X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=4e14202cf080082b5ebf3d041378074f4930485f;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=5c658949ebc3ec6a2a9cd39566f06a34f835c628;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 5c65894..4e14202 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,35 +1,87 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * 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.*;
 
-public class NucleotideColourScheme extends ResidueColourScheme
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme
+    extends ResidueColourScheme
 {
-  public NucleotideColourScheme() {
-  super(ResidueProperties.nucleotide,0);
+  /**
+   * Creates a new NucleotideColourScheme object.
+   */
+  public NucleotideColourScheme()
+  {
+    super(ResidueProperties.nucleotide, 0);
   }
 
-
-  public Color findColour(String n)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c)
   {
     // System.out.println("called"); log.debug
-    return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];
+    return colors[ResidueProperties.nucleotideIndex[c]];
   }
 
-
-  public Color findColour(String n, int j) {
-
-    if (threshold == 0 || aboveThreshold( n, j))
+  /**
+   * 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
       {
-        return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
       }
       catch (Exception ex)
       {
         return Color.white;
       }
+    }
     else
+    {
       return Color.white;
+    }
 
-  }
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
 
+    return currentColour;
+  }
 }