apply gpl development license

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

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 26aea21..7906ed1 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,37 +1,88 @@
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-\r
-public class NucleotideColourScheme extends ResidueColourScheme\r
-{\r
-  public NucleotideColourScheme() {\r
-  super(ResidueProperties.nucleotide,0);\r
-  }\r
-\r
-\r
-  public Color findColour(String n)\r
-  {\r
-    System.out.println("called");\r
-    return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];\r
-  }\r
-\r
-\r
-  public Color findColour(String n, int j) {\r
-\r
-    if (threshold == 0 || aboveThreshold( n, j))\r
-      try\r
-      {\r
-        return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
-      }\r
-      catch (Exception ex)\r
-      {\r
-        return Color.white;\r
-      }\r
-    else\r
-      return Color.white;\r
-\r
-  }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
+{
+  /**
+   * Creates a new NucleotideColourScheme object.
+   */
+  public NucleotideColourScheme()
+  {
+    super(ResidueProperties.nucleotide, 0);
+  }
+
+  /**
+   * 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]];
+  }
+
+  /**
+   * 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;
+  }
+}