Format changes

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

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 942e55b..4afb321 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -47,7 +47,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
     public Color findColour(String n)\r
     {\r
         // System.out.println("called"); log.debug\r
-        return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
+        return colors[ResidueProperties.nucleotideIndex[n.charAt(0)]];\r
     }\r
 \r
     /**\r
@@ -60,11 +60,12 @@ public class NucleotideColourScheme extends ResidueColourScheme
      */\r
     public Color findColour(String n, int j)\r
     {\r
+        Color currentColour;\r
         if ((threshold == 0) || aboveThreshold(n, j))\r
         {\r
             try\r
             {\r
-                currentColour = colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
+                currentColour = colors[ ResidueProperties.nucleotideIndex[n.charAt(0)]];\r
             }\r
             catch (Exception ex)\r
             {\r
@@ -77,7 +78,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
         }\r
 \r
         if(conservationColouring)\r
-         applyConservation(j);\r
+         currentColour = applyConservation(currentColour, j);\r
 \r
        return currentColour;\r
     }\r