+/*\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