1 | #ifndef _theplu_yat_utility_aligner_ |
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2 | #define _theplu_yat_utility_aligner_ |
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3 | |
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4 | // $Id: Aligner.h 2986 2013-02-18 08:07:44Z peter $ |
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5 | |
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6 | /* |
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7 | Copyright (C) 2012 Peter Johansson |
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8 | Copyright (C) 2013 Jari Häkkinen |
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9 | |
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10 | This file is part of the yat library, http://dev.thep.lu.se/yat |
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11 | |
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12 | The yat library is free software; you can redistribute it and/or |
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13 | modify it under the terms of the GNU General Public License as |
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14 | published by the Free Software Foundation; either version 3 of the |
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15 | License, or (at your option) any later version. |
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16 | |
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17 | The yat library is distributed in the hope that it will be useful, |
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18 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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19 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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20 | General Public License for more details. |
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21 | |
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22 | You should have received a copy of the GNU General Public License |
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23 | along with yat. If not, see <http://www.gnu.org/licenses/>. |
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24 | */ |
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25 | |
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26 | #include <cstddef> |
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27 | #include <vector> |
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28 | |
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29 | namespace theplu { |
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30 | namespace yat { |
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31 | namespace utility { |
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32 | |
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33 | class Matrix; |
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34 | |
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35 | /** |
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36 | \brief Aligning two sequences |
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37 | |
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38 | General class aligning two sequences described in a dot-matrix, |
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39 | D, in which \f$ D(i,j) \f$ describes how similar element \c i in |
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40 | the first sequence is with element \c j in the second sequence. A |
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41 | path through this matrix corresponds to an alignment of the two |
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42 | sequences, in which a diagonal step correspoinds to a match |
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43 | between corresponding sequence elements, and a vertical or |
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44 | horizontal step correspond correspond to inserting a gap into one |
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45 | of the sequences. |
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46 | |
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47 | \since New in yat 0.9 |
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48 | */ |
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49 | class Aligner |
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50 | { |
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51 | public: |
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52 | /** |
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53 | Enum used to describe alignment. |
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54 | |
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55 | \see alignment |
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56 | */ |
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57 | enum direction { none, right, down, diagonal }; |
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58 | |
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59 | /** |
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60 | \brief Constructor |
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61 | |
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62 | Same as Aligner(gap, open_gap, gap, open_gap) |
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63 | */ |
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64 | Aligner(double gap=0, double open_gap=0); |
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65 | |
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66 | /** |
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67 | \brief constructor |
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68 | |
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69 | \param vertical_gap Penalty for extending a vertical gap |
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70 | |
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71 | \param open_vertical_gap Penalty for open a vertical gap. Total |
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72 | cost for a vertical gap is open_vertical_gap + N * |
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73 | vertical_gap. |
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74 | |
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75 | \param horizon_gap Penalty for extending a horizontal gap |
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76 | |
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77 | \param open_horizon_gap Penalty for open a horizontal |
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78 | gap. Total penalty for a horizontal gap is open_horizon_gap + N |
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79 | * horizon_gap. |
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80 | */ |
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81 | Aligner(double vertical_gap, double open_vertical_gap, |
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82 | double horizon_gap, double open_horizon_gap); |
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83 | |
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84 | /** |
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85 | Initialize a score matrix with \f$ S_{k,0} = - |
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86 | \textrm{open\_vertical\_gap} - k * \textrm{vertical\_gap} \f$ |
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87 | and \f$ S_{0,k} = - \textrm{open\_horizon\_gap} - k * |
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88 | \textrm{horizon\_gap} \f$ and align using operator(). |
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89 | |
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90 | \return most lower right element of score matrix |
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91 | */ |
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92 | double needleman_wunsch(const Matrix& d); |
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93 | |
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94 | /** |
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95 | Initialize a score matrix with all elements equal to zero, |
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96 | align using operator(). |
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97 | |
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98 | \return max element in score matrix. |
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99 | */ |
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100 | double smith_waterman(const Matrix& d); |
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101 | |
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102 | /** |
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103 | \brief calculate score matrix based on the \a dot matrix |
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104 | |
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105 | The algorithm calculates a maximum \a score matrix as |
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106 | |
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107 | \f$ S_{i,j} = \textrm{max} \{ S_{ij}; S_{i,j-1} - F(\textrm{gap}_V); |
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108 | S_{i-1,j-1} + D_{i-1,j-1}; S_{i-1,j} - F(\textrm{gap}_H) \} \f$ |
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109 | |
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110 | where \f$ F(\textrm{gap}) \f$ is gap if there was already a |
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111 | gap, and gap + open_gap otherwise. |
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112 | |
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113 | */ |
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114 | void operator()(const Matrix& dot, Matrix& score); |
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115 | |
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116 | /** |
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117 | \brief access cigar element i, j |
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118 | |
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119 | If, for example, cigar(i,j) returned Aligner::diagonal, implies |
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120 | that score(i,j) was maximized as score(i-1,j-1) + dot(i-1, |
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121 | j-1), which in turn implies that element i-1 in first sequence |
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122 | was aligned with element j-1 in second sequence. |
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123 | */ |
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124 | const direction& alignment(size_t i, size_t j) const; |
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125 | |
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126 | private: |
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127 | direction& cigar(size_t i, size_t j); |
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128 | |
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129 | size_t columns_; |
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130 | double vertical_gap_; |
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131 | double open_vertical_gap_; |
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132 | double horizon_gap_; |
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133 | double open_horizon_gap_; |
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134 | std::vector<direction> alignment_; |
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135 | }; |
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136 | |
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137 | }}} // of namespace utility, yat, and theplu |
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138 | |
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139 | #endif |
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