X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=8785954c60a271a2e3bdcd0a868e8fd2b2923024;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=dc061756c782e8f3145bb383de4c35c58156bb90;hpb=85867b5d46751cfce6500002e098a431fec0950e;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index dc06175..8785954 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,35 +1,79 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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.*;
 
+
+/**
+ * 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");
-    return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];
-  }
-
-
-  public Color findColour(String n, int j) {
-
-    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;
+    /**
+     * Creates a new NucleotideColourScheme object.
+     */
+    public NucleotideColourScheme()
+    {
+        super(ResidueProperties.nucleotide, 0);
+    }
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n)
+    {
+        // System.out.println("called"); log.debug
+        return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n, int j)
+    {
+        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;
+        }
+    }
 }