Commented out code removed

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