18namespace seqan3::detail
26template <
typename alignment_configuration_t,
typename... policies_t>
27 requires is_type_specialisation_of_v<alignment_configuration_t, configuration>
28class pairwise_alignment_algorithm_banded :
29 protected pairwise_alignment_algorithm<alignment_configuration_t, policies_t...>
33 using base_algorithm_t = pairwise_alignment_algorithm<alignment_configuration_t, policies_t...>;
36 using typename base_algorithm_t::alignment_result_type;
37 using typename base_algorithm_t::score_type;
38 using typename base_algorithm_t::traits_type;
40 static_assert(!std::same_as<alignment_result_type, empty_type>,
"Alignment result type was not configured.");
41 static_assert(traits_type::is_banded,
"Alignment configuration must have band configured.");
47 pairwise_alignment_algorithm_banded() =
default;
48 pairwise_alignment_algorithm_banded(pairwise_alignment_algorithm_banded
const &) =
default;
49 pairwise_alignment_algorithm_banded(pairwise_alignment_algorithm_banded &&) =
default;
50 pairwise_alignment_algorithm_banded &
51 operator=(pairwise_alignment_algorithm_banded
const &) =
default;
52 pairwise_alignment_algorithm_banded & operator=(pairwise_alignment_algorithm_banded &&) =
default;
53 ~pairwise_alignment_algorithm_banded() =
default;
64 pairwise_alignment_algorithm_banded(alignment_configuration_t
const & config) : base_algorithm_t(config)
72 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
73 requires std::invocable<callback_t, alignment_result_type>
74 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
78 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
80 size_t sequence1_size = std::ranges::distance(get<0>(sequence_pair));
81 size_t const sequence2_size = std::ranges::distance(get<1>(sequence_pair));
83 auto && [alignment_matrix, index_matrix] =
84 this->acquire_matrices(sequence1_size, sequence2_size, this->lowest_viable_score());
87 this->compare_and_set_optimum.set_target_indices(row_index_type{sequence2_size},
88 column_index_type{sequence1_size});
91 sequence1_size =
std::min(sequence1_size, this->upper_diagonal + sequence2_size);
93 using sequence1_difference_t = std::ranges::range_difference_t<decltype(get<0>(sequence_pair))>;
95 compute_matrix(std::views::take(get<0>(sequence_pair),
static_cast<sequence1_difference_t
>(sequence1_size)),
96 get<1>(sequence_pair),
99 this->make_result_and_invoke(
std::forward<
decltype(sequence_pair)>(sequence_pair),
102 this->optimal_coordinate,
109 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
110 requires traits_type::is_vectorised && std::invocable<callback_t, alignment_result_type>
111 auto operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
113 using simd_collection_t =
std::vector<score_type, aligned_allocator<score_type,
alignof(score_type)>>;
114 using original_score_t =
typename traits_type::original_score_type;
117 auto seq1_collection = indexed_sequence_pairs | views::elements<0> | views::elements<0>;
118 auto seq2_collection = indexed_sequence_pairs | views::elements<0> | views::elements<1>;
120 this->initialise_tracker(seq1_collection, seq2_collection);
123 thread_local simd_collection_t simd_seq1_collection{};
124 thread_local simd_collection_t simd_seq2_collection{};
126 this->convert_batch_of_sequences_to_simd_vector(simd_seq1_collection,
128 this->scoring_scheme.padding_symbol);
129 this->convert_batch_of_sequences_to_simd_vector(simd_seq2_collection,
131 this->scoring_scheme.padding_symbol);
133 size_t const sequence1_size = std::ranges::distance(simd_seq1_collection);
134 size_t const sequence2_size = std::ranges::distance(simd_seq2_collection);
136 auto && [alignment_matrix, index_matrix] =
137 this->acquire_matrices(sequence1_size, sequence2_size, this->lowest_viable_score());
139 compute_matrix(simd_seq1_collection, simd_seq2_collection, alignment_matrix, index_matrix);
142 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
144 original_score_t score = this->optimal_score[index]
145 - (this->padding_offsets[index] * this->scoring_scheme.padding_match_score());
146 matrix_coordinate coordinate{row_index_type{
size_t{this->optimal_coordinate.row[index]}},
147 column_index_type{
size_t{this->optimal_coordinate.col[index]}}};
148 this->make_result_and_invoke(
std::forward<
decltype(sequence_pair)>(sequence_pair),
151 std::move(coordinate),
212 template <std::ranges::forward_range sequence1_t,
213 std::ranges::forward_range sequence2_t,
214 std::ranges::input_range alignment_matrix_t,
215 std::ranges::input_range index_matrix_t>
216 requires std::ranges::forward_range<std::ranges::range_reference_t<alignment_matrix_t>>
217 && std::ranges::forward_range<std::ranges::range_reference_t<index_matrix_t>>
218 void compute_matrix(sequence1_t && sequence1,
219 sequence2_t && sequence2,
220 alignment_matrix_t && alignment_matrix,
221 index_matrix_t && index_matrix)
227 this->reset_optimum();
229 auto alignment_matrix_it = alignment_matrix.begin();
230 auto indexed_matrix_it = index_matrix.begin();
232 using row_index_t = std::ranges::range_difference_t<sequence2_t>;
233 using column_index_t = std::ranges::range_difference_t<sequence1_t>;
235 row_index_t row_size = std::max<int32_t>(0, -this->lower_diagonal);
236 column_index_t
const column_size = std::max<int32_t>(0, this->upper_diagonal);
237 this->initialise_column(*alignment_matrix_it, *indexed_matrix_it, std::views::take(sequence2, row_size));
243 for (
auto alphabet1 :
std::views::
take(sequence1, column_size))
245 this->compute_column(*++alignment_matrix_it,
246 *++indexed_matrix_it,
248 std::views::take(sequence2, ++row_size));
255 row_index_t first_row_index = 0u;
256 for (
auto alphabet1 :
std::views::
drop(sequence1, column_size))
258 compute_band_column(*++alignment_matrix_it,
259 std::views::drop(*++indexed_matrix_it, first_row_index + 1),
269 auto alignment_column = *alignment_matrix_it;
270 auto cell_index_column = std::views::drop(*indexed_matrix_it, first_row_index);
272 auto alignment_column_it = alignment_column.begin();
273 auto cell_index_column_it = cell_index_column.begin();
275 this->track_last_column_cell(*alignment_column_it, *cell_index_column_it);
277 for (row_index_t last_row = std::min<row_index_t>(std::ranges::distance(sequence2), row_size);
278 first_row_index < last_row;
280 this->track_last_column_cell(*++alignment_column_it, *++cell_index_column_it);
282 this->track_final_cell(*alignment_column_it, *cell_index_column_it);
336 template <std::ranges::forward_range alignment_column_t,
337 std::ranges::input_range cell_index_column_t,
338 typename alphabet1_t,
339 std::ranges::input_range sequence2_t>
340 void compute_band_column(alignment_column_t && alignment_column,
341 cell_index_column_t && cell_index_column,
342 alphabet1_t
const & alphabet1,
343 sequence2_t && sequence2)
349 auto current_alignment_column_it = alignment_column.begin();
350 auto cell_index_column_it = cell_index_column.begin();
353 decltype(current_alignment_column_it) next_alignment_column_it{current_alignment_column_it};
354 auto cell = *current_alignment_column_it;
355 cell = this->track_cell(
356 this->initialise_band_first_cell(cell.best_score(),
357 *++next_alignment_column_it,
359 *cell_index_column_it);
365 for (
auto && alphabet2 :
std::views::
drop(sequence2, 1))
367 current_alignment_column_it = next_alignment_column_it;
368 auto cell = *current_alignment_column_it;
369 cell = this->track_cell(this->compute_inner_cell(cell.best_score(),
370 *++next_alignment_column_it,
371 this->scoring_scheme.score(alphabet1, alphabet2)),
372 *++cell_index_column_it);
379 this->track_last_row_cell(*current_alignment_column_it, *cell_index_column_it);
typename decltype(detail::split_after< i >(list_t{}))::first_type take
Return a seqan3::type_list of the first n types in the input type list.
Definition type_list/traits.hpp:374
typename decltype(detail::split_after< i >(list_t{}))::second_type drop
Return a seqan3::type_list of the types in the input type list, except the first n.
Definition type_list/traits.hpp:392
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition slice.hpp:175
SeqAn specific customisations in the standard namespace.
Provides seqan3::detail::pairwise_alignment_algorithm.
Provides seqan3::views::slice.