From a03e7cf54816cf5c05b68e5dee297d4223f20f00 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 28 Apr 2005 15:30:28 +0000
Subject: [PATCH] Menu names changed

---
 src/jalview/gui/PopupMenu.java |   49 +++++++++++++++++++++++++---------------
 1 file changed, 31 insertions(+), 18 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 398294b..3177bfc 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -42,6 +42,7 @@ public class PopupMenu extends JPopupMenu
   JMenuItem unGroupMenuItem = new JMenuItem();
   JMenuItem pdbMenuItem = new JMenuItem();
   JMenuItem outline = new JMenuItem();
+  JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 
   public PopupMenu(AlignmentPanel ap, Sequence seq)
   {
@@ -182,6 +183,14 @@ public class PopupMenu extends JPopupMenu
         outline_actionPerformed(e);
       }
     });
+    nucleotideMenuItem.setText("Nucleotide");
+    nucleotideMenuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        nucleotideMenuItem_actionPerformed(e);
+      }
+    });
     add(groupMenu);
     this.add(sequenceMenu);
     this.add(residueMenu);
@@ -196,6 +205,9 @@ public class PopupMenu extends JPopupMenu
     defineMenu.addSeparator();
     defineMenu.add(noColourmenuItem);
     defineMenu.add(clustalColour);
+    defineMenu.add(BLOSUM62Colour);
+    defineMenu.add(PIDColour);
+
     defineMenu.add(zappoColour);
     defineMenu.add(taylorColour);
     defineMenu.add(hydrophobicityColour);
@@ -203,9 +215,10 @@ public class PopupMenu extends JPopupMenu
     defineMenu.add(strandColour);
     defineMenu.add(turnColour);
     defineMenu.add(buriedColour);
+    defineMenu.add(nucleotideMenuItem);
+
     defineMenu.add(userDefinedColour);
-    defineMenu.add(PIDColour);
-    defineMenu.add(BLOSUM62Colour);
+
     defineMenu.addSeparator();
     defineMenu.add(abovePIDColour);
     defineMenu.add(conservationMenuItem);
@@ -231,7 +244,7 @@ public class PopupMenu extends JPopupMenu
         clustalColour_actionPerformed(e);
       }
     });
-    zappoColour.setText("Zappo colour scheme");
+    zappoColour.setText("Zappo");
     zappoColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -239,7 +252,7 @@ public class PopupMenu extends JPopupMenu
         zappoColour_actionPerformed(e);
       }
     });
-    taylorColour.setText("Taylor colour scheme");
+    taylorColour.setText("Taylor");
     taylorColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -247,7 +260,7 @@ public class PopupMenu extends JPopupMenu
         taylorColour_actionPerformed(e);
       }
     });
-    hydrophobicityColour.setText("By hydrophobicity");
+    hydrophobicityColour.setText("Hydrophobicity");
     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -279,7 +292,7 @@ public class PopupMenu extends JPopupMenu
         turnColour_actionPerformed(e);
       }
     });
-    buriedColour.setText("Buried index");
+    buriedColour.setText("Buried Index");
     buriedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -287,7 +300,7 @@ public class PopupMenu extends JPopupMenu
         buriedColour_actionPerformed(e);
       }
     });
-    abovePIDColour.setText("Above PID threshold only");
+    abovePIDColour.setText("Above % Identity");
     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -295,7 +308,7 @@ public class PopupMenu extends JPopupMenu
         abovePIDColour_actionPerformed(e);
       }
     });
-    userDefinedColour.setText("User defined colours");
+    userDefinedColour.setText("User Defined");
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -311,7 +324,7 @@ public class PopupMenu extends JPopupMenu
         PIDColour_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText("BLOSUM62 score");
+    BLOSUM62Colour.setText("BLOSUM62");
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -319,7 +332,7 @@ public class PopupMenu extends JPopupMenu
         BLOSUM62Colour_actionPerformed(e);
       }
     });
-    conservationMenuItem.setText("By conservation");
+    conservationMenuItem.setText("Conservation");
    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
@@ -392,6 +405,13 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
+  public void nucleotideMenuItem_actionPerformed(ActionEvent e)
+  {
+    getGroup().cs = new NucleotideColourScheme();
+    refresh();
+  }
+
+
 
   protected void abovePIDColour_actionPerformed(ActionEvent e)
   {
@@ -424,14 +444,7 @@ public class PopupMenu extends JPopupMenu
 
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
-
+    UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());
   }
 
   protected void PIDColour_actionPerformed(ActionEvent e)
-- 
1.7.10.2