    changeColour();
-  }
-
-
-  public void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
-    changeColour();
-  }
-
-  public void helixColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new HelixColourScheme()  );
-    changeColour();
-  }
-
-
-  public void strandColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new StrandColourScheme() );
-    changeColour();
-  }
-
-
-  public void turnColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new TurnColourScheme() );
-    changeColour();
-  }
-
-
-  public void buriedColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new BuriedColourScheme() );
-    changeColour();
-  }
-
-  void changeColour()
-  {
-    if(abovePIDThreshold.isSelected())
-      abovePIDThreshold_actionPerformed(null);
-    else if(conservationMenuItem.isSelected())
-      conservationMenuItem_actionPerformed(null);
-
-     alignPanel.seqPanel.seqCanvas.paintFlag = true;
-     alignPanel.repaint();
-  }
-
-  void addConservationOrPIDColour()
-  {
-    int x=0, y=0, threshold = 70;
-
-    if(sliderFrame!=null)
-       try
-       {
-         x = sliderFrame.getX();
-         y = sliderFrame.getY();
-         SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
-         threshold = sp.getValue();
-         sliderFrame.setClosed(true);
-       }
-       catch (Exception ex)
-       {    ex.printStackTrace();   }
-
-     ColourSchemeI oldCs = viewport.getGlobalColourScheme();
-
-     ConservationColourScheme ccs = null;
-     if (oldCs instanceof ConservationColourScheme)
-       ccs = (ConservationColourScheme) oldCs;
-
-     if(conservationMenuItem.isSelected())
-     {
-       Alignment al = (Alignment)viewport.alignment;
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
-
-       c.calculate();
-       c.verdict(false, 100);
-
-       if(ccs!=null)
-         ccs = new ConservationColourScheme(c, ccs.cs);
-       else
-         ccs = new ConservationColourScheme(c, oldCs);
-
-        viewport.setGlobalColourScheme( ccs );
-
-     }
-     else if(oldCs instanceof ConservationColourScheme)
-     {
-       oldCs = ccs.cs;
-       viewport.setGlobalColourScheme( oldCs );
-     }
-
-
-     if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
-     {
-       sliderFrame = new JInternalFrame();
-       sliderFrame.setMaximizable(false);
-       sliderFrame.setResizable(false);
-
-       SliderPanel sp = null;
-       if (conservationMenuItem.isSelected())
-       {
-        if(threshold > 50)
-          threshold = 30;
-        sp = new SliderPanel(alignPanel, threshold, true,ccs);
-        Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);
-        threshold = 0;
-       }
-       else if (abovePIDThreshold.isSelected())
-       {
-         sp = new SliderPanel(alignPanel, threshold, false, oldCs);
-         sp.cs = oldCs;
-         Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
-       }
-
-       sliderFrame.setContentPane(sp);
-       if(x!=0 && y!=0)
-               sliderFrame.setLocation(x,y);
-
-     }
-     else
-       threshold = 0;
-
-
-     if (oldCs instanceof ResidueColourScheme)
-     {
-       ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
-       rcs.setThreshold(threshold);
-     }
-     else if (oldCs instanceof ScoreColourScheme)
-     {
-       ScoreColourScheme scs = (ScoreColourScheme) oldCs;
-       scs.setThreshold(threshold);
-     }
-
-     alignPanel.seqPanel.seqCanvas.paintFlag = true;
-     alignPanel.repaint();
-
-  }
-
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-   if(abovePIDThreshold.isSelected())
-    abovePIDThreshold.setSelected(false);
-
-   viewport.setConservationSelected(conservationMenuItem.isSelected());
-
-   addConservationOrPIDColour();
-  }
-
-  JInternalFrame sliderFrame;
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)
-  {
-      if(conservationMenuItem.isSelected())
-        conservationMenuItem.setSelected(false);
-
-      addConservationOrPIDColour();
-  }
-
-
-
-  public void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
-  }
-
-  public void PIDColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new PIDColourScheme() );
-    alignPanel.setColourScheme( );
-  }
-
-
-  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
-    alignPanel.setColourScheme();
-  }
-*/
-//////////////////////////////////////
   protected void groupAnnotation_actionPerformed(ActionEvent e)
   {
 
-- 
1.7.10.2