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root/PrimerMatch/select.h
Revision: 1.2
Committed: Wed May 4 18:03:45 2005 UTC (11 years ago) by nje01
Branch: MAIN
CVS Tags: HEAD
Changes since 1.1: +1 -0 lines
Log Message:
Small bug fixes, plus codon based edit distance for peptide searching.

Line File contents
1 /**************************************************************************
2 * This code is part of the supporting infrastructure for ATA Mapper.
3 * Copyright (C) 2002,2003,2004 Applera Corporation. All rights reserved.
4 * Author: Nathan Edwards
5 *
6 * This program is free software; you can redistribute it and/or modify
7 * it under the terms of the GNU General Public License as published by
8 * the Free Software Foundation; either version 2 of the License, or
9 * (at your option) any later version.
10 *
11 * This program is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received (LICENSE.txt) a copy of the GNU General Public
17 * License along with this program; if not, write to the Free Software
18 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
19 *************************************************************************/
20
21
22 #ifndef _IBPEP_SELECT_H_
23 #define _IBPEP_SELECT_H_
24
25 #include "char_io.h"
26 #include "pattern_match.h"
27
28 PatternMatch *pick_pattern_index(CharacterProducer * const & ff,
29 int pmselect,
30 int nmismatch,
31 std::vector<std::pair<int,int> > *exact_const,
32 std::vector<int> *patlen,
33 int seedlen,
34 bool wildcard,
35 bool textn,
36 bool indels,
37 bool dna_mut,
38 char eos,
39 bool verbose);
40 #endif