JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places...

[jalview.git] / src / jalview / appletgui / UserDefinedColours.java

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index d1c0e1b..83d6fd6 100644 (file)
--- 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);