/*\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
+ * 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
-\r
/**\r
* DOCUMENT ME!\r
*\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class NucleotideColourScheme extends ResidueColourScheme\r
+public class NucleotideColourScheme\r
+ extends ResidueColourScheme\r
{\r
- /**\r
- * Creates a new NucleotideColourScheme object.\r
- */\r
- public NucleotideColourScheme()\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
- super(ResidueProperties.nucleotide, 0);\r
+ try\r
+ {\r
+ currentColour = colors[ResidueProperties.nucleotideIndex[c]];\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ return Color.white;\r
+ }\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String n)\r
+ else\r
{\r
- // System.out.println("called"); log.debug\r
- return colors[ResidueProperties.nucleotideIndex[n.charAt(0)]];\r
+ return Color.white;\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(String n, int j)\r
+ if (conservationColouring)\r
{\r
- Color currentColour;\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
- if(conservationColouring)\r
- applyConservation(currentColour, j);\r
-\r
- return currentColour;\r
+ currentColour = applyConservation(currentColour, j);\r
}\r
+\r
+ return currentColour;\r
+ }\r
}\r