+/*\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
+ * \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
public class ScoreMatrix\r
{\r
String name;\r
+\r
/**\r
* reference to integer score matrix\r
*/\r
int[][] matrix;\r
+\r
/**\r
* 0 for Protein Score matrix. 1 for dna score matrix\r
*/\r
int type;\r
+\r
ScoreMatrix(String name, int[][] matrix, int type)\r
{\r
this.matrix = matrix;\r
}\r
\r
/**\r
- *\r
+ * \r
* @param A1\r
* @param A2\r
* @return score for substituting first char in A1 with first char in A2\r
\r
try\r
{\r
- int a = (type == 0) ? ResidueProperties.aaIndex[c] :\r
- ResidueProperties.nucleotideIndex[c];\r
- int b = (type == 0) ? ResidueProperties.aaIndex[d] :\r
- ResidueProperties.nucleotideIndex[d];\r
+ int a = (type == 0) ? ResidueProperties.aaIndex[c]\r
+ : ResidueProperties.nucleotideIndex[c];\r
+ int b = (type == 0) ? ResidueProperties.aaIndex[d]\r
+ : ResidueProperties.nucleotideIndex[d];\r
\r
pog = matrix[a][b];\r
- }\r
- catch (Exception e)\r
+ } catch (Exception e)\r
{\r
- //System.out.println("Unknown residue in " + A1 + " " + A2);\r
+ // System.out.println("Unknown residue in " + A1 + " " + A2);\r
}\r
\r
return pog;\r