JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 899fc60..dd99f8a 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,85 +1,95 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class NucleotideColourScheme extends ResidueColourScheme\r
-{\r
-    /**\r
-     * Creates a new NucleotideColourScheme object.\r
-     */\r
-    public NucleotideColourScheme()\r
-    {\r
-        super(ResidueProperties.nucleotide, 0);\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param n DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public Color findColour(char c)\r
-    {\r
-        // System.out.println("called"); log.debug\r
-        return colors[ResidueProperties.nucleotideIndex[c]];\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param n DOCUMENT ME!\r
-     * @param j DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public Color findColour(char c, int j)\r
-    {\r
-        Color currentColour;\r
-        if ((threshold == 0) || aboveThreshold(c, j))\r
-        {\r
-            try\r
-            {\r
-                currentColour = colors[ ResidueProperties.nucleotideIndex[c]];\r
-            }\r
-            catch (Exception ex)\r
-            {\r
-                return Color.white;\r
-            }\r
-        }\r
-        else\r
-        {\r
-            return Color.white;\r
-        }\r
-\r
-        if(conservationColouring)\r
-         currentColour = applyConservation(currentColour, j);\r
-\r
-       return currentColour;\r
-    }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme extends ResidueColourScheme
+{
+  /**
+   * Creates a new NucleotideColourScheme object.
+   */
+  public NucleotideColourScheme()
+  {
+    super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
+            0);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  @Override
+  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!
+   */
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    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;
+  }
+}