yat  0.14.5pre
Alignment.h
1 #ifndef _theplu_yat_utility_alignment_
2 #define _theplu_yat_utility_alignment_
3 
4 // $Id: Alignment.h 3210 2014-05-05 06:10:02Z peter $
5 
6 /*
7  Copyright (C) 2004 Jari Häkkinen, Peter Johansson
8  Copyright (C) 2005 Peter Johansson
9  Copyright (C) 2006 Jari Häkkinen
10  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
11  Copyright (C) 2012, 2014 Peter Johansson
12 
13  This file is part of the yat library, http://dev.thep.lu.se/yat
14 
15  The yat library is free software; you can redistribute it and/or
16  modify it under the terms of the GNU General Public License as
17  published by the Free Software Foundation; either version 3 of the
18  License, or (at your option) any later version.
19 
20  The yat library is distributed in the hope that it will be useful,
21  but WITHOUT ANY WARRANTY; without even the implied warranty of
22  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
23  General Public License for more details.
24 
25  You should have received a copy of the GNU General Public License
26  along with yat. If not, see <http://www.gnu.org/licenses/>.
27 */
28 
29 #include "deprecate.h"
30 
31 #include <string>
32 #include <utility>
33 #include <vector>
34 
35 namespace theplu {
36 namespace yat {
37 namespace utility {
38 
39  class Matrix;
40 
63  double NeedlemanWunsch(const utility::Matrix& s,
64  std::vector<std::pair<size_t, size_t> >& path,
65  const double gap);
66 
90  double SmithWaterman(const utility::Matrix& s,
91  double gap, double open_gap) YAT_DEPRECATE;
92 
108  double ssearch(std::string first, std::string second, double gap,
109  double open_gap, double mismatch=0.0);
110 
111 }}} // of namespace utility, yat, and theplu
112 
113 #endif
double NeedlemanWunsch(const utility::Matrix &s, std::vector< std::pair< size_t, size_t > > &path, const double gap)
double ssearch(std::string first, std::string second, double gap, double open_gap, double mismatch=0.0)
double SmithWaterman(const utility::Matrix &s, double gap, double open_gap)
Local alignment following the Smith-Waterman algorithm.

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