Works out exisiting colur of a group

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

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index 1cbc0d4..ab5a808 100755 (executable)
--- 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;\r
   int colourThreshold =  7;\r
 \r
-  public ConservationColourScheme(SequenceGroup sg)\r
+  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
   {\r
     super();\r
-    this.conserve = sg.getConservation();\r
-    colourThreshold = 7;\r
-    this.cs = sg.cs;\r
+    conserve = cons;\r
+    cs = oldcs;\r
   }\r
 \r
   public void setColours(DrawableSequence seq, int j) {\r
@@ -68,7 +67,7 @@ public class ConservationColourScheme extends ResidueColourScheme {
 \r
       seq.setColor(c);\r
   }\r
-   public Color findColour(SequenceI seq, String s, int i, java.util.Vector whatever)\r
+   public Color findColour(String s, int i, java.util.Vector whatever)\r
    {\r
      Color c = null;\r
      if (colourThreshold > 0 && conserve.getConsSequence() != null)\r
@@ -106,7 +105,7 @@ public class ConservationColourScheme extends ResidueColourScheme {
    }\r
 \r
   public Color findColour(DrawableSequence seq, String s, int j) {\r
-    return cs.findColour(null, s, -1, null);\r
+    return cs.findColour( s, -1, null);\r
   }\r
   public boolean fullConservation(int j) {\r
     String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);\r