source: trunk/yat/utility/Alignment.h @ 687

Last change on this file since 687 was 687, checked in by Jari Häkkinen, 16 years ago

Clean up of namespace comments.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.3 KB
Line 
1#ifndef _theplu_yat_utility_alignment_
2#define _theplu_yat_utility_alignment_
3
4// $Id: Alignment.h 687 2006-10-16 23:51:10Z jari $
5
6/*
7  Copyright (C) The authors contributing to this file.
8
9  This file is part of the yat library, http://lev.thep.lu.se/trac/yat
10
11  The yat library is free software; you can redistribute it and/or
12  modify it under the terms of the GNU General Public License as
13  published by the Free Software Foundation; either version 2 of the
14  License, or (at your option) any later version.
15
16  The yat library is distributed in the hope that it will be useful,
17  but WITHOUT ANY WARRANTY; without even the implied warranty of
18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19  General Public License for more details.
20
21  You should have received a copy of the GNU General Public License
22  along with this program; if not, write to the Free Software
23  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
24  02111-1307, USA.
25*/
26
27#include <utility>
28#include <vector>
29
30namespace theplu {
31namespace yat {
32namespace utility {
33
34  class matrix;
35
36  ///
37  /// Function performing alignment following the Needleman-Wunch
38  /// algorithm. The algorithm starts from the dot-matrix, \a s, where
39  /// \f$ s_{ij} \f$ describes how well element \f$ i \f$ in the first
40  /// sequence match to element \f$ j \f$ in the second sequence. A
41  /// path through this matrix corresponds to an alignment of the two
42  /// sequences, in which a diagonal step over a matrix element
43  /// corresponds to a match between the corresponding sequnce
44  /// elements and a vertical or a horizontal step corresponds to
45  /// inserting a gap in one of the sequnces. The function maximizes
46  /// \f$ \sum s_{ij}-n \f$ \a gap, where the first sum goes over all
47  /// matches and the second term is a penalty term for inserting \f$
48  /// n \f$ gaps. Default is to have the \a gap cost set to zero. The
49  /// vector \a path contains information about which elements that
50  /// were matched. If the first element in the first sequence was
51  /// matched to the first element in the second sequence, the last
52  /// element in \a path is pair(0,0).
53  ///
54  /// @return the global maximum alignment score.
55  ///
56  double NeedlemanWunsch(const utility::matrix& s,
57                         std::vector<std::pair<size_t, size_t> >& path,
58                         const double gap);
59
60}}} // of namespace utility, yat, and theplu
61
62#endif
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