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

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

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 0c1e688..62dfec5 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -19,6 +19,7 @@ package jalview.schemes;
 
 import java.awt.Color;
 import java.util.StringTokenizer;
+import jalview.datamodel.SequenceI;
 
 public class UserColourScheme extends ResidueColourScheme
 {
@@ -201,7 +202,7 @@ public class UserColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public Color findColour(char c, int j, int sequenceIndex)
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
     int index = ResidueProperties.aaIndex[c];