39namespace seqan3::detail
75template <
typename config_t,
typename ...algorithm_policies_t>
76class alignment_algorithm :
77 public invoke_deferred_crtp_base<algorithm_policies_t, alignment_algorithm<config_t, algorithm_policies_t...>>...
82 using traits_t = alignment_configuration_traits<config_t>;
84 using alignment_column_t =
decltype(std::declval<alignment_algorithm>().current_alignment_column());
86 using alignment_column_iterator_t = std::ranges::iterator_t<alignment_column_t>;
88 using alignment_result_t =
typename traits_t::alignment_result_type;
90 static_assert(!std::same_as<alignment_result_t, empty_type>,
"Alignment result type was not configured.");
93 using score_debug_matrix_t =
95 two_dimensional_matrix<std::optional<typename traits_t::original_score_type>,
97 matrix_major_order::column>,
100 using trace_debug_matrix_t =
102 two_dimensional_matrix<std::optional<trace_directions>,
104 matrix_major_order::column>,
111 constexpr alignment_algorithm() =
default;
112 constexpr alignment_algorithm(alignment_algorithm
const &) =
default;
113 constexpr alignment_algorithm(alignment_algorithm &&) =
default;
114 constexpr alignment_algorithm & operator=(alignment_algorithm
const &) =
default;
115 constexpr alignment_algorithm & operator=(alignment_algorithm &&) =
default;
116 ~alignment_algorithm() =
default;
126 explicit constexpr alignment_algorithm(config_t
const & cfg) :
127 invoke_deferred_crtp_base<algorithm_policies_t, alignment_algorithm<config_t, algorithm_policies_t...>>{cfg}...,
128 cfg_ptr{std::make_shared<config_t>(cfg)}
130 this->scoring_scheme = seqan3::get<align_cfg::scoring_scheme>(*cfg_ptr).scheme;
131 this->initialise_alignment_state(*cfg_ptr);
180 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
182 requires (!traits_t::is_vectorised) && std::invocable<callback_t, alignment_result_t>
184 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
188 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
189 compute_single_pair(idx, get<0>(sequence_pair), get<1>(sequence_pair), callback);
193 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
195 requires traits_t::is_vectorised && std::invocable<callback_t, alignment_result_t>
197 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
199 assert(cfg_ptr !=
nullptr);
201 static_assert(simd_concept<typename traits_t::score_type>,
"Expected simd score type.");
202 static_assert(simd_concept<typename traits_t::trace_type>,
"Expected simd trace type.");
205 auto sequence1_range = indexed_sequence_pairs | views::elements<0> | views::elements<0>;
206 auto sequence2_range = indexed_sequence_pairs | views::elements<0> | views::elements<1>;
209 this->initialise_find_optimum_policy(sequence1_range,
211 this->scoring_scheme.padding_match_score());
214 auto simd_sequences1 = convert_batch_of_sequences_to_simd_vector(sequence1_range);
215 auto simd_sequences2 = convert_batch_of_sequences_to_simd_vector(sequence2_range);
217 max_size_in_collection =
std::pair{simd_sequences1.size(), simd_sequences2.size()};
219 this->alignment_state.reset_optimum();
221 compute_matrix(simd_sequences1, simd_sequences2);
223 make_alignment_result(indexed_sequence_pairs, callback);
241 template <
typename sequence_range_t>
242 constexpr auto convert_batch_of_sequences_to_simd_vector(sequence_range_t & sequences)
244 assert(
static_cast<size_t>(std::ranges::distance(sequences)) <= traits_t::alignments_per_vector);
246 using simd_score_t =
typename traits_t::score_type;
248 std::vector<simd_score_t, aligned_allocator<simd_score_t,
alignof(simd_score_t)>> simd_sequence{};
250 for (
auto && simd_vector_chunk : sequences | views::to_simd<simd_score_t>(this->scoring_scheme.padding_symbol))
251 for (
auto && simd_vector : simd_vector_chunk)
252 simd_sequence.
push_back(std::move(simd_vector));
254 return simd_sequence;
274 template <std::ranges::forward_range sequence1_t,
275 std::ranges::forward_range sequence2_t,
277 constexpr void compute_single_pair(
size_t const idx,
278 sequence1_t && sequence1,
279 sequence2_t && sequence2,
280 callback_t & callback)
282 assert(cfg_ptr !=
nullptr);
284 if constexpr (traits_t::is_debug)
285 initialise_debug_matrices(sequence1, sequence2);
288 this->alignment_state.reset_optimum();
290 if constexpr (traits_t::is_banded)
294 auto const & band = get<align_cfg::band_fixed_size>(*cfg_ptr);
295 check_valid_band_parameter(sequence1, sequence2, band);
296 auto && [subsequence1, subsequence2] = this->slice_sequences(sequence1, sequence2, band);
298 compute_matrix(subsequence1, subsequence2, band);
299 make_alignment_result(idx, subsequence1, subsequence2, callback);
303 compute_matrix(sequence1, sequence2);
304 make_alignment_result(idx, sequence1, sequence2, callback);
324 template <
typename sequence1_t,
typename sequence2_t>
325 constexpr void check_valid_band_parameter(sequence1_t && sequence1,
326 sequence2_t && sequence2,
327 align_cfg::band_fixed_size
const & band)
329 static_assert(config_t::template exists<align_cfg::band_fixed_size>(),
330 "The band configuration is required for the banded alignment algorithm.");
333 static_assert(std::is_signed_v<diff_type>,
"Only signed types can be used to test the band parameters.");
335 if (
static_cast<diff_type
>(band.lower_diagonal) > std::ranges::distance(sequence1))
337 throw invalid_alignment_configuration
339 "Invalid band error: The lower diagonal excludes the whole alignment matrix."
343 if (
static_cast<diff_type
>(band.upper_diagonal) < -std::ranges::distance(sequence2))
345 throw invalid_alignment_configuration
347 "Invalid band error: The upper diagonal excludes the whole alignment matrix."
364 template <
typename sequence1_t,
typename sequence2_t>
365 constexpr void initialise_debug_matrices(sequence1_t & sequence1, sequence2_t & sequence2)
367 size_t rows = std::ranges::distance(sequence2) + 1;
368 size_t cols = std::ranges::distance(sequence1) + 1;
370 score_debug_matrix = score_debug_matrix_t{number_rows{rows}, number_cols{cols}};
371 trace_debug_matrix = trace_debug_matrix_t{number_rows{rows}, number_cols{cols}};
381 template <
typename sequence1_t,
typename sequence2_t>
382 void compute_matrix(sequence1_t & sequence1, sequence2_t & sequence2)
384 requires (!traits_t::is_banded)
391 this->allocate_matrix(sequence1, sequence2);
392 initialise_first_alignment_column(sequence2);
398 for (
auto const & alphabet1 : sequence1)
400 compute_alignment_column<true>(this->scoring_scheme_profile_column(alphabet1), sequence2);
401 finalise_last_cell_in_column(
true);
408 finalise_alignment();
412 template <
typename sequence1_t,
typename sequence2_t>
413 void compute_matrix(sequence1_t & sequence1, sequence2_t & sequence2, align_cfg::band_fixed_size
const & band)
415 requires traits_t::is_banded
423 this->allocate_matrix(sequence1, sequence2, band, this->alignment_state);
424 using row_index_t = std::ranges::range_difference_t<sequence2_t>;
425 row_index_t last_row_index = this->score_matrix.band_row_index;
426 initialise_first_alignment_column(
std::views::take(sequence2, last_row_index));
432 row_index_t sequence2_size = std::ranges::distance(sequence2);
433 for (
auto const & seq1_value :
std::views::take(sequence1, this->score_matrix.band_col_index))
435 compute_alignment_column<true>(seq1_value,
std::views::take(sequence2, ++last_row_index));
437 finalise_last_cell_in_column(last_row_index >= sequence2_size);
444 size_t first_row_index = 0;
445 for (
auto const & seq1_value :
std::views::drop(sequence1, this->score_matrix.band_col_index))
448 compute_alignment_column<false>(seq1_value, sequence2 |
views::slice(first_row_index++, ++last_row_index));
450 finalise_last_cell_in_column(last_row_index >= sequence2_size);
457 finalise_alignment();
472 template <
typename sequence2_t>
473 auto initialise_first_alignment_column(sequence2_t && sequence2)
476 alignment_column = this->current_alignment_column();
477 assert(!alignment_column.empty());
480 alignment_column_it = alignment_column.begin();
481 this->init_origin_cell(*alignment_column_it, this->alignment_state);
484 for (
auto it = std::ranges::begin(sequence2); it != std::ranges::end(sequence2); ++it)
485 this->init_column_cell(*++alignment_column_it, this->alignment_state);
488 bool at_last_row =
true;
489 if constexpr (traits_t::is_banded)
490 at_last_row =
static_cast<size_t>(this->score_matrix.band_row_index) == this->score_matrix.num_rows - 1;
492 finalise_last_cell_in_column(at_last_row);
510 template <
bool initialise_first_cell,
typename sequence1_value_t,
typename sequence2_t>
511 void compute_alignment_column(sequence1_value_t
const & seq1_value, sequence2_t && sequence2)
513 this->next_alignment_column();
514 alignment_column = this->current_alignment_column();
515 alignment_column_it = alignment_column.begin();
519 if constexpr (initialise_first_cell)
521 this->init_row_cell(*alignment_column_it, this->alignment_state);
525 this->compute_first_band_cell(*alignment_column_it,
526 this->alignment_state,
527 this->scoring_scheme.score(seq1_value, *seq2_it));
531 for (; seq2_it != std::ranges::end(sequence2); ++seq2_it)
532 this->compute_cell(*++alignment_column_it,
533 this->alignment_state,
534 this->scoring_scheme.score(seq1_value, *seq2_it));
547 constexpr void finalise_last_cell_in_column(
bool const at_last_row)
noexcept
550 this->check_score_of_last_row_cell(*alignment_column_it, this->alignment_state);
552 if constexpr (traits_t::is_debug)
553 dump_alignment_column();
557 constexpr void finalise_alignment() noexcept
563 this->check_score_of_cells_in_last_column(alignment_column, this->alignment_state);
564 this->check_score_of_last_cell(*alignment_column_it, this->alignment_state);
593 template <
typename index_t,
typename sequence1_t,
typename sequence2_t,
typename callback_t>
595 requires (!traits_t::is_vectorised)
597 constexpr void make_alignment_result([[maybe_unused]] index_t
const idx,
598 [[maybe_unused]] sequence1_t & sequence1,
599 [[maybe_unused]] sequence2_t & sequence2,
600 callback_t & callback)
602 using result_value_t =
typename alignment_result_value_type_accessor<alignment_result_t>::type;
608 static_assert(seqan3::detail::alignment_configuration_traits<config_t>::has_output_configuration,
609 "The configuration must contain at least one align_cfg::output_* element.");
611 result_value_t res{};
613 if constexpr (traits_t::output_sequence1_id)
614 res.sequence1_id = idx;
616 if constexpr (traits_t::output_sequence2_id)
617 res.sequence2_id = idx;
620 if constexpr (traits_t::compute_score)
621 res.score = this->alignment_state.optimum.score;
623 if constexpr (traits_t::compute_end_positions)
625 using alignment_coordinate_t = detail::advanceable_alignment_coordinate<>;
626 res.end_positions = alignment_coordinate_t{column_index_type{this->alignment_state.optimum.column_index},
627 row_index_type{this->alignment_state.optimum.row_index}};
629 if constexpr (traits_t::is_banded)
630 res.end_positions.second += res.end_positions.first - this->trace_matrix.band_col_index;
633 if constexpr (traits_t::compute_begin_positions)
636 aligned_sequence_builder builder{sequence1, sequence2};
638 detail::matrix_coordinate
const optimum_coordinate
640 detail::row_index_type{this->alignment_state.optimum.row_index},
641 detail::column_index_type{this->alignment_state.optimum.column_index}
643 auto trace_res = builder(this->trace_matrix.trace_path(optimum_coordinate));
644 res.begin_positions.first = trace_res.first_sequence_slice_positions.first;
645 res.begin_positions.second = trace_res.second_sequence_slice_positions.first;
647 if constexpr (traits_t::compute_sequence_alignment)
648 res.alignment = std::move(trace_res.alignment);
652 if constexpr (traits_t::is_debug)
654 res.score_debug_matrix = std::move(score_debug_matrix);
655 if constexpr (traits_t::compute_sequence_alignment)
656 res.trace_debug_matrix = std::move(trace_debug_matrix);
659 callback(std::move(res));
687 template <
typename indexed_sequence_pair_range_t,
typename callback_t>
689 requires traits_t::is_vectorised
691 constexpr auto make_alignment_result(indexed_sequence_pair_range_t && index_sequence_pairs,
692 callback_t & callback)
694 using result_value_t =
typename alignment_result_value_type_accessor<alignment_result_t>::type;
696 size_t simd_index = 0;
697 for (
auto && [sequence_pairs, alignment_index] : index_sequence_pairs)
699 (void) sequence_pairs;
700 result_value_t res{};
702 if constexpr (traits_t::output_sequence1_id)
703 res.sequence1_id = alignment_index;
705 if constexpr (traits_t::output_sequence2_id)
706 res.sequence2_id = alignment_index;
708 if constexpr (traits_t::compute_score)
709 res.score = this->alignment_state.optimum.score[simd_index];
711 if constexpr (traits_t::compute_end_positions)
713 res.end_positions.first = this->alignment_state.optimum.column_index[simd_index];
714 res.end_positions.second = this->alignment_state.optimum.row_index[simd_index];
717 callback(std::move(res));
730 void dump_alignment_column()
734 auto column = this->current_alignment_column();
736 auto coord = get<1>(column.front()).coordinate;
737 if constexpr (traits_t::is_banded)
738 coord.second += coord.first - this->score_matrix.band_col_index;
740 matrix_offset offset{row_index_type{
static_cast<std::ptrdiff_t>(coord.second)},
746 return get<0>(tpl).current;
747 }), score_debug_matrix.begin() +
offset);
750 if constexpr (traits_t::compute_sequence_alignment)
752 auto trace_matrix_it = trace_debug_matrix.begin() +
offset;
756 return get<1>(tpl).current;
757 }), trace_debug_matrix.begin() +
offset);
764 alignment_column_t alignment_column{};
766 alignment_column_iterator_t alignment_column_it{};
768 score_debug_matrix_t score_debug_matrix{};
770 trace_debug_matrix_t trace_debug_matrix{};
Provides seqan3::detail::align_config_band.
Provides seqan3::align_cfg::scoring_scheme.
Provides seqan3::detail::align_result_selector.
Provides seqan3::aligned_allocator.
Provides seqan3::detail::aligned_sequence_builder.
Includes customized exception types for the alignment module .
Provides concepts needed internally for the alignment algorithms.
Provides helper type traits for the configuration and execution of the alignment algorithm.
Provides seqan3::detail::deferred_crtp_base.
Provides seqan3::views::elements.
Provides seqan3::detail::empty_type.
Provides various type traits for use on functions.
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
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: traits.hpp:368
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: traits.hpp:388
decltype(detail::transform< trait_t >(list_t{})) transform
Apply a transformation trait to every type in the list and return a seqan3::type_list of the results.
Definition: traits.hpp:471
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition: slice.hpp:183
The <iterator> header from C++20's standard library.
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:429
The <ranges> header from C++20's standard library.
Provides seqan3::simd::simd_type.
Provides seqan3::simd::simd_traits.
Provides seqan3::detail::to_simd view.
Provides the declaration of seqan3::detail::trace_directions.
Provides seqan3::simd::simd_concept.