X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=899fc60ae99d22f2cc372d99e22a543480dd3534;hb=1b1a1007c534a02fdbae76df0c084f215c7c4c21;hp=0f2101e06a089a7fe5d8a1ab3788ba00746b17aa;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 0f2101e..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
@@ -16,39 +16,70 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package jalview.schemes;
 
 import java.awt.*;
 
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class NucleotideColourScheme extends ResidueColourScheme
 {
-  public NucleotideColourScheme() {
-  super(ResidueProperties.nucleotide,0);
-  }
-
-
-  public Color findColour(String n)
-  {
-    // System.out.println("called"); log.debug
-    return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];
-  }
-
+    /**
+     * Creates a new NucleotideColourScheme object.
+     */
+    public NucleotideColourScheme()
+    {
+        super(ResidueProperties.nucleotide, 0);
+    }
 
-  public Color findColour(String n, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(char c)
+    {
+        // System.out.println("called"); log.debug
+        return colors[ResidueProperties.nucleotideIndex[c]];
+    }
 
-    if (threshold == 0 || aboveThreshold( n, j))
-      try
-      {
-        return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
-      }
-      catch (Exception ex)
-      {
-        return Color.white;
-      }
-    else
-      return Color.white;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(char c, int j)
+    {
+        Color currentColour;
+        if ((threshold == 0) || aboveThreshold(c, j))
+        {
+            try
+            {
+                currentColour = colors[ ResidueProperties.nucleotideIndex[c]];
+            }
+            catch (Exception ex)
+            {
+                return Color.white;
+            }
+        }
+        else
+        {
+            return Color.white;
+        }
 
-  }
+        if(conservationColouring)
+         currentColour = applyConservation(currentColour, j);
 
+       return currentColour;
+    }
 }