/*
- * 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 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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.
*
- * 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
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.analysis;
* Keys are Name, Start, End, SeqFeatures, PdbId
*
* @param seq
- * SequenceI
+ * SequenceI
* @return Hashtable
*/
public static Hashtable SeqCharacterHash(SequenceI seq)
* these methods with something more elegant.
*
* @param sq
- * SequenceI
+ * SequenceI
* @param sqinfo
- * Hashtable
+ * Hashtable
* @return boolean true if name was not updated from sqinfo Name entry
*/
public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
* ordered vector of sequences.
*
* @param i
- * int
+ * int
* @return String
*/
public static String unique_name(int i)
* name.
*
* @param sequences
- * SequenceI[]
+ * SequenceI[]
* @param write_names
- * boolean set this to rename each of the sequences to its
- * unique_name(index) name
+ * boolean set this to rename each of the sequences to its
+ * unique_name(index) name
* @return Hashtable to be passed to
* @see deuniquify to recover original names (and properties) for renamed
* sequences
*
* @see uniquify(sequences,true)
* @param map
- * Hashtable
+ * Hashtable
* @param sequences
- * SequenceI[]
+ * SequenceI[]
* @return boolean
*/
public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
*
* @see uniquify(sequences,true)
* @param map
- * Hashtable
+ * Hashtable
* @param sequences
- * SequenceI[]
+ * SequenceI[]
* @param quiet
- * when false, don't complain about sequences without any data
- * in the map.
+ * when false, don't complain about sequences without any data in the
+ * map.
* @return boolean
*/
public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
* contain at least one residue.
*
* @param sequences
- * SequenceI[]
+ * SequenceI[]
* @return SequenceI[]
*/
public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)