aaIndex replaces aaHash

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

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 0f2101e..6aaef7d 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
@@ -16,39 +16,69 @@
 * 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
-\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
-  public NucleotideColourScheme() {\r
-  super(ResidueProperties.nucleotide,0);\r
-  }\r
-\r
-\r
-  public Color findColour(String n)\r
-  {\r
-    // System.out.println("called"); log.debug\r
-    return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];\r
-  }\r
-\r
+    /**\r
+     * Creates a new NucleotideColourScheme object.\r
+     */\r
+    public NucleotideColourScheme()\r
+    {\r
+        super(ResidueProperties.nucleotide, 0);\r
+    }\r
 \r
-  public Color findColour(String n, int j) {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param n DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public Color findColour(String n)\r
+    {\r
+        // System.out.println("called"); log.debug\r
+        return colors[ResidueProperties.nucleotideIndex[n.charAt(0)]];\r
+    }\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
+     * DOCUMENT ME!\r
+     *\r
+     * @param n DOCUMENT ME!\r
+     * @param j DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public Color findColour(String n, int j)\r
+    {\r
+        if ((threshold == 0) || aboveThreshold(n, j))\r
+        {\r
+            try\r
+            {\r
+                currentColour = colors[ ResidueProperties.nucleotideIndex[n.charAt(0)]];\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
+         applyConservation(j);\r
 \r
+       return currentColour;\r
+    }\r
 }\r