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>;
94 template <
typename alignment_algorithm_t = alignment_algorithm>
95 static auto _alignment_column_t() ->
decltype(std::declval<alignment_algorithm_t>().current_alignment_column());
98 using alignment_column_t =
decltype(_alignment_column_t());
100 using alignment_column_iterator_t = std::ranges::iterator_t<alignment_column_t>;
102 using alignment_result_t =
typename traits_t::alignment_result_type;
104 static_assert(!std::same_as<alignment_result_t, empty_type>,
"Alignment result type was not configured.");
107 using score_debug_matrix_t =
109 two_dimensional_matrix<std::optional<typename traits_t::original_score_type>,
111 matrix_major_order::column>,
114 using trace_debug_matrix_t =
116 two_dimensional_matrix<std::optional<trace_directions>,
118 matrix_major_order::column>,
125 constexpr alignment_algorithm() =
default;
126 constexpr alignment_algorithm(alignment_algorithm
const &) =
default;
127 constexpr alignment_algorithm(alignment_algorithm &&) =
default;
128 constexpr alignment_algorithm & operator=(alignment_algorithm
const &) =
default;
129 constexpr alignment_algorithm & operator=(alignment_algorithm &&) =
default;
130 ~alignment_algorithm() =
default;
140 explicit constexpr alignment_algorithm(config_t
const & cfg) :
141 invoke_deferred_crtp_base<algorithm_policies_t, alignment_algorithm<config_t, algorithm_policies_t...>>{cfg}...,
142 cfg_ptr{std::make_shared<config_t>(cfg)}
144 this->scoring_scheme = seqan3::get<align_cfg::scoring_scheme>(*cfg_ptr).scheme;
145 this->initialise_alignment_state(*cfg_ptr);
194 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
196 requires (!traits_t::is_vectorised) && std::invocable<callback_t, alignment_result_t>
198 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
202 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
203 compute_single_pair(idx, get<0>(sequence_pair), get<1>(sequence_pair), callback);
207 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
209 requires traits_t::is_vectorised && std::invocable<callback_t, alignment_result_t>
211 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
213 assert(cfg_ptr !=
nullptr);
215 static_assert(simd_concept<typename traits_t::score_type>,
"Expected simd score type.");
216 static_assert(simd_concept<typename traits_t::trace_type>,
"Expected simd trace type.");
219 auto sequence1_range = indexed_sequence_pairs | views::elements<0> | views::elements<0>;
220 auto sequence2_range = indexed_sequence_pairs | views::elements<0> | views::elements<1>;
223 this->initialise_find_optimum_policy(sequence1_range,
225 this->scoring_scheme.padding_match_score());
228 auto simd_sequences1 = convert_batch_of_sequences_to_simd_vector(sequence1_range);
229 auto simd_sequences2 = convert_batch_of_sequences_to_simd_vector(sequence2_range);
231 max_size_in_collection =
std::pair{simd_sequences1.size(), simd_sequences2.size()};
233 this->alignment_state.reset_optimum();
235 compute_matrix(simd_sequences1, simd_sequences2);
237 make_alignment_result(indexed_sequence_pairs, callback);
255 template <
typename sequence_range_t>
256 constexpr auto convert_batch_of_sequences_to_simd_vector(sequence_range_t & sequences)
258 assert(
static_cast<size_t>(std::ranges::distance(sequences)) <= traits_t::alignments_per_vector);
260 using simd_score_t =
typename traits_t::score_type;
262 std::vector<simd_score_t, aligned_allocator<simd_score_t,
alignof(simd_score_t)>> simd_sequence{};
264 for (
auto && simd_vector_chunk : sequences | views::to_simd<simd_score_t>(this->scoring_scheme.padding_symbol))
265 for (
auto && simd_vector : simd_vector_chunk)
266 simd_sequence.
push_back(std::move(simd_vector));
268 return simd_sequence;
288 template <std::ranges::forward_range sequence1_t,
289 std::ranges::forward_range sequence2_t,
291 constexpr void compute_single_pair(
size_t const idx,
292 sequence1_t && sequence1,
293 sequence2_t && sequence2,
294 callback_t & callback)
296 assert(cfg_ptr !=
nullptr);
298 if constexpr (traits_t::is_debug)
299 initialise_debug_matrices(sequence1, sequence2);
302 this->alignment_state.reset_optimum();
304 if constexpr (traits_t::is_banded)
308 auto const & band = get<align_cfg::band_fixed_size>(*cfg_ptr);
309 check_valid_band_parameter(sequence1, sequence2, band);
310 auto && [subsequence1, subsequence2] = this->slice_sequences(sequence1, sequence2, band);
312 compute_matrix(subsequence1, subsequence2, band);
313 make_alignment_result(idx, subsequence1, subsequence2, callback);
317 compute_matrix(sequence1, sequence2);
318 make_alignment_result(idx, sequence1, sequence2, callback);
338 template <
typename sequence1_t,
typename sequence2_t>
339 constexpr void check_valid_band_parameter(sequence1_t && sequence1,
340 sequence2_t && sequence2,
341 align_cfg::band_fixed_size
const & band)
343 static_assert(config_t::template exists<align_cfg::band_fixed_size>(),
344 "The band configuration is required for the banded alignment algorithm.");
347 static_assert(std::is_signed_v<diff_type>,
"Only signed types can be used to test the band parameters.");
349 if (
static_cast<diff_type
>(band.lower_diagonal) > std::ranges::distance(sequence1))
351 throw invalid_alignment_configuration
353 "Invalid band error: The lower diagonal excludes the whole alignment matrix."
357 if (
static_cast<diff_type
>(band.upper_diagonal) < -std::ranges::distance(sequence2))
359 throw invalid_alignment_configuration
361 "Invalid band error: The upper diagonal excludes the whole alignment matrix."
378 template <
typename sequence1_t,
typename sequence2_t>
379 constexpr void initialise_debug_matrices(sequence1_t & sequence1, sequence2_t & sequence2)
381 size_t rows = std::ranges::distance(sequence2) + 1;
382 size_t cols = std::ranges::distance(sequence1) + 1;
384 score_debug_matrix = score_debug_matrix_t{number_rows{rows}, number_cols{cols}};
385 trace_debug_matrix = trace_debug_matrix_t{number_rows{rows}, number_cols{cols}};
395 template <
typename sequence1_t,
typename sequence2_t>
396 void compute_matrix(sequence1_t & sequence1, sequence2_t & sequence2)
398 requires (!traits_t::is_banded)
405 this->allocate_matrix(sequence1, sequence2);
406 initialise_first_alignment_column(sequence2);
412 for (
auto const & alphabet1 : sequence1)
414 compute_alignment_column<true>(this->scoring_scheme_profile_column(alphabet1), sequence2);
415 finalise_last_cell_in_column(
true);
422 finalise_alignment();
426 template <
typename sequence1_t,
typename sequence2_t>
427 void compute_matrix(sequence1_t & sequence1, sequence2_t & sequence2, align_cfg::band_fixed_size
const & band)
429 requires traits_t::is_banded
437 this->allocate_matrix(sequence1, sequence2, band, this->alignment_state);
438 using row_index_t = std::ranges::range_difference_t<sequence2_t>;
439 row_index_t last_row_index = this->score_matrix.band_row_index;
440 initialise_first_alignment_column(
std::views::take(sequence2, last_row_index));
446 row_index_t sequence2_size = std::ranges::distance(sequence2);
447 for (
auto const & seq1_value :
std::views::take(sequence1, this->score_matrix.band_col_index))
449 compute_alignment_column<true>(seq1_value,
std::views::take(sequence2, ++last_row_index));
451 finalise_last_cell_in_column(last_row_index >= sequence2_size);
458 size_t first_row_index = 0;
459 for (
auto const & seq1_value :
std::views::drop(sequence1, this->score_matrix.band_col_index))
462 compute_alignment_column<false>(seq1_value, sequence2 |
views::slice(first_row_index++, ++last_row_index));
464 finalise_last_cell_in_column(last_row_index >= sequence2_size);
471 finalise_alignment();
486 template <
typename sequence2_t>
487 auto initialise_first_alignment_column(sequence2_t && sequence2)
490 alignment_column = this->current_alignment_column();
491 assert(!alignment_column.empty());
494 alignment_column_it = alignment_column.begin();
495 this->init_origin_cell(*alignment_column_it, this->alignment_state);
498 for (
auto it = std::ranges::begin(sequence2); it != std::ranges::end(sequence2); ++it)
499 this->init_column_cell(*++alignment_column_it, this->alignment_state);
502 bool at_last_row =
true;
503 if constexpr (traits_t::is_banded)
504 at_last_row =
static_cast<size_t>(this->score_matrix.band_row_index) == this->score_matrix.num_rows - 1;
506 finalise_last_cell_in_column(at_last_row);
524 template <
bool initialise_first_cell,
typename sequence1_value_t,
typename sequence2_t>
525 void compute_alignment_column(sequence1_value_t
const & seq1_value, sequence2_t && sequence2)
527 this->next_alignment_column();
528 alignment_column = this->current_alignment_column();
529 alignment_column_it = alignment_column.begin();
533 if constexpr (initialise_first_cell)
535 this->init_row_cell(*alignment_column_it, this->alignment_state);
539 this->compute_first_band_cell(*alignment_column_it,
540 this->alignment_state,
541 this->scoring_scheme.score(seq1_value, *seq2_it));
545 for (; seq2_it != std::ranges::end(sequence2); ++seq2_it)
546 this->compute_cell(*++alignment_column_it,
547 this->alignment_state,
548 this->scoring_scheme.score(seq1_value, *seq2_it));
561 constexpr void finalise_last_cell_in_column(
bool const at_last_row)
noexcept
564 this->check_score_of_last_row_cell(*alignment_column_it, this->alignment_state);
566 if constexpr (traits_t::is_debug)
567 dump_alignment_column();
571 constexpr void finalise_alignment() noexcept
577 this->check_score_of_cells_in_last_column(alignment_column, this->alignment_state);
578 this->check_score_of_last_cell(*alignment_column_it, this->alignment_state);
607 template <
typename index_t,
typename sequence1_t,
typename sequence2_t,
typename callback_t>
609 requires (!traits_t::is_vectorised)
611 constexpr void make_alignment_result([[maybe_unused]] index_t
const idx,
612 [[maybe_unused]] sequence1_t & sequence1,
613 [[maybe_unused]] sequence2_t & sequence2,
614 callback_t & callback)
616 using result_value_t =
typename alignment_result_value_type_accessor<alignment_result_t>::type;
622 static_assert(seqan3::detail::alignment_configuration_traits<config_t>::has_output_configuration,
623 "The configuration must contain at least one align_cfg::output_* element.");
625 result_value_t res{};
627 if constexpr (traits_t::output_sequence1_id)
628 res.sequence1_id = idx;
630 if constexpr (traits_t::output_sequence2_id)
631 res.sequence2_id = idx;
634 if constexpr (traits_t::compute_score)
635 res.score = this->alignment_state.optimum.score;
637 if constexpr (traits_t::compute_end_positions)
639 using alignment_coordinate_t = detail::advanceable_alignment_coordinate<>;
640 res.end_positions = alignment_coordinate_t{column_index_type{this->alignment_state.optimum.column_index},
641 row_index_type{this->alignment_state.optimum.row_index}};
643 if constexpr (traits_t::is_banded)
644 res.end_positions.second += res.end_positions.first - this->trace_matrix.band_col_index;
647 if constexpr (traits_t::compute_begin_positions)
650 aligned_sequence_builder builder{sequence1, sequence2};
652 detail::matrix_coordinate
const optimum_coordinate
654 detail::row_index_type{this->alignment_state.optimum.row_index},
655 detail::column_index_type{this->alignment_state.optimum.column_index}
657 auto trace_res = builder(this->trace_matrix.trace_path(optimum_coordinate));
658 res.begin_positions.first = trace_res.first_sequence_slice_positions.first;
659 res.begin_positions.second = trace_res.second_sequence_slice_positions.first;
661 if constexpr (traits_t::compute_sequence_alignment)
662 res.alignment = std::move(trace_res.alignment);
666 if constexpr (traits_t::is_debug)
668 res.score_debug_matrix = std::move(score_debug_matrix);
669 if constexpr (traits_t::compute_sequence_alignment)
670 res.trace_debug_matrix = std::move(trace_debug_matrix);
673 callback(std::move(res));
701 template <
typename indexed_sequence_pair_range_t,
typename callback_t>
703 requires traits_t::is_vectorised
705 constexpr auto make_alignment_result(indexed_sequence_pair_range_t && index_sequence_pairs,
706 callback_t & callback)
708 using result_value_t =
typename alignment_result_value_type_accessor<alignment_result_t>::type;
710 size_t simd_index = 0;
711 for (
auto && [sequence_pairs, alignment_index] : index_sequence_pairs)
713 (void) sequence_pairs;
714 result_value_t res{};
716 if constexpr (traits_t::output_sequence1_id)
717 res.sequence1_id = alignment_index;
719 if constexpr (traits_t::output_sequence2_id)
720 res.sequence2_id = alignment_index;
722 if constexpr (traits_t::compute_score)
723 res.score = this->alignment_state.optimum.score[simd_index];
725 if constexpr (traits_t::compute_end_positions)
727 res.end_positions.first = this->alignment_state.optimum.column_index[simd_index];
728 res.end_positions.second = this->alignment_state.optimum.row_index[simd_index];
731 callback(std::move(res));
744 void dump_alignment_column()
748 auto column = this->current_alignment_column();
750 auto coord = get<1>(column.front()).coordinate;
751 if constexpr (traits_t::is_banded)
752 coord.second += coord.first - this->score_matrix.band_col_index;
754 matrix_offset offset{row_index_type{
static_cast<std::ptrdiff_t>(coord.second)},
760 return get<0>(tpl).current;
761 }), score_debug_matrix.begin() +
offset);
764 if constexpr (traits_t::compute_sequence_alignment)
766 auto trace_matrix_it = trace_debug_matrix.begin() +
offset;
770 return get<1>(tpl).current;
771 }), trace_debug_matrix.begin() +
offset);
778 alignment_column_t alignment_column{};
780 alignment_column_iterator_t alignment_column_it{};
782 score_debug_matrix_t score_debug_matrix{};
784 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:392
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:412
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:495
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition: slice.hpp:183
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.