/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
+ * This file is part of Jalview.\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
+ * Jalview 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 3 of the License, or (at your option) any later version.\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
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.schemes;\r
\r
return pog;\r
}\r
\r
+ /**\r
+ * pretty print the matrix\r
+ */\r
+ public String toString()\r
+ {\r
+ return outputMatrix(false);\r
+ }\r
+\r
+ public String outputMatrix(boolean html)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ int[] symbols = (type == 0) ? ResidueProperties.aaIndex\r
+ : ResidueProperties.nucleotideIndex;\r
+ int symMax = (type == 0) ? ResidueProperties.maxProteinIndex\r
+ : ResidueProperties.maxNucleotideIndex;\r
+ boolean header = true;\r
+ if (html)\r
+ {\r
+ sb.append("<table>");\r
+ }\r
+ for (char sym = 'A'; sym <= 'Z'; sym++)\r
+ {\r
+ if (symbols[sym] >= 0 && symbols[sym] < symMax)\r
+ {\r
+ if (header)\r
+ {\r
+ sb.append(html ? "<tr><td></td>" : "");\r
+ for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)\r
+ {\r
+ if (symbols[sym2] >= 0 && symbols[sym2] < symMax)\r
+ {\r
+ sb.append((html ? "<td> " : "\t") + sym2\r
+ + (html ? " </td>" : ""));\r
+ }\r
+ }\r
+ header = false;\r
+ sb.append(html ? "</tr>\n" : "\n");\r
+ }\r
+ if (html)\r
+ {\r
+ sb.append("<tr>");\r
+ }\r
+ sb.append((html ? "<td>" : "") + sym + (html ? "</td>" : ""));\r
+ for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)\r
+ {\r
+ if (symbols[sym2] >= 0 && symbols[sym2] < symMax)\r
+ {\r
+ sb.append((html ? "<td>" : "\t")\r
+ + matrix[symbols[sym]][symbols[sym2]]\r
+ + (html ? "</td>" : ""));\r
+ }\r
+ }\r
+ sb.append(html ? "</tr>\n" : "\n");\r
+ }\r
+ }\r
+ if (html)\r
+ {\r
+ sb.append("</table>");\r
+ }\r
+ return sb.toString();\r
+ }\r
}\r