/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.datamodel;
* create a new mapping from
*
* @param to
- * the sequence being mapped
+ * the sequence being mapped
* @param exon
- * int[] {start,end,start,end} series on associated sequence
+ * int[] {start,end,start,end} series on associated sequence
* @param is
- * int[] {start,end,...} ranges on the reference frame being
- * mapped to
+ * int[] {start,end,...} ranges on the reference frame being mapped
+ * to
* @param i
- * step size on associated sequence
+ * step size on associated sequence
* @param j
- * step size on mapped frame
+ * step size on mapped frame
*/
public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)
{
/**
* @param map
- * the map to set
+ * the map to set
*/
public void setMap(MapList map)
{
* gets boundary in direction of mapping
*
* @param position
- * in mapped reference frame
+ * in mapped reference frame
* @return int{start, end} positions in associated sequence (in direction of
* mapped word)
*/