X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=899fc60ae99d22f2cc372d99e22a543480dd3534;hb=4984b6e2d15c5983e8d3177425cfbe31329d750c;hp=8785954c60a271a2e3bdcd0a868e8fd2b2923024;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 8785954..899fc60 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -44,10 +44,10 @@ public class NucleotideColourScheme extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n)
+    public Color findColour(char c)
     {
         // System.out.println("called"); log.debug
-        return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+        return colors[ResidueProperties.nucleotideIndex[c]];
     }
 
     /**
@@ -58,13 +58,14 @@ public class NucleotideColourScheme extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n, int j)
+    public Color findColour(char c, int j)
     {
-        if ((threshold == 0) || aboveThreshold(n, j))
+        Color currentColour;
+        if ((threshold == 0) || aboveThreshold(c, j))
         {
             try
             {
-                return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+                currentColour = colors[ ResidueProperties.nucleotideIndex[c]];
             }
             catch (Exception ex)
             {
@@ -75,5 +76,10 @@ public class NucleotideColourScheme extends ResidueColourScheme
         {
             return Color.white;
         }
+
+        if(conservationColouring)
+         currentColour = applyConservation(currentColour, j);
+
+       return currentColour;
     }
 }