25 namespace seqan3::detail
38 struct max_score_updater
55 template <
typename score_t,
typename coordinate_t>
57 requires (std::totally_ordered<score_t> && std::assignable_from<score_t &, score_t const &> &&
58 std::assignable_from<coordinate_t &, coordinate_t const &>)
60 void operator()(score_t & optimal_score,
61 coordinate_t & optimal_coordinate,
62 score_t current_score,
63 coordinate_t current_coordinate)
const noexcept
65 bool const is_better_score = current_score >= optimal_score;
66 optimal_score = (is_better_score) ?
std::move(current_score) : optimal_score;
67 optimal_coordinate = (is_better_score) ?
std::move(current_coordinate) : optimal_coordinate;
111 struct max_score_banded_updater
115 size_t target_row_index{};
117 size_t target_col_index{};
137 template <
typename score_t,
typename coordinate_t>
139 requires (std::totally_ordered<score_t> && std::assignable_from<score_t &, score_t const &> &&
140 std::assignable_from<coordinate_t &, coordinate_t const &>)
142 void operator()(score_t & optimal_score,
143 coordinate_t & optimal_coordinate,
144 score_t current_score,
145 coordinate_t current_coordinate)
const noexcept
147 bool const is_better_score = (target_row_index == current_coordinate.row ||
148 target_col_index == current_coordinate.col) &&
149 (current_score >= optimal_score);
150 optimal_score = (is_better_score) ?
std::move(current_score) : optimal_score;
151 optimal_coordinate = (is_better_score) ?
std::move(current_coordinate) : optimal_coordinate;
158 void set_target_indices(row_index_type<size_t> row_index, column_index_type<size_t> col_index) noexcept
160 target_row_index = row_index.get();
161 target_col_index = col_index.get();
184 template <
typename alignment_configuration_t, std::semiregular optimum_updater_t>
186 requires is_type_specialisation_of_v<alignment_configuration_t, configuration> &&
187 std::invocable<optimum_updater_t,
188 typename alignment_configuration_traits<alignment_configuration_t>::score_type &,
189 typename alignment_configuration_traits<alignment_configuration_t>::matrix_coordinate_type &,
190 typename alignment_configuration_traits<alignment_configuration_t>::score_type,
191 typename alignment_configuration_traits<alignment_configuration_t>::matrix_coordinate_type>
193 class policy_optimum_tracker
197 using traits_type = alignment_configuration_traits<alignment_configuration_t>;
199 using score_type =
typename traits_type::score_type;
201 using matrix_coordinate_type =
typename traits_type::matrix_coordinate_type;
204 score_type optimal_score{};
206 matrix_coordinate_type optimal_coordinate{};
208 optimum_updater_t compare_and_set_optimum{};
211 bool test_every_cell{
false};
213 bool test_last_row_cell{
false};
215 bool test_last_column_cell{
false};
220 policy_optimum_tracker() =
default;
221 policy_optimum_tracker(policy_optimum_tracker
const &) =
default;
222 policy_optimum_tracker(policy_optimum_tracker &&) =
default;
223 policy_optimum_tracker & operator=(policy_optimum_tracker
const &) =
default;
224 policy_optimum_tracker & operator=(policy_optimum_tracker &&) =
default;
225 ~policy_optimum_tracker() =
default;
235 policy_optimum_tracker(alignment_configuration_t
const & config)
237 auto method_global_config = config.get_or(align_cfg::method_global{});
238 test_last_row_cell = method_global_config.free_end_gaps_sequence1_trailing;
239 test_last_column_cell = method_global_config.free_end_gaps_sequence2_trailing;
257 template <
typename cell_t>
258 decltype(
auto) track_cell(cell_t && cell, matrix_coordinate_type coordinate) noexcept
261 invoke_comparator(cell,
std::move(coordinate));
263 return std::forward<cell_t>(cell);
280 template <
typename cell_t>
281 decltype(
auto) track_last_row_cell(cell_t && cell, matrix_coordinate_type coordinate) noexcept
283 if (test_last_row_cell && !test_every_cell)
284 invoke_comparator(cell,
std::move(coordinate));
300 template <
typename cell_t>
301 decltype(
auto) track_last_column_cell(cell_t && cell, matrix_coordinate_type coordinate) noexcept
303 if (test_last_column_cell && !test_every_cell)
304 invoke_comparator(cell,
std::move(coordinate));
306 return std::forward<cell_t>(cell);
323 template <
typename cell_t>
324 decltype(
auto) track_final_cell(cell_t && cell, matrix_coordinate_type coordinate) noexcept
326 if (!(test_every_cell || test_last_row_cell || test_last_column_cell))
327 invoke_comparator(cell,
std::move(coordinate));
330 void reset_optimum() noexcept
333 optimal_coordinate = {};
347 template <
typename cell_t>
348 void invoke_comparator(cell_t && cell, matrix_coordinate_type coordinate) noexcept
350 compare_and_set_optimum(optimal_score, optimal_coordinate, cell.best_score(),
std::move(coordinate));
Provides helper type traits for the configuration and execution of the alignment algorithm.
Provides seqan3::configuration and utility functions.
Provides seqan3::detail::coordinate_matrix.
Provides type traits for working with templates.
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:74
Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and associated strong types.
Provides seqan3::tuple_like.