1 | #ifndef _theplu_yat_utility_aligner_ |
---|
2 | #define _theplu_yat_utility_aligner_ |
---|
3 | |
---|
4 | // $Id: Aligner.h 3200 2014-05-03 11:36:31Z peter $ |
---|
5 | |
---|
6 | /* |
---|
7 | Copyright (C) 2012 Peter Johansson |
---|
8 | Copyright (C) 2013 Jari Häkkinen, Peter Johansson |
---|
9 | Copyright (C) 2014 Peter Johansson |
---|
10 | |
---|
11 | This file is part of the yat library, http://dev.thep.lu.se/yat |
---|
12 | |
---|
13 | The yat library is free software; you can redistribute it and/or |
---|
14 | modify it under the terms of the GNU General Public License as |
---|
15 | published by the Free Software Foundation; either version 3 of the |
---|
16 | License, or (at your option) any later version. |
---|
17 | |
---|
18 | The yat library is distributed in the hope that it will be useful, |
---|
19 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
---|
20 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
---|
21 | General Public License for more details. |
---|
22 | |
---|
23 | You should have received a copy of the GNU General Public License |
---|
24 | along with yat. If not, see <http://www.gnu.org/licenses/>. |
---|
25 | */ |
---|
26 | |
---|
27 | #include <boost/cstdint.hpp> |
---|
28 | |
---|
29 | #include <deque> |
---|
30 | #include <cstddef> |
---|
31 | #include <iosfwd> |
---|
32 | #include <vector> |
---|
33 | |
---|
34 | namespace theplu { |
---|
35 | namespace yat { |
---|
36 | namespace utility { |
---|
37 | |
---|
38 | class Matrix; |
---|
39 | |
---|
40 | /** |
---|
41 | \brief Aligning two sequences |
---|
42 | |
---|
43 | General class aligning two sequences described in a dot-matrix, |
---|
44 | D, in which \f$ D(i,j) \f$ describes how similar element \c i in |
---|
45 | the first sequence is with element \c j in the second sequence. A |
---|
46 | path through this matrix corresponds to an alignment of the two |
---|
47 | sequences, in which a diagonal step correspoinds to a match |
---|
48 | between corresponding sequence elements, and a vertical or |
---|
49 | horizontal step correspond correspond to inserting a gap into one |
---|
50 | of the sequences. |
---|
51 | |
---|
52 | \since New in yat 0.9 |
---|
53 | */ |
---|
54 | class Aligner |
---|
55 | { |
---|
56 | public: |
---|
57 | /** |
---|
58 | Enum used to describe alignment. |
---|
59 | |
---|
60 | \see alignment |
---|
61 | */ |
---|
62 | enum direction { none, right, down, diagonal }; |
---|
63 | |
---|
64 | /** |
---|
65 | \brief Constructor |
---|
66 | |
---|
67 | Same as Aligner(gap, open_gap, gap, open_gap) |
---|
68 | */ |
---|
69 | Aligner(double gap=0, double open_gap=0); |
---|
70 | |
---|
71 | /** |
---|
72 | \brief constructor |
---|
73 | |
---|
74 | \param vertical_gap Penalty for extending a vertical gap. A |
---|
75 | vertical gap means alignment consumes an element in second |
---|
76 | element and not, in the first element, i.e., an element has |
---|
77 | been inserted to the second element or equivalently an element |
---|
78 | has been deleted in first sequence. |
---|
79 | |
---|
80 | \param open_vertical_gap Penalty for open a vertical gap. Total |
---|
81 | cost for a vertical gap is open_vertical_gap + N * |
---|
82 | vertical_gap. |
---|
83 | |
---|
84 | \param horizon_gap Penalty for extending a horizontal gap |
---|
85 | |
---|
86 | \param open_horizon_gap Penalty for open a horizontal |
---|
87 | gap. Total penalty for a horizontal gap is open_horizon_gap + N |
---|
88 | * horizon_gap. |
---|
89 | */ |
---|
90 | Aligner(double vertical_gap, double open_vertical_gap, |
---|
91 | double horizon_gap, double open_horizon_gap); |
---|
92 | |
---|
93 | /** |
---|
94 | Initialize a score matrix with \f$ S_{k,0} = - |
---|
95 | \textrm{open\_vertical\_gap} - k * \textrm{vertical\_gap} \f$ |
---|
96 | and \f$ S_{0,k} = - \textrm{open\_horizon\_gap} - k * |
---|
97 | \textrm{horizon\_gap} \f$ and align using operator(). |
---|
98 | |
---|
99 | \return most lower right element of score matrix |
---|
100 | */ |
---|
101 | double needleman_wunsch(const Matrix& d); |
---|
102 | |
---|
103 | /** |
---|
104 | Initialize a score matrix with all elements equal to zero, |
---|
105 | align using operator(). |
---|
106 | |
---|
107 | \return max element in score matrix. |
---|
108 | */ |
---|
109 | double smith_waterman(const Matrix& d); |
---|
110 | |
---|
111 | /** |
---|
112 | \brief calculate score matrix based on the \a dot matrix |
---|
113 | |
---|
114 | The algorithm calculates a maximum \a score matrix as |
---|
115 | |
---|
116 | \f$ S_{i,j} = \textrm{max} \{ S_{ij}; S_{i,j-1} - F(\textrm{gap}_V); |
---|
117 | S_{i-1,j-1} + D_{i-1,j-1}; S_{i-1,j} - F(\textrm{gap}_H) \} \f$ |
---|
118 | |
---|
119 | where \f$ F(\textrm{gap}) \f$ is gap if there was already a |
---|
120 | gap, and gap + open_gap otherwise. |
---|
121 | |
---|
122 | */ |
---|
123 | void operator()(const Matrix& dot, Matrix& score); |
---|
124 | |
---|
125 | /** |
---|
126 | If, for example, alignment(i,j) returns Aligner::diagonal, |
---|
127 | implies that score(i,j) was maximized as score(i-1,j-1) + |
---|
128 | dot(i-1, j-1), in other words, element i-1 in first sequence |
---|
129 | was aligned with element j-1 in second sequence. |
---|
130 | */ |
---|
131 | const direction& alignment(size_t i, size_t j) const; |
---|
132 | |
---|
133 | /** |
---|
134 | \since new in yat 0.12 |
---|
135 | */ |
---|
136 | class Cigar |
---|
137 | { |
---|
138 | public: |
---|
139 | /** |
---|
140 | Erases all elements. |
---|
141 | */ |
---|
142 | void clear(void); |
---|
143 | |
---|
144 | /** |
---|
145 | \return operation i |
---|
146 | */ |
---|
147 | uint8_t op(size_t i) const; |
---|
148 | |
---|
149 | /** |
---|
150 | \return character describing operation i |
---|
151 | */ |
---|
152 | char opchr(size_t i) const; |
---|
153 | |
---|
154 | /** |
---|
155 | \return length of element i |
---|
156 | */ |
---|
157 | uint32_t oplen(size_t i) const; |
---|
158 | |
---|
159 | /** |
---|
160 | Erase last operation. |
---|
161 | */ |
---|
162 | void pop_back(uint32_t len=1); |
---|
163 | |
---|
164 | /** |
---|
165 | Erase first operation. |
---|
166 | */ |
---|
167 | void pop_front(uint32_t len=1); |
---|
168 | |
---|
169 | /** |
---|
170 | Add an operation \a op of length \a len at back of cigar. |
---|
171 | */ |
---|
172 | void push_back(uint8_t op, uint32_t len=1); |
---|
173 | |
---|
174 | /** |
---|
175 | Add an operation \a op of length \a len at front of cigar. |
---|
176 | */ |
---|
177 | void push_front(uint8_t op, uint32_t len=1); |
---|
178 | |
---|
179 | /** |
---|
180 | \return cigar element i |
---|
181 | */ |
---|
182 | uint32_t operator[](size_t) const; |
---|
183 | |
---|
184 | /** |
---|
185 | \return number of elements in cigar |
---|
186 | */ |
---|
187 | size_t size(void) const; |
---|
188 | private: |
---|
189 | std::deque<uint32_t> cigar_; |
---|
190 | |
---|
191 | // using compiler generated copy |
---|
192 | // Cigar(const Cigar& other); |
---|
193 | // Cigar& operator=(const Cigar&); |
---|
194 | }; |
---|
195 | |
---|
196 | /** |
---|
197 | \since new in yat 0.12 |
---|
198 | */ |
---|
199 | const Cigar cigar(size_t i, size_t j) const; |
---|
200 | |
---|
201 | private: |
---|
202 | direction& directions(size_t i, size_t j); |
---|
203 | |
---|
204 | size_t columns_; |
---|
205 | double vertical_gap_; |
---|
206 | double open_vertical_gap_; |
---|
207 | double horizon_gap_; |
---|
208 | double open_horizon_gap_; |
---|
209 | std::vector<direction> alignment_; |
---|
210 | }; |
---|
211 | |
---|
212 | |
---|
213 | /** |
---|
214 | Output e.g. '5S44M5I98M' if the cigar has four elements. Each |
---|
215 | element is output as the length followed by the character |
---|
216 | descibing the operation (see opchr). |
---|
217 | |
---|
218 | \relates Aligner::Cigar |
---|
219 | */ |
---|
220 | std::ostream& operator<<(std::ostream& os, const Aligner::Cigar& cigar); |
---|
221 | |
---|
222 | }}} // of namespace utility, yat, and theplu |
---|
223 | |
---|
224 | #endif |
---|