/*\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 2.5)\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.util;\r
\r
* addShift\r
* \r
* @param pos\r
- * start position for shift (in original reference frame)\r
+ * start position for shift (in original reference frame)\r
* @param shift\r
- * length of shift\r
+ * length of shift\r
*/\r
public void addShift(int pos, int shift)\r
{\r
* shift\r
* \r
* @param pos\r
- * int\r
+ * int\r
* @return int shifted position\r
*/\r
public int shift(int pos)\r
}\r
\r
/**\r
- * parse a 1d map of position 1<i<n to L<pos[i]<N such as that returned\r
- * from SequenceI.gapMap()\r
+ * parse a 1d map of position 1<i<n to L<pos[i]<N such as that returned from\r
+ * SequenceI.gapMap()\r
* \r
* @param gapMap\r
* @return shifts from map index to mapped position\r