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 5d12cce..b0365ce 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -19,6 +19,7 @@ package jalview.schemes;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
 
@@ -154,7 +155,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
    * @return DOCUMENT ME!
    */
   @Override
-  public Color findColour(char c, int j, int sequenceIndex)
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour = Color.white;
 
@@ -204,7 +205,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
           if (colourScheme != null)
           {
-            currentColour = colourScheme.findColour(c, j, sequenceIndex);
+            currentColour = colourScheme.findColour(c, j, seq);
           }
           else if (range != 0)
           {