X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FUserDefinedColours.java;h=83d6fd6a999db66062e4db1be1c4b2879b2e1d7e;hb=483ecb5e4541537778844529cc93204f9124b68d;hp=d1c0e1bf7b7fd0d3c9bdbdf49c753b7feaadadd6;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index d1c0e1b..83d6fd6 100644
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -64,13 +64,13 @@ public class UserDefinedColours extends Panel
 
   Button selectedButton;
 
-  Vector<Color> oldColours = new Vector<Color>();
+  Vector<Color> oldColours = new Vector<>();
 
   ColourSchemeI oldColourScheme;
 
   Frame frame;
 
-  MCview.AppletPDBCanvas pdbcanvas;
+  mc_view.AppletPDBCanvas pdbcanvas;
 
   AppletJmol jmol;
 
@@ -107,7 +107,7 @@ public class UserDefinedColours extends Panel
     init();
   }
 
-  public UserDefinedColours(MCview.AppletPDBCanvas pdb)
+  public UserDefinedColours(mc_view.AppletPDBCanvas pdb)
   {
     this.pdbcanvas = pdb;
     init();
@@ -520,11 +520,11 @@ public class UserDefinedColours extends Panel
                 ap.av.isIgnoreGapsConsensus());
       }
       ap.seqPanel.seqCanvas.img = null;
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
     else if (jmol != null)
     {
-      jmol.setJalviewColourScheme(ucs);
+      jmol.colourByJalviewColourScheme(ucs);
     }
     else if (pdbcanvas != null)
     {
@@ -599,7 +599,7 @@ public class UserDefinedColours extends Panel
       {
         ap.av.setGlobalColourScheme(oldColourScheme);
       }
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
 
     frame.setVisible(false);