25namespace seqan3::detail
44template <
typename alignment_configuration_t,
typename... policies_t>
45 requires is_type_specialisation_of_v<alignment_configuration_t, configuration>
46class pairwise_alignment_algorithm :
protected policies_t...
50 using traits_type = alignment_configuration_traits<alignment_configuration_t>;
52 using score_type =
typename traits_type::score_type;
54 using alignment_result_type =
typename traits_type::alignment_result_type;
56 static_assert(!std::same_as<alignment_result_type, empty_type>,
"Alignment result type was not configured.");
62 pairwise_alignment_algorithm() =
default;
63 pairwise_alignment_algorithm(pairwise_alignment_algorithm
const &) =
default;
64 pairwise_alignment_algorithm(pairwise_alignment_algorithm &&) =
default;
65 pairwise_alignment_algorithm & operator=(pairwise_alignment_algorithm
const &) =
default;
66 pairwise_alignment_algorithm & operator=(pairwise_alignment_algorithm &&) =
default;
67 ~pairwise_alignment_algorithm() =
default;
76 pairwise_alignment_algorithm(alignment_configuration_t
const & config) : policies_t(config)...
125 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
126 requires std::invocable<callback_t, alignment_result_type>
127 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
131 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
133 size_t const sequence1_size = std::ranges::distance(get<0>(sequence_pair));
134 size_t const sequence2_size = std::ranges::distance(get<1>(sequence_pair));
136 auto && [alignment_matrix, index_matrix] = this->acquire_matrices(sequence1_size, sequence2_size);
138 compute_matrix(get<0>(sequence_pair), get<1>(sequence_pair), alignment_matrix, index_matrix);
139 this->make_result_and_invoke(
std::forward<
decltype(sequence_pair)>(sequence_pair),
142 this->optimal_coordinate,
150 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
151 requires traits_type::is_vectorised && std::invocable<callback_t, alignment_result_type>
152 auto operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
154 using simd_collection_t =
std::vector<score_type, aligned_allocator<score_type,
alignof(score_type)>>;
155 using original_score_t =
typename traits_type::original_score_type;
158 auto seq1_collection = indexed_sequence_pairs | views::elements<0> | views::elements<0>;
159 auto seq2_collection = indexed_sequence_pairs | views::elements<0> | views::elements<1>;
161 this->initialise_tracker(seq1_collection, seq2_collection);
164 thread_local simd_collection_t simd_seq1_collection{};
165 thread_local simd_collection_t simd_seq2_collection{};
167 convert_batch_of_sequences_to_simd_vector(simd_seq1_collection,
169 this->scoring_scheme.padding_symbol);
170 convert_batch_of_sequences_to_simd_vector(simd_seq2_collection,
172 this->scoring_scheme.padding_symbol);
174 size_t const sequence1_size = std::ranges::distance(simd_seq1_collection);
175 size_t const sequence2_size = std::ranges::distance(simd_seq2_collection);
177 auto && [alignment_matrix, index_matrix] = this->acquire_matrices(sequence1_size, sequence2_size);
179 compute_matrix(simd_seq1_collection, simd_seq2_collection, alignment_matrix, index_matrix);
182 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
184 original_score_t score = this->optimal_score[index]
185 - (this->padding_offsets[index] * this->scoring_scheme.padding_match_score());
186 matrix_coordinate coordinate{row_index_type{
size_t{this->optimal_coordinate.row[index]}},
187 column_index_type{
size_t{this->optimal_coordinate.col[index]}}};
188 this->make_result_and_invoke(
std::forward<
decltype(sequence_pair)>(sequence_pair),
191 std::move(coordinate),
218 template <
typename simd_sequence_t, std::ranges::forward_range sequence_collection_t, arithmetic padding_symbol_t>
219 requires std::ranges::output_range<simd_sequence_t, score_type>
220 void convert_batch_of_sequences_to_simd_vector(simd_sequence_t & simd_sequence,
221 sequence_collection_t & sequences,
222 padding_symbol_t
const & padding_symbol)
224 assert(
static_cast<size_t>(std::ranges::distance(sequences)) <= traits_type::alignments_per_vector);
226 simd_sequence.clear();
227 for (
auto && simd_vector_chunk : sequences | views::to_simd<score_type>(padding_symbol))
244 template <std::ranges::forward_range sequence1_t,
245 std::ranges::forward_range sequence2_t,
246 std::ranges::input_range alignment_matrix_t,
247 std::ranges::input_range index_matrix_t>
248 requires std::ranges::forward_range<std::ranges::range_reference_t<alignment_matrix_t>>
249 && std::ranges::forward_range<std::ranges::range_reference_t<index_matrix_t>>
250 void compute_matrix(sequence1_t && sequence1,
251 sequence2_t && sequence2,
252 alignment_matrix_t && alignment_matrix,
253 index_matrix_t && index_matrix)
259 this->reset_optimum();
261 auto alignment_matrix_it = alignment_matrix.begin();
262 auto indexed_matrix_it = index_matrix.begin();
264 initialise_column(*alignment_matrix_it, *indexed_matrix_it, sequence2);
270 for (
auto alphabet1 : sequence1)
271 compute_column(*++alignment_matrix_it,
272 *++indexed_matrix_it,
273 this->scoring_scheme_profile_column(alphabet1),
280 auto && alignment_column = *alignment_matrix_it;
281 auto && cell_index_column = *indexed_matrix_it;
283 auto alignment_column_it = alignment_column.begin();
284 auto cell_index_column_it = cell_index_column.begin();
286 this->track_last_column_cell(*alignment_column_it, *cell_index_column_it);
288 for ([[maybe_unused]]
auto && unused : sequence2)
289 this->track_last_column_cell(*++alignment_column_it, *++cell_index_column_it);
291 this->track_final_cell(*alignment_column_it, *cell_index_column_it);
312 template <std::ranges::input_range alignment_column_t,
313 std::ranges::input_range cell_index_column_t,
314 std::ranges::input_range sequence2_t>
315 void initialise_column(alignment_column_t && alignment_column,
316 cell_index_column_t && cell_index_column,
317 sequence2_t && sequence2)
323 auto first_column_it = alignment_column.begin();
324 auto cell_index_column_it = cell_index_column.begin();
325 *first_column_it = this->track_cell(this->initialise_origin_cell(), *cell_index_column_it);
331 for ([[maybe_unused]]
auto const & unused : sequence2)
335 this->track_cell(this->initialise_first_column_cell(*first_column_it), *++cell_index_column_it);
342 this->track_last_row_cell(*first_column_it, *cell_index_column_it);
363 template <std::ranges::input_range alignment_column_t,
364 std::ranges::input_range cell_index_column_t,
365 typename alphabet1_t,
366 std::ranges::input_range sequence2_t>
368 void compute_column(alignment_column_t && alignment_column,
369 cell_index_column_t && cell_index_column,
370 alphabet1_t
const & alphabet1,
371 sequence2_t && sequence2)
373 using score_type =
typename traits_type::score_type;
379 auto alignment_column_it = alignment_column.begin();
380 auto cell_index_column_it = cell_index_column.begin();
382 auto cell = *alignment_column_it;
383 score_type diagonal = cell.best_score();
384 *alignment_column_it = this->track_cell(this->initialise_first_row_cell(cell), *cell_index_column_it);
390 for (
auto const & alphabet2 : sequence2)
392 auto cell = *++alignment_column_it;
393 score_type next_diagonal = cell.best_score();
394 *alignment_column_it = this->track_cell(
395 this->compute_inner_cell(diagonal, cell, this->scoring_scheme.score(alphabet1, alphabet2)),
396 *++cell_index_column_it);
397 diagonal = next_diagonal;
404 this->track_last_row_cell(*alignment_column_it, *cell_index_column_it);
Provides seqan3::aligned_allocator.
Provides helper type traits for the configuration and execution of the alignment algorithm.
T back_inserter(T... args)
Provides seqan3::views::elements.
Provides seqan3::detail::empty_type.
The basis for seqan3::alphabet, but requires only rank interface (not char).
constexpr auto const & get(configuration< configs_t... > const &config) noexcept
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: configuration.hpp:415
Provides seqan3::detail::to_simd view.
Provides traits to inspect some information of a type, for example its name.