X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=7eab3dde3e2069ee86fc60ae08c3037b6694c9f8;hb=ac4bbf6dd2bfccdaae9067fb4765c73600dea729;hp=b0a5caa81f8f172cb75d9d326521c5cd65fb63a0;hpb=c300ec003b843d3166983a893effc1f4faafed08;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index b0a5caa..7eab3dd 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -7,13 +7,19 @@ import java.awt.*;
 public class ResidueColourScheme implements ColourSchemeI{
     Color    [] colors;
     int       threshold = 0;
+    public Vector   consensus;
 
     public ResidueColourScheme(Color[] colors, int threshold) {
-	this.colors    = colors;
+        this.colors    = colors;
 	this.threshold = threshold;
     }
 
-    public ResidueColourScheme() {
+    public ResidueColourScheme()
+    {   }
+
+    public void setConsensus(Vector consensus)
+    {
+      this.consensus = consensus;
     }
 
     public Color findColour(String aa)
@@ -21,9 +27,9 @@ public class ResidueColourScheme implements ColourSchemeI{
       return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
     }
 
-    public Color findColour(String s, int j, Vector aa) {
+    public Color findColour(String s, int j) {
 
-       if( threshold==0 || aboveThreshold(aa,s,j))
+       if( threshold==0 || aboveThreshold(s,j))
           return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
        else
           return Color.white;
@@ -38,10 +44,9 @@ public class ResidueColourScheme implements ColourSchemeI{
 	threshold = ct;
     }
 
-    public boolean aboveThreshold(Vector aa,String s, int j)
+    public boolean aboveThreshold(String s, int j)
     {
-
-	Hashtable hash = (Hashtable)aa.elementAt(j);
+	Hashtable hash = (Hashtable)consensus.elementAt(j);
 
         if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))
         {