| 1 | /* |
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| 2 | Copyright (c) 2006-2018 Elmar Pruesse <elmar.pruesse@ucdenver.edu> |
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| 3 | |
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| 4 | This file is part of SINA. |
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| 5 | SINA is free software: you can redistribute it and/or modify it under |
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| 6 | the terms of the GNU General Public License as published by the Free |
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| 7 | Software Foundation, either version 3 of the License, or (at your |
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| 8 | option) any later version. |
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| 9 | |
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| 10 | SINA is distributed in the hope that it will be useful, but WITHOUT ANY |
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| 11 | WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 12 | FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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| 13 | for more details. |
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| 14 | |
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| 15 | You should have received a copy of the GNU General Public License |
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| 16 | along with SINA. If not, see <http://www.gnu.org/licenses/>. |
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| 17 | |
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| 18 | Additional permission under GNU GPL version 3 section 7 |
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| 19 | |
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| 20 | If you modify SINA, or any covered work, by linking or combining it |
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| 21 | with components of ARB (or a modified version of that software), |
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| 22 | containing parts covered by the terms of the |
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| 23 | ARB-public-library-license, the licensors of SINA grant you additional |
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| 24 | permission to convey the resulting work. Corresponding Source for a |
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| 25 | non-source form of such a combination shall include the source code |
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| 26 | for the parts of ARB used as well as that of the covered work. |
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| 27 | */ |
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| 28 | |
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| 29 | #ifndef _SCORING_SCHEMES_H_ |
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| 30 | #define _SCORING_SCHEMES_H_ |
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| 31 | |
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| 32 | #include <vector> |
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| 33 | |
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| 34 | namespace sina { |
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| 35 | |
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| 36 | |
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| 37 | class scoring_scheme_profile { |
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| 38 | public: |
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| 39 | using value_type = float; |
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| 40 | |
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| 41 | scoring_scheme_profile(const value_type& _m, const value_type& _mm, |
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| 42 | const value_type& _gp, const value_type& _gpe) |
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| 43 | : match_score(_m), mismatch_score(_mm), |
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| 44 | gap_penalty(_gp), gap_extension_penalty(_gpe) |
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| 45 | {} |
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| 46 | |
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| 47 | template<typename base_type_a, typename base_type_b> |
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| 48 | value_type |
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| 49 | insertion(const value_type& prev, |
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| 50 | const base_type_a& /*b1*/, |
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| 51 | const base_type_b& /*b2*/) const |
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| 52 | { |
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| 53 | return prev + gap_penalty; |
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| 54 | } |
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| 55 | |
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| 56 | template<typename base_type_a, typename base_type_b> |
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| 57 | value_type |
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| 58 | insertion_ext(const value_type& prev, |
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| 59 | const base_type_a& /*b1*/, |
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| 60 | const base_type_b& /*b2*/, |
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| 61 | int /*offset*/) const |
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| 62 | { |
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| 63 | return prev + gap_extension_penalty; |
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| 64 | } |
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| 65 | |
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| 66 | template<typename base_type_a, typename base_type_b> |
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| 67 | value_type |
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| 68 | deletion(const value_type& prev, |
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| 69 | const base_type_a& /*b1*/, |
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| 70 | const base_type_b& /*b2*/) const |
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| 71 | { |
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| 72 | return prev + gap_penalty; |
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| 73 | } |
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| 74 | |
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| 75 | template<typename base_type_a, typename base_type_b> |
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| 76 | value_type |
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| 77 | deletion_ext(const value_type& prev, |
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| 78 | const base_type_a& /*b1*/, |
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| 79 | const base_type_b& /*b2*/, |
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| 80 | int /*offset*/) const |
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| 81 | { |
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| 82 | return prev + gap_extension_penalty; |
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| 83 | } |
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| 84 | |
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| 85 | template<typename base_type_a, typename base_type_b> |
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| 86 | value_type |
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| 87 | match(const value_type& prev, |
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| 88 | const base_type_a& b1, |
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| 89 | const base_type_b& b2) const |
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| 90 | { |
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| 91 | return prev + (b1.comp(b2, match_score, mismatch_score, |
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| 92 | gap_penalty, gap_extension_penalty)); |
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| 93 | } |
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| 94 | |
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| 95 | private: |
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| 96 | const value_type match_score; |
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| 97 | const value_type mismatch_score; |
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| 98 | const value_type gap_penalty; |
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| 99 | const value_type gap_extension_penalty; |
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| 100 | }; |
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| 101 | |
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| 102 | class scoring_scheme_simple { |
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| 103 | public: |
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| 104 | using value_type = float; |
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| 105 | |
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| 106 | scoring_scheme_simple(const value_type& _m, const value_type& _mm, |
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| 107 | const value_type& _gp, const value_type& _gpe) |
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| 108 | : match_score(_m), mismatch_score(_mm), |
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| 109 | gap_penalty(_gp), gap_extension_penalty(_gpe) |
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| 110 | {} |
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| 111 | |
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| 112 | template<typename base_type_a, typename base_type_b> |
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| 113 | value_type |
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| 114 | insertion(const value_type& prev, |
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| 115 | const base_type_a& /*b1*/, |
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| 116 | const base_type_b& /*b2*/) const |
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| 117 | { |
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| 118 | return prev + gap_penalty; |
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| 119 | } |
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| 120 | |
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| 121 | template<typename base_type_a, typename base_type_b> |
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| 122 | value_type |
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| 123 | insertion_ext(const value_type& prev, |
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| 124 | const base_type_a& /*b1*/, |
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| 125 | const base_type_b& /*b2*/, |
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| 126 | int /*offset*/) const |
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| 127 | { |
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| 128 | return prev + gap_extension_penalty; |
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| 129 | } |
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| 130 | |
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| 131 | template<typename base_type_a, typename base_type_b> |
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| 132 | value_type |
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| 133 | deletion(const value_type& prev, |
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| 134 | const base_type_a& /*b1*/, |
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| 135 | const base_type_b& /*b2*/) const |
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| 136 | { |
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| 137 | return prev + gap_penalty;// * b1.getWeight(); |
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| 138 | } |
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| 139 | |
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| 140 | template<typename base_type_a, typename base_type_b> |
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| 141 | value_type |
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| 142 | deletion_ext(const value_type& prev, |
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| 143 | const base_type_a& /*b1*/, |
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| 144 | const base_type_b& /*b2*/, |
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| 145 | int /*offset*/) const |
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| 146 | { |
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| 147 | return prev + gap_extension_penalty;// * b1.getWeight(); |
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| 148 | } |
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| 149 | |
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| 150 | template<typename base_type_a,typename base_type_b> |
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| 151 | value_type |
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| 152 | match(const value_type& prev, |
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| 153 | const base_type_a& b1, |
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| 154 | const base_type_b& b2) const |
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| 155 | { |
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| 156 | return prev + (b1.comp(b2)?match_score:mismatch_score) * b1.getWeight(); |
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| 157 | } |
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| 158 | |
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| 159 | private: |
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| 160 | const value_type match_score; |
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| 161 | const value_type mismatch_score; |
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| 162 | const value_type gap_penalty; |
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| 163 | const value_type gap_extension_penalty; |
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| 164 | }; |
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| 165 | |
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| 166 | class scoring_scheme_weighted { |
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| 167 | public: |
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| 168 | using value_type = float; |
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| 169 | |
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| 170 | scoring_scheme_weighted(const value_type& _m, const value_type& _mm, |
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| 171 | const value_type& _gp, const value_type& _gpe, |
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| 172 | std::vector<value_type>& _weights) |
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| 173 | : match_score(_m), mismatch_score(_mm), |
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| 174 | gap_penalty(_gp), gap_extension_penalty(_gpe), |
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| 175 | weights(_weights) |
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| 176 | {} |
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| 177 | |
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| 178 | template<typename base_type_a, typename base_type_b> |
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| 179 | value_type |
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| 180 | insertion(const value_type& prev, |
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| 181 | const base_type_a& b1, |
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| 182 | const base_type_b& /*b2*/) const |
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| 183 | { |
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| 184 | // the insertion will be placed in the column |
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| 185 | // immediately following the current column. use |
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| 186 | // the weight from that column. |
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| 187 | return prev + gap_penalty * weights[b1.getPosition() +1]; |
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| 188 | } |
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| 189 | |
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| 190 | template<typename base_type_a, typename base_type_b> |
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| 191 | value_type |
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| 192 | insertion_ext(const value_type& prev, |
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| 193 | const base_type_a& b1, |
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| 194 | const base_type_b& /*b2*/, |
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| 195 | int offset) const |
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| 196 | { |
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| 197 | // the insertion will be placed in the column |
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| 198 | // immediately following the current column plus |
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| 199 | // offset (number of previous insertions) |
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| 200 | return prev + gap_extension_penalty |
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| 201 | * weights[b1.getPosition() + 1 + offset]; |
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| 202 | } |
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| 203 | |
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| 204 | template<typename base_type_a, typename base_type_b> |
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| 205 | value_type |
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| 206 | deletion(const value_type& prev, |
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| 207 | const base_type_a& b1, |
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| 208 | const base_type_b& /*b2*/) const |
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| 209 | { |
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| 210 | // deletions always happen in current column |
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| 211 | return prev + gap_penalty * weights[b1.getPosition()];// * b1.getWeight(); |
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| 212 | } |
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| 213 | |
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| 214 | template<typename base_type_a, typename base_type_b> |
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| 215 | value_type |
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| 216 | deletion_ext(const value_type& prev, |
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| 217 | const base_type_a& b1, |
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| 218 | const base_type_b& /*b2*/, |
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| 219 | int /*offset*/) const |
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| 220 | { |
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| 221 | // deletions always happen in current column |
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| 222 | return prev + gap_extension_penalty |
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| 223 | * weights[b1.getPosition()] ;//* b1.getWeight(); |
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| 224 | } |
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| 225 | |
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| 226 | template<typename base_type_a, typename base_type_b> |
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| 227 | value_type |
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| 228 | match(const value_type& prev, |
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| 229 | const base_type_a& b1, |
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| 230 | const base_type_b& b2) const |
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| 231 | { |
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| 232 | return prev + (b1.comp(b2)?match_score:mismatch_score) * weights[b1.getPosition()] * b1.getWeight(); |
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| 233 | } |
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| 234 | |
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| 235 | private: |
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| 236 | const value_type match_score; |
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| 237 | const value_type mismatch_score; |
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| 238 | const value_type gap_penalty; |
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| 239 | const value_type gap_extension_penalty; |
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| 240 | std::vector<value_type>& weights; |
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| 241 | }; |
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| 242 | |
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| 243 | |
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| 244 | template<typename MATRIX_TYPE> |
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| 245 | class scoring_scheme_matrix { |
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| 246 | public: |
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| 247 | using value_type = float; |
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| 248 | using matrix_type = MATRIX_TYPE; |
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| 249 | |
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| 250 | scoring_scheme_matrix(const value_type& _gp, const value_type& _gpe, |
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| 251 | std::vector<value_type>& _weights, |
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| 252 | const matrix_type& _matrix) |
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| 253 | : gap_penalty(_gp), |
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| 254 | gap_extension_penalty(_gpe), |
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| 255 | weights(_weights), |
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| 256 | matrix(_matrix) |
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| 257 | {} |
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| 258 | |
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| 259 | template<typename base_type_a, typename base_type_b> |
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| 260 | value_type |
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| 261 | insertion(const value_type& prev, |
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| 262 | const base_type_a& b1, |
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| 263 | const base_type_b& /*b2*/) const |
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| 264 | { |
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| 265 | return prev + gap_penalty * weights[b1.getPosition()]; |
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| 266 | } |
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| 267 | |
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| 268 | template<typename base_type_a, typename base_type_b> |
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| 269 | value_type |
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| 270 | insertion_ext(const value_type& prev, |
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| 271 | const base_type_a& b1, |
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| 272 | const base_type_b& /*b2*/, |
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| 273 | int /*offset*/) const |
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| 274 | { |
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| 275 | return prev + gap_extension_penalty * weights[b1.getPosition()]; |
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| 276 | } |
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| 277 | |
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| 278 | template<typename base_type_a, typename base_type_b> |
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| 279 | value_type |
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| 280 | deletion(const value_type& prev, |
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| 281 | const base_type_a& b1, |
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| 282 | const base_type_b& b2) const |
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| 283 | { |
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| 284 | return insertion(prev, b1, b2); |
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| 285 | } |
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| 286 | |
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| 287 | template<typename base_type_a, typename base_type_b> |
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| 288 | value_type |
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| 289 | deletion_ext(const value_type& prev, |
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| 290 | const base_type_a& b1, |
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| 291 | const base_type_b& b2, |
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| 292 | int offset) const |
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| 293 | { |
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| 294 | return insertion_ext(prev, b1, b2, offset); |
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| 295 | } |
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| 296 | |
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| 297 | template<typename base_type_a, typename base_type_b> |
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| 298 | value_type |
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| 299 | match(const value_type& prev, |
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| 300 | const base_type_a& b1, |
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| 301 | const base_type_b& b2) const |
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| 302 | { |
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| 303 | return prev + b1.comp(b2,matrix) * weights[b1.getPosition()]; |
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| 304 | } |
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| 305 | |
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| 306 | private: |
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| 307 | const value_type gap_penalty; |
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| 308 | const value_type gap_extension_penalty; |
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| 309 | const std::vector<value_type>& weights; |
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| 310 | const matrix_type& matrix; |
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| 311 | }; |
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| 312 | |
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| 313 | |
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| 314 | } // namespace sina |
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| 315 | |
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| 316 | #endif // _MESH_H_ |
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| 317 | |
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| 318 | /* |
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| 319 | Local Variables: |
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| 320 | mode:c++ |
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| 321 | c-file-style:"stroustrup" |
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| 322 | c-file-offsets:((innamespace . 0)(inline-open . 0)(case-label . 0)) |
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| 323 | indent-tabs-mode:nil |
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| 324 | fill-column:99 |
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| 325 | End: |
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| 326 | */ |
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| 327 | // vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=99 : |
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