X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=133dcafc16e0a139e961a84473d6b1a19f92187e;hb=6173092ff5cb03f039cac674bfc8bc4f969976a5;hp=001b2323d34be58ef353804711951da2efa357ab;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 001b232..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);
 
@@ -418,16 +418,15 @@ public class UserDefinedColours
     if (seqGroup != null)
     {
       seqGroup.cs = ucs;
-      ap.repaint();
+      ap.paintAlignment(true);
     }
     else if (ap != null)
     {
       ap.alignFrame.changeColour(ucs);
     }
-    else if (pdbcanvas != null)
+    else if (jmol != null)
     {
-      pdbcanvas.pdb.setColours(ucs);
-      pdbcanvas.updateSeqColours();
+      jmol.setJalviewColourScheme(ucs);
     }
   }
 
@@ -789,12 +788,12 @@ public class UserDefinedColours
       {
         ap.av.setGlobalColourScheme(oldColourScheme);
       }
-      ap.repaint();
+      ap.paintAlignment(true);
     }
 
-    if (pdbcanvas != null)
+    if (jmol != null)
     {
-      pdbcanvas.pdb.setColours(oldColourScheme);
+      jmol.setJalviewColourScheme(oldColourScheme);
     }
 
     try