JAL-1065 JAL-1066 - use direct object reference rather then index into alignment

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 36c1f95..b0365ce 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,9 +17,11 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Color;
 
 public class AnnotationColourGradient extends ResidueColourScheme
 {
@@ -152,7 +154,8 @@ public class AnnotationColourGradient extends ResidueColourScheme
    * 
    * @return DOCUMENT ME!
    */
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour = Color.white;
 
@@ -202,7 +205,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
           if (colourScheme != null)
           {
-            currentColour = colourScheme.findColour(c, j);
+            currentColour = colourScheme.findColour(c, j, seq);
           }
           else if (range != 0)
           {