25 namespace seqan3::detail
43 template <
typename alignment_configuration_t>
44 class policy_affine_gap_recursion
48 using traits_type = alignment_configuration_traits<alignment_configuration_t>;
50 using original_score_type =
typename traits_type::original_score_type;
52 using score_type =
typename traits_type::score_type;
56 using affine_cell_type = affine_cell_proxy<affine_score_tuple_t>;
59 score_type gap_extension_score{};
61 score_type gap_open_score{};
64 bool first_row_is_free{};
66 bool first_column_is_free{};
71 policy_affine_gap_recursion() =
default;
72 policy_affine_gap_recursion(policy_affine_gap_recursion
const &) =
default;
73 policy_affine_gap_recursion(policy_affine_gap_recursion &&) =
default;
74 policy_affine_gap_recursion & operator=(policy_affine_gap_recursion
const &) =
default;
75 policy_affine_gap_recursion & operator=(policy_affine_gap_recursion &&) =
default;
76 ~policy_affine_gap_recursion() =
default;
87 explicit policy_affine_gap_recursion(alignment_configuration_t
const & config)
90 auto const & selected_gap_scheme = config.get_or(align_cfg::gap_cost_affine{align_cfg::open_score{-10},
91 align_cfg::extension_score{-1}});
93 gap_extension_score = maybe_convert_to_simd(selected_gap_scheme.extension_score);
94 gap_open_score = maybe_convert_to_simd(selected_gap_scheme.open_score) + gap_extension_score;
96 auto method_global_config = config.get_or(align_cfg::method_global{});
97 first_row_is_free = method_global_config.free_end_gaps_sequence1_leading;
98 first_column_is_free = method_global_config.free_end_gaps_sequence2_leading;
119 template <
typename affine_cell_t>
120 affine_cell_type compute_inner_cell(score_type diagonal_score,
121 affine_cell_t previous_cell,
122 score_type
const sequence_score)
const noexcept
124 diagonal_score += sequence_score;
125 score_type horizontal_score = previous_cell.horizontal_score();
126 score_type vertical_score = previous_cell.vertical_score();
128 diagonal_score = (diagonal_score < vertical_score) ? vertical_score : diagonal_score;
129 diagonal_score = (diagonal_score < horizontal_score) ? horizontal_score : diagonal_score;
131 score_type tmp = diagonal_score + gap_open_score;
132 vertical_score += gap_extension_score;
133 horizontal_score += gap_extension_score;
136 vertical_score = (vertical_score < tmp) ? tmp : vertical_score;
137 horizontal_score = (horizontal_score < tmp) ? tmp : horizontal_score;
139 return {diagonal_score, horizontal_score, vertical_score};
152 affine_cell_type initialise_origin_cell() const noexcept
154 return {score_type{},
155 first_row_is_free ? score_type{} : gap_open_score,
156 first_column_is_free ? score_type{} : gap_open_score};
173 template <
typename affine_cell_t>
174 affine_cell_type initialise_first_column_cell(affine_cell_t previous_cell)
const noexcept
176 score_type new_vertical = previous_cell.vertical_score() + gap_extension_score;
177 return {previous_cell.vertical_score(),
178 previous_cell.vertical_score() + gap_open_score,
179 first_column_is_free ? previous_cell.vertical_score() : new_vertical};
196 template <
typename affine_cell_t>
197 affine_cell_type initialise_first_row_cell(affine_cell_t previous_cell)
const noexcept
199 score_type new_horizontal_score = previous_cell.horizontal_score() + gap_extension_score;
200 return {previous_cell.horizontal_score(),
201 first_row_is_free ? previous_cell.horizontal_score() : new_horizontal_score,
202 previous_cell.horizontal_score() + gap_open_score};
215 score_type lowest_viable_score() const noexcept
217 if constexpr (simd_concept<score_type>)
218 assert(gap_open_score[0] <= 0 && gap_extension_score[0] <= 0);
220 assert(gap_open_score <= 0 && gap_extension_score <= 0);
223 (gap_open_score + gap_extension_score);
233 template <
typename score_t>
237 constexpr
auto maybe_convert_to_simd(score_t && score)
const noexcept
239 if constexpr (simd_concept<score_type>)
240 return simd::fill<score_type>(std::forward<score_t>(score));
242 return std::forward<score_t>(score);
Provides seqan3::detail::affine_cell_proxy.
Provides algorithms to modify seqan3::simd::simd_type.
Provides seqan3::align_config::gap_cost_affine.
Provides helper type traits for the configuration and execution of the alignment algorithm.
Provides type traits for working with templates.
A type that satisfies std::is_arithmetic_v<t>.
Provides seqan3::simd::simd_concept.