/*\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
import java.awt.*;\r
\r
\r
-public class NucleotideColourScheme extends ResidueColourScheme {\r
- public NucleotideColourScheme() {\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
- 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(String n)\r
+ {\r
// System.out.println("called"); log.debug\r
- return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
+ return colors[ResidueProperties.nucleotideIndex[n.charAt(0)]];\r
}\r
\r
- public Color findColour(String n, int j) {\r
- if ((threshold == 0) || aboveThreshold(n, j)) {\r
- try {\r
- return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
- } catch (Exception ex) {\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
- } else {\r
+ }\r
+ else\r
+ {\r
return Color.white;\r
}\r
+\r
+ if(conservationColouring)\r
+ applyConservation(j);\r
+\r
+ return currentColour;\r
}\r
}\r