X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=133dcafc16e0a139e961a84473d6b1a19f92187e;hb=6173092ff5cb03f039cac674bfc8bc4f969976a5;hp=d5a92112cdeb96d93eccab1bd7b5fec916ed3028;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index d5a9211..133dcaf 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -45,7 +45,7 @@ public class UserDefinedColours
   Vector selectedButtons;
   ColourSchemeI oldColourScheme;
   JInternalFrame frame;
-  MCview.PDBCanvas pdbcanvas;
+  AppJmol jmol;
   Vector upperCaseButtons;
   Vector lowerCaseButtons;
 
@@ -95,10 +95,10 @@ public class UserDefinedColours
     showFrame();
   }
 
-  public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
+  public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs)
   {
     super();
-    pdbcanvas = pdb;
+    this.jmol = jmol;
 
     colorChooser.getSelectionModel().addChangeListener(this);
 
@@ -424,10 +424,9 @@ public class UserDefinedColours
     {
       ap.alignFrame.changeColour(ucs);
     }
-    else if (pdbcanvas != null)
+    else if (jmol != null)
     {
-      pdbcanvas.pdb.setColours(ucs);
-      pdbcanvas.updateSeqColours();
+      jmol.setJalviewColourScheme(ucs);
     }
   }
 
@@ -792,9 +791,9 @@ public class UserDefinedColours
       ap.paintAlignment(true);
     }
 
-    if (pdbcanvas != null)
+    if (jmol != null)
     {
-      pdbcanvas.pdb.setColours(oldColourScheme);
+      jmol.setJalviewColourScheme(oldColourScheme);
     }
 
     try