X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConservationColourScheme.java;h=ab5a8083e19da4f1106fad4dd5cc16632d2571ad;hb=44d9bd9b511490baec5302be3b7756be0adebde3;hp=0eac54be7e14c89dae568ecbaa1d21a229f46fac;hpb=6a4192007f93c030726298295037f6eac97cf4f3;p=jalview.git

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index 0eac54b..ab5a808 100755
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -29,12 +29,11 @@ public class ConservationColourScheme extends ResidueColourScheme {
   public int inc = 30;
   int colourThreshold =  7;
 
-  public ConservationColourScheme(SequenceGroup sg)
+  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
   {
     super();
-    this.conserve = sg.getConservation();
-    colourThreshold = 7;
-    this.cs = sg.cs;
+    conserve = cons;
+    cs = oldcs;
   }
 
   public void setColours(DrawableSequence seq, int j) {
@@ -67,9 +66,8 @@ public class ConservationColourScheme extends ResidueColourScheme {
       }
 
       seq.setColor(c);
-
   }
-   public Color findColour(SequenceI seq, String s, int i, java.util.Vector whatever)
+   public Color findColour(String s, int i, java.util.Vector whatever)
    {
      Color c = null;
      if (colourThreshold > 0 && conserve.getConsSequence() != null)
@@ -107,7 +105,7 @@ public class ConservationColourScheme extends ResidueColourScheme {
    }
 
   public Color findColour(DrawableSequence seq, String s, int j) {
-    return cs.findColour(null, s, -1, null);
+    return cs.findColour( s, -1, null);
   }
   public boolean fullConservation(int j) {
     String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);