X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=1c9525c3a3c2726d448bb7881b475d6d7f3e89b1;hb=c1e70ea0a01d2c916675aa8020970c6696d0dba5;hp=e238d797d83860d17a6cd62b2317c885e426a601;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index e238d79..1c9525c 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -82,27 +82,25 @@ public class ScoreColourScheme extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String s, int j)
+    public Color findColour(char c, int j)
     {
         if (threshold > 0)
         {
-            if (!aboveThreshold(s, j))
+            if (!aboveThreshold(c, j))
             {
                 return Color.white;
             }
         }
 
-        char c = s.charAt(0);
-
-        if (jalview.util.Comparison.isGap((c)))
+        if (jalview.util.Comparison.isGap(c))
         {
             return Color.white;
         }
 
-        currentColour = colors[((Integer) ResidueProperties.aaHash.get(s)).intValue()];
+        Color currentColour = colors[ ResidueProperties.aaIndex[c] ];
 
         if(conservationColouring)
-         applyConservation(j);
+          currentColour =  applyConservation(currentColour, j);
 
         return currentColour;
     }