/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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.datamodel;\r
\r
public int[][] codons = null;\r
\r
/**\r
- * width of protein sequence alignement implicit assertion that codons.length >=\r
- * aaWidth\r
+ * width of protein sequence alignement implicit assertion that codons.length\r
+ * >= aaWidth\r
*/\r
public int aaWidth = 0;\r
\r
* test to see if codon frame involves seq in any way\r
* \r
* @param seq\r
- * a nucleotide or protein sequence\r
+ * a nucleotide or protein sequence\r
* @return true if a mapping exists to or from this sequence to any translated\r
* sequence\r
*/\r
* \r
* @param seq\r
* @param index\r
- * position in seq\r
+ * position in seq\r
* @param results\r
- * where highlighted regions go\r
+ * where highlighted regions go\r
*/\r
public void markMappedRegion(SequenceI seq, int index,\r
SearchResults results)\r