source: trunk/yat/utility/Alignment.cc @ 865

Last change on this file since 865 was 865, checked in by Peter, 14 years ago

changing URL to http://trac.thep.lu.se/trac/yat

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1// $Id: Alignment.cc 865 2007-09-10 19:41:04Z peter $
2
3/*
4  Copyright (C) 2004 Jari Häkkinen
5  Copyright (C) 2005 Peter Johansson
6  Copyright (C) 2006 Jari Häkkinen
7
8  This file is part of the yat library, http://trac.thep.lu.se/trac/yat
9
10  The yat library is free software; you can redistribute it and/or
11  modify it under the terms of the GNU General Public License as
12  published by the Free Software Foundation; either version 2 of the
13  License, or (at your option) any later version.
14
15  The yat library is distributed in the hope that it will be useful,
16  but WITHOUT ANY WARRANTY; without even the implied warranty of
17  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18  General Public License for more details.
19
20  You should have received a copy of the GNU General Public License
21  along with this program; if not, write to the Free Software
22  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
23  02111-1307, USA.
24*/
25
26#include "Alignment.h"
27#include "matrix.h"
28
29#include <utility>
30#include <vector>
31
32namespace theplu {
33namespace yat {
34namespace utility {
35
36  double NeedlemanWunsch(const utility::matrix& s,
37                         std::vector<std::pair<size_t, size_t> >& path,
38                         const double gap)
39  {
40    utility::matrix m(s.rows()+1,s.columns()+1);
41    // Init upper and left border of matrix
42    for (size_t i=1; i<m.rows(); i++) 
43      m(i,0)=-i*gap;
44    for (size_t i=1; i<m.columns(); i++) 
45      m(0,i)=-i*gap;
46    // choice(i,j) tells us how we came to s(i,j). 1 is diagonal, 2
47    // vertical, and 3 horizontal,
48    utility::matrix choice(m.rows(),m.columns());
49
50    // Calculating NeedlemanWunsch matrix
51    for (size_t i=1; i<m.rows(); i++) 
52      for (size_t j=1; j<m.columns(); j++){ 
53        if (m(i-1,j-1) + s(i-1,j-1) > m(i-1,j)-gap && 
54            m(i-1,j-1) + s(i-1,j-1) > m(i,j-1)-gap){
55          m(i,j)=m(i-1,j-1) + s(i-1,j-1);
56          choice(i,j)=1;
57        }
58        else if (m(i-1,j) > m(i,j-1)){
59          m(i,j)=m(i-1,j)-gap;
60          choice(i,j)=2;
61        }
62        else{
63          m(i,j)=m(i,j-1)-gap;
64          choice(i,j)=3;
65        }
66      }
67    // Going backwards to find best path
68    size_t i = m.rows()-1;
69    size_t j= m.columns()-1;
70    path.resize(0);
71    while (i && j){
72      if (choice(i,j)==1){
73        i--;
74        j--;
75        path.push_back(std::make_pair(i,j));
76      }
77      else if (choice(i,j)==2)
78        i--;
79      else
80        j--;
81    }
82
83    return m(m.rows()-1,m.columns()-1);
84  }
85
86}}} // of namespace utility, yat, and theplu
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