From 0af39ffc83a804e0f3f0d7618fcdc9e5073c0a0b Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 22 Apr 2011 11:37:55 +0000
Subject: [PATCH] option for enabling Jmol colouring mode JAL-824

---
 src/jalview/appletgui/AppletJmol.java |   15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 619d522..9efe17e 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -52,6 +52,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
 
+  CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false);
+  
   MenuItem chain = new MenuItem("By Chain");
 
   MenuItem charge = new MenuItem("Charge & Cysteine");
@@ -185,7 +187,8 @@ public class AppletJmol extends EmbmenuFrame implements
     turn.addActionListener(this);
     buried.addActionListener(this);
     user.addActionListener(this);
-
+    jmolColour.addActionListener(this);
+    
     jmolHelp.addActionListener(this);
 
     coloursMenu.add(seqColour);
@@ -199,7 +202,7 @@ public class AppletJmol extends EmbmenuFrame implements
     coloursMenu.add(turn);
     coloursMenu.add(buried);
     coloursMenu.add(user);
-
+    coloursMenu.add(jmolColour);
     helpMenu.add(jmolHelp);
     this.setLayout(new BorderLayout());
 
@@ -474,19 +477,25 @@ public class AppletJmol extends EmbmenuFrame implements
   }
 
   /**
-   * tick or untick the seqColour menu entry depending upon if it was selected
+   * tick or untick the seqColour menu entry or jmoColour entry depending upon if it was selected
    * or not.
    * 
    * @param itm
    */
   private void setEnabled(MenuItem itm)
   {
+    jmolColour.setState(itm == jmolColour);
     seqColour.setState(itm == seqColour);
     jmb.setColourBySequence(itm == seqColour);
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
+    if (evt.getSource() == jmolColour)
+    {
+      setEnabled(jmolColour);
+      jmb.setColourBySequence(false);
+    } else
     if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-- 
1.7.10.2