From 5486259bcccbe21aebd36e70a6695e710679fb7f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 26 Mar 2007 17:29:37 +0000
Subject: [PATCH] Jmol calls user colours

---
 src/jalview/appletgui/UserDefinedColours.java |   19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index de1cff7..ecb3265 100755
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -38,8 +38,9 @@ public class UserDefinedColours
   ColourSchemeI oldColourScheme;
   Frame frame;
   MCview.AppletPDBCanvas pdbcanvas;
+  AppletJmol jmol;
 
-  Component caller;
+  Object caller;
   String originalLabel;
   Color originalColour;
 
@@ -74,7 +75,13 @@ public class UserDefinedColours
     init();
   }
 
-  public UserDefinedColours(Component caller,
+  public UserDefinedColours(AppletJmol jmol)
+  {
+    this.jmol = jmol;
+    init();
+  }
+
+  public UserDefinedColours(Object caller,
                             String label,
                             Color colour)
   {
@@ -345,6 +352,10 @@ public class UserDefinedColours
       ap.seqPanel.seqCanvas.img = null;
       ap.paintAlignment(true);
     }
+    else if(jmol!=null)
+    {
+      jmol.setJalviewColourScheme(ucs);
+    }
     else if (pdbcanvas != null)
     {
       pdbcanvas.setColours(ucs);
@@ -398,6 +409,10 @@ public class UserDefinedColours
       }
       ap.paintAlignment(true);
     }
+    else if(jmol !=null)
+    {
+      jmol.setJalviewColourScheme(ucs);
+    }
     else if (pdbcanvas != null)
     {
       pdbcanvas.pdb.setColours(ucs);
-- 
1.7.10.2