Formatting

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

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index dc06175..4e14202 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,35 +1,87 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
-public class NucleotideColourScheme extends ResidueColourScheme\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class NucleotideColourScheme\r
+    extends ResidueColourScheme\r
 {\r
-  public NucleotideColourScheme() {\r
-  super(ResidueProperties.nucleotide,0);\r
+  /**\r
+   * Creates a new NucleotideColourScheme object.\r
+   */\r
+  public NucleotideColourScheme()\r
+  {\r
+    super(ResidueProperties.nucleotide, 0);\r
   }\r
 \r
-\r
-  public Color findColour(String n)\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");\r
-    return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];\r
+    // System.out.println("called"); log.debug\r
+    return colors[ResidueProperties.nucleotideIndex[c]];\r
   }\r
 \r
-\r
-  public Color findColour(String n, int j) {\r
-\r
-    if (threshold == 0 || aboveThreshold( n, j))\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
-        return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\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
-  }\r
+    if (conservationColouring)\r
+    {\r
+      currentColour = applyConservation(currentColour, j);\r
+    }\r
 \r
+    return currentColour;\r
+  }\r
 }\r