X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=462b9c64bc41d0f272e54a1556da250cfd8b1d12;hb=f52d7fc6ab9bf2c926f0208c225d3dc6e65c8ecf;hp=b6602ea15c01ad44a58c12066c7b48b4dd3a52eb;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index b6602ea..462b9c6 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -17,9 +17,9 @@
  */
 package jalview.schemes;
 
-import java.util.*;
-
-import java.awt.*;
+import java.awt.Color;
+import java.util.StringTokenizer;
+import jalview.datamodel.SequenceI;
 
 public class UserColourScheme extends ResidueColourScheme
 {
@@ -29,15 +29,18 @@ public class UserColourScheme extends ResidueColourScheme
 
   public UserColourScheme()
   {
+    super(ResidueProperties.aaIndex);
   }
 
   public UserColourScheme(Color[] newColors)
   {
+    super(ResidueProperties.aaIndex);
     colors = newColors;
   }
 
   public UserColourScheme(String colour)
   {
+    super(ResidueProperties.aaIndex);
     Color col = getColourFromString(colour);
 
     if (col == null)
@@ -201,7 +204,8 @@ public class UserColourScheme extends ResidueColourScheme
 
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
     int index = ResidueProperties.aaIndex[c];