From a4685bdf439ef8c5b61593c9dbb574e884385a2b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 17 Aug 2005 09:09:18 +0000
Subject: [PATCH] User colours

---
 src/jalview/gui/PopupMenu.java     |   39 ++++++++++++++++++++---
 src/jalview/jbgui/GAlignFrame.java |   61 ++++++++++++++++++++++++------------
 2 files changed, 76 insertions(+), 24 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 26fc93c..40c51cb 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -339,6 +339,28 @@ public class PopupMenu extends JPopupMenu
         colourMenu.add(buriedColour);
         colourMenu.add(nucleotideMenuItem);
         colourMenu.add(userDefinedColour);
+
+        if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+        {
+          java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+              getUserColourSchemes().keys();
+
+          while (userColours.hasMoreElements())
+          {
+            JMenuItem item = new JMenuItem(userColours.
+                nextElement().toString());
+            item.addActionListener(new ActionListener()
+            {
+              public void actionPerformed(ActionEvent evt)
+              {
+                userDefinedColour_actionPerformed(evt);
+              }
+            });
+            colourMenu.add(item);
+          }
+        }
+
+
         colourMenu.addSeparator();
         colourMenu.add(abovePIDColour);
         colourMenu.add(conservationMenuItem);
@@ -423,7 +445,7 @@ public class PopupMenu extends JPopupMenu
                     abovePIDColour_actionPerformed(e);
                 }
             });
-        userDefinedColour.setText("User Defined");
+        userDefinedColour.setText("User Defined...");
         userDefinedColour.addActionListener(new java.awt.event.ActionListener()
             {
                 public void actionPerformed(ActionEvent e)
@@ -621,9 +643,18 @@ public class PopupMenu extends JPopupMenu
      */
     protected void userDefinedColour_actionPerformed(ActionEvent e)
     {
-        new UserDefinedColours(ap, getGroup());
-    }
-
+       SequenceGroup sg = getGroup();
+
+       if (e.getActionCommand().equals("User Defined..."))
+         new UserDefinedColours(ap, sg);
+       else
+       {
+         UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+             getUserColourSchemes().get(e.getActionCommand());
+
+         sg.cs = udc;
+       }
+     }
     /**
      * DOCUMENT ME!
      *
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 26e5326..345bcf5 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,7 +23,6 @@ import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
 
-import jalview.gui.*;
 import jalview.schemes.*;
 
 public class GAlignFrame
@@ -115,25 +114,10 @@ public class GAlignFrame
   JMenu jMenu2 = new JMenu();
   JMenuItem padGapsMenuitem = new JMenuItem();
   JMenuItem ClustalRealign = new JMenuItem();
+  protected ButtonGroup colours = new ButtonGroup();
 
   public GAlignFrame()
   {
-    ButtonGroup colours = new ButtonGroup();
-    colours.add(noColourmenuItem);
-    colours.add(clustalColour);
-    colours.add(zappoColour);
-    colours.add(taylorColour);
-    colours.add(hydrophobicityColour);
-    colours.add(helixColour);
-    colours.add(strandColour);
-    colours.add(turnColour);
-    colours.add(buriedColour);
-    colours.add(userDefinedColour);
-    colours.add(PIDColour);
-    colours.add(BLOSUM62Colour);
-    colours.add(nucleotideColour);
-
-    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
 
 
     try
@@ -141,12 +125,10 @@ public class GAlignFrame
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
-      JMenuItem item;
-
       // dynamically fill save as menu with available formats
       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
       {
-        item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
+        JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
                              elementAt(
                                  i));
         item.addActionListener(new java.awt.event.ActionListener()
@@ -164,6 +146,45 @@ public class GAlignFrame
     {
     }
 
+
+    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+            nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.insert(radioItem, 15);
+        colours.add(radioItem);
+      }
+    }
+    colours.add(noColourmenuItem);
+    colours.add(clustalColour);
+    colours.add(zappoColour);
+    colours.add(taylorColour);
+    colours.add(hydrophobicityColour);
+    colours.add(helixColour);
+    colours.add(strandColour);
+    colours.add(turnColour);
+    colours.add(buriedColour);
+    colours.add(userDefinedColour);
+    colours.add(PIDColour);
+    colours.add(BLOSUM62Colour);
+    colours.add(nucleotideColour);
+
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+
+
   }
 
   public void setColourSelected(String defaultColour)
-- 
1.7.10.2