JAL-958 store/recover normalised flag

[jalview.git] / src / jalview / schemes / UserColourScheme.java

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index b6602ea..25c849e 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -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];