25 namespace seqan3::detail
44 template <
typename alignment_configuration_t,
typename ...policies_t>
46 requires is_type_specialisation_of_v<alignment_configuration_t, configuration>
48 class pairwise_alignment_algorithm :
protected policies_t...
52 using traits_type = alignment_configuration_traits<alignment_configuration_t>;
54 using score_type =
typename traits_type::score_type;
56 using alignment_result_type =
typename traits_type::alignment_result_type;
58 static_assert(!std::same_as<alignment_result_type, empty_type>,
"Alignment result type was not configured.");
64 pairwise_alignment_algorithm() =
default;
65 pairwise_alignment_algorithm(pairwise_alignment_algorithm
const &) =
default;
66 pairwise_alignment_algorithm(pairwise_alignment_algorithm &&) =
default;
67 pairwise_alignment_algorithm & operator=(pairwise_alignment_algorithm
const &) =
default;
68 pairwise_alignment_algorithm & operator=(pairwise_alignment_algorithm &&) =
default;
69 ~pairwise_alignment_algorithm() =
default;
78 pairwise_alignment_algorithm(alignment_configuration_t
const & config) : policies_t(config)...
127 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
129 requires std::invocable<callback_t, alignment_result_type>
131 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
135 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
137 size_t const sequence1_size = std::ranges::distance(get<0>(sequence_pair));
138 size_t const sequence2_size = std::ranges::distance(get<1>(sequence_pair));
140 auto && [alignment_matrix, index_matrix] = this->acquire_matrices(sequence1_size, sequence2_size);
142 compute_matrix(get<0>(sequence_pair), get<1>(sequence_pair), alignment_matrix, index_matrix);
143 this->make_result_and_invoke(
std::forward<decltype(sequence_pair)>(sequence_pair),
146 this->optimal_coordinate,
154 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
156 requires traits_type::is_vectorised && std::invocable<callback_t, alignment_result_type>
158 auto operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
160 using simd_collection_t =
std::vector<score_type, aligned_allocator<score_type,
alignof(score_type)>>;
161 using original_score_t =
typename traits_type::original_score_type;
164 auto seq1_collection = indexed_sequence_pairs | views::elements<0> | views::elements<0>;
165 auto seq2_collection = indexed_sequence_pairs | views::elements<0> | views::elements<1>;
167 this->initialise_tracker(seq1_collection, seq2_collection);
170 thread_local simd_collection_t simd_seq1_collection{};
171 thread_local simd_collection_t simd_seq2_collection{};
173 convert_batch_of_sequences_to_simd_vector(simd_seq1_collection,
175 this->scoring_scheme.padding_symbol);
176 convert_batch_of_sequences_to_simd_vector(simd_seq2_collection,
178 this->scoring_scheme.padding_symbol);
180 size_t const sequence1_size = std::ranges::distance(simd_seq1_collection);
181 size_t const sequence2_size = std::ranges::distance(simd_seq2_collection);
183 auto && [alignment_matrix, index_matrix] = this->acquire_matrices(sequence1_size, sequence2_size);
185 compute_matrix(simd_seq1_collection, simd_seq2_collection, alignment_matrix, index_matrix);
188 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
190 original_score_t score = this->optimal_score[index] -
191 (this->padding_offsets[index] * this->scoring_scheme.padding_match_score());
192 matrix_coordinate coordinate{row_index_type{
size_t{this->optimal_coordinate.row[index]}},
193 column_index_type{
size_t{this->optimal_coordinate.col[index]}}};
194 this->make_result_and_invoke(
std::forward<decltype(sequence_pair)>(sequence_pair),
224 template <
typename simd_sequence_t,
225 std::ranges::forward_range sequence_collection_t,
228 requires std::ranges::output_range<simd_sequence_t, score_type>
230 void convert_batch_of_sequences_to_simd_vector(simd_sequence_t & simd_sequence,
231 sequence_collection_t & sequences,
232 padding_symbol_t
const & padding_symbol)
234 assert(
static_cast<size_t>(std::ranges::distance(sequences)) <= traits_type::alignments_per_vector);
236 simd_sequence.clear();
237 for (
auto && simd_vector_chunk : sequences | views::to_simd<score_type>(padding_symbol))
254 template <std::ranges::forward_range sequence1_t,
255 std::ranges::forward_range sequence2_t,
256 std::ranges::input_range alignment_matrix_t,
257 std::ranges::input_range index_matrix_t>
259 requires std::ranges::forward_range<std::ranges::range_reference_t<alignment_matrix_t>> &&
260 std::ranges::forward_range<std::ranges::range_reference_t<index_matrix_t>>
262 void compute_matrix(sequence1_t && sequence1,
263 sequence2_t && sequence2,
264 alignment_matrix_t && alignment_matrix,
265 index_matrix_t && index_matrix)
271 this->reset_optimum();
273 auto alignment_matrix_it = alignment_matrix.begin();
274 auto indexed_matrix_it = index_matrix.begin();
276 initialise_column(*alignment_matrix_it, *indexed_matrix_it, sequence2);
282 for (
auto alphabet1 : sequence1)
283 compute_column(*++alignment_matrix_it,
284 *++indexed_matrix_it,
285 this->scoring_scheme_profile_column(alphabet1),
292 auto && alignment_column = *alignment_matrix_it;
293 auto && cell_index_column = *indexed_matrix_it;
295 auto alignment_column_it = alignment_column.begin();
296 auto cell_index_column_it = cell_index_column.begin();
298 this->track_last_column_cell(*alignment_column_it, *cell_index_column_it);
300 for ([[maybe_unused]]
auto && unused : sequence2)
301 this->track_last_column_cell(*++alignment_column_it, *++cell_index_column_it);
303 this->track_final_cell(*alignment_column_it, *cell_index_column_it);
324 template <std::ranges::input_range alignment_column_t,
325 std::ranges::input_range cell_index_column_t,
326 std::ranges::input_range sequence2_t>
327 void initialise_column(alignment_column_t && alignment_column,
328 cell_index_column_t && cell_index_column,
329 sequence2_t && sequence2)
335 auto first_column_it = alignment_column.begin();
336 auto cell_index_column_it = cell_index_column.begin();
337 *first_column_it = this->track_cell(this->initialise_origin_cell(), *cell_index_column_it);
343 for ([[maybe_unused]]
auto const & unused : sequence2)
346 *first_column_it = this->track_cell(this->initialise_first_column_cell(*first_column_it),
347 *++cell_index_column_it);
354 this->track_last_row_cell(*first_column_it, *cell_index_column_it);
375 template <std::ranges::input_range alignment_column_t,
376 std::ranges::input_range cell_index_column_t,
377 typename alphabet1_t,
378 std::ranges::input_range sequence2_t>
382 void compute_column(alignment_column_t && alignment_column,
383 cell_index_column_t && cell_index_column,
384 alphabet1_t
const & alphabet1,
385 sequence2_t && sequence2)
387 using score_type =
typename traits_type::score_type;
393 auto alignment_column_it = alignment_column.begin();
394 auto cell_index_column_it = cell_index_column.begin();
396 auto cell = *alignment_column_it;
397 score_type diagonal = cell.best_score();
398 *alignment_column_it = this->track_cell(this->initialise_first_row_cell(cell), *cell_index_column_it);
404 for (
auto const & alphabet2 : sequence2)
406 auto cell = *++alignment_column_it;
407 score_type next_diagonal = cell.best_score();
408 *alignment_column_it = this->track_cell(
409 this->compute_inner_cell(diagonal, cell, this->scoring_scheme.score(alphabet1, alphabet2)),
410 *++cell_index_column_it);
411 diagonal = next_diagonal;
418 this->track_last_row_cell(*alignment_column_it, *cell_index_column_it);
Provides helper type traits for the configuration and execution of the alignment algorithm.
Provides seqan3::views::elements.
Provides seqan3::detail::empty_type.
constexpr auto get
A view calling get on each element in a range.
Definition: elements.hpp:114
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:74
A type that satisfies std::is_arithmetic_v<t>.
The basis for seqan3::alphabet, but requires only rank interface (not char).
Adaptations of concepts from the Ranges TS.
Provides seqan3::detail::to_simd view.
Provides traits to inspect some information of a type, for example its name.
Provides seqan3::aligned_allocator.