X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FUserDefinedColours.java;h=342c065261eeb7ca1280c7d8739a0ad8fd5200ee;hb=e5b2fbdb4ecc9faaadcc3e18fabad8794fca44aa;hp=9ffe1698ce5869462f5743d4191b301a3d9d8ab7;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 9ffe169..342c065 100644
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -427,7 +427,9 @@ public class UserDefinedColours extends Panel implements ActionListener,
   {
     applyButton_actionPerformed();
     if (dialog != null)
+    {
       dialog.setVisible(false);
+    }
 
     frame.setVisible(false);
   }
@@ -489,7 +491,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     UserColourScheme ucs = new UserColourScheme(newColours);
     if (ap != null)
     {
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     if (ap != null)
@@ -557,7 +559,9 @@ public class UserDefinedColours extends Panel implements ActionListener,
         }
       }
       if (dialog != null)
+      {
         dialog.setVisible(false);
+      }
 
       frame.setVisible(false);
       return;