From 90bd6677b1f44a0608dcccde1ff59632cc9a54a1 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 27 Jan 2005 18:34:38 +0000
Subject: [PATCH] ColourSchemeKey now in documentation

---
 src/jalview/gui/AlignFrame.java    |    7 -------
 src/jalview/gui/Desktop.java       |   27 ++++++++++++++++-----------
 src/jalview/jbgui/GAlignFrame.java |   15 ---------------
 src/jalview/jbgui/GDesktop.java    |   14 --------------
 4 files changed, 16 insertions(+), 47 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b0d1b32..5173fed 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -687,13 +687,6 @@ public class AlignFrame extends GAlignFrame
 
 
 
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
-  {
-    ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
-    Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
-  }
-
-
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("sort");
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index b0f000e..464ec59 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -214,7 +214,6 @@ public class Desktop extends jalview.jbgui.GDesktop
                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);
 
-
    }
  }
 
@@ -230,12 +229,6 @@ public class Desktop extends jalview.jbgui.GDesktop
  }
 
 
- protected void colourIndexMenuItem_actionPerformed(ActionEvent e)
- {
-   ColourKey colourKey = new ColourKey(null);
-   addInternalFrame(colourKey, "Colour scheme key", 400, 320);
- }
-
 
  public void aboutMenuItem_actionPerformed(ActionEvent e)
  {
@@ -250,10 +243,22 @@ public class Desktop extends jalview.jbgui.GDesktop
 
  public void documentationMenuItem_actionPerformed(ActionEvent e)
  {
-   try{
-     jalview.util.BrowserLauncher.openURL("http://www.jalview.org/documentation.html");
-   }catch(Exception ex){}
+   try
+   {
+      ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+      java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
+      javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);
+
+      javax.help.HelpBroker hb = hs.createHelpBroker();
+      hb.setLocation(new Point(200, 50));
+      hb.setSize(new Dimension(800,700));
+      hb.setCurrentID("home");
+      hb.setDisplayed(true);
+   }
+   catch (Exception ex)
+   {
+     ex.printStackTrace();
+   }
  }
 
-
 }
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a74c5e7..484287c 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -68,7 +68,6 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
   JMenuItem htmlMenuItem = new JMenuItem();
-  JMenuItem schemeKeyMenuItem = new JMenuItem();
   JMenuItem overviewMenuItem = new JMenuItem();
   protected JMenuItem undoMenuItem = new JMenuItem();
   protected JMenuItem redoMenuItem = new JMenuItem();
@@ -500,14 +499,6 @@ public class GAlignFrame extends JInternalFrame
         htmlMenuItem_actionPerformed(e);
       }
     });
-    schemeKeyMenuItem.setText("Colour Scheme Key");
-    schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        schemeKeyMenuItem_actionPerformed(e);
-      }
-    });
     overviewMenuItem.setText("Overview window");
     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -687,8 +678,6 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.addSeparator();
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(conservationMenuItem);
-    colourMenu.addSeparator();
-    colourMenu.add(schemeKeyMenuItem);
     calculateMenu.add(sortPairwiseMenuItem);
     calculateMenu.add(sortIDMenuItem);
     calculateMenu.add(sortGroupMenuItem);
@@ -968,10 +957,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 475153d..2ef7ad6 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -24,7 +24,6 @@ public class GDesktop extends JFrame
   JMenuItem quit = new JMenuItem();
   JMenuItem aboutMenuItem = new JMenuItem();
   JMenuItem documentationMenuItem = new JMenuItem();
-  JMenuItem colourIndexMenuItem = new JMenuItem();
   FlowLayout flowLayout1 = new FlowLayout();
   protected static JMenu windowMenu = new JMenu();
   public GDesktop()
@@ -97,14 +96,6 @@ public class GDesktop extends JFrame
         documentationMenuItem_actionPerformed(e);
       }
     });
-    colourIndexMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        colourIndexMenuItem_actionPerformed(e);
-      }
-    });
-    colourIndexMenuItem.setText("Colour Scheme Key");
     this.getContentPane().setLayout(flowLayout1);
     windowMenu.setText("Window");
     DesktopMenubar.add(FileMenu);
@@ -115,7 +106,6 @@ public class GDesktop extends JFrame
     FileMenu.add(inputTextboxMenuItem);
     FileMenu.addSeparator();
     FileMenu.add(quit);
-    HelpMenu.add(colourIndexMenuItem);
     HelpMenu.add(aboutMenuItem);
     HelpMenu.add(documentationMenuItem);
   }
@@ -138,8 +128,4 @@ public class GDesktop extends JFrame
   protected void documentationMenuItem_actionPerformed(ActionEvent e)
   {  }
 
-  protected void colourIndexMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
 }
-- 
1.7.10.2