19 #include <type_traits>
40 namespace seqan3::detail
76 template <
typename config_t,
typename ...algorithm_policies_t>
77 class alignment_algorithm :
78 public invoke_deferred_crtp_base<algorithm_policies_t, alignment_algorithm<config_t, algorithm_policies_t...>>...
83 using traits_t = alignment_configuration_traits<config_t>;
85 using alignment_column_t = decltype(std::declval<alignment_algorithm>().current_alignment_column());
87 using alignment_column_iterator_t = std::ranges::iterator_t<alignment_column_t>;
89 using alignment_result_t =
typename traits_t::alignment_result_type;
91 static_assert(!std::same_as<alignment_result_t, empty_type>,
"Alignment result type was not configured.");
94 using score_debug_matrix_t =
96 two_dimensional_matrix<std::optional<typename traits_t::original_score_type>,
98 matrix_major_order::column>,
101 using trace_debug_matrix_t =
103 two_dimensional_matrix<std::optional<trace_directions>,
105 matrix_major_order::column>,
112 constexpr alignment_algorithm() =
default;
113 constexpr alignment_algorithm(alignment_algorithm
const &) =
default;
114 constexpr alignment_algorithm(alignment_algorithm &&) =
default;
115 constexpr alignment_algorithm & operator=(alignment_algorithm
const &) =
default;
116 constexpr alignment_algorithm & operator=(alignment_algorithm &&) =
default;
117 ~alignment_algorithm() =
default;
127 explicit constexpr alignment_algorithm(config_t
const & cfg) :
128 invoke_deferred_crtp_base<algorithm_policies_t, alignment_algorithm<config_t, algorithm_policies_t...>>{cfg}...,
129 cfg_ptr{std::make_shared<config_t>(cfg)}
131 this->scoring_scheme = seqan3::get<align_cfg::scoring_scheme>(*cfg_ptr).scheme;
132 this->initialise_alignment_state(*cfg_ptr);
181 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
183 requires (!traits_t::is_vectorised) && std::invocable<callback_t, alignment_result_t>
185 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
189 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
190 compute_single_pair(idx, get<0>(sequence_pair), get<1>(sequence_pair), callback);
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)
200 assert(cfg_ptr !=
nullptr);
202 static_assert(simd_concept<typename traits_t::score_type>,
"Expected simd score type.");
203 static_assert(simd_concept<typename traits_t::trace_type>,
"Expected simd trace type.");
206 auto sequence1_range = indexed_sequence_pairs | views::elements<0> | views::elements<0>;
207 auto sequence2_range = indexed_sequence_pairs | views::elements<0> | views::elements<1>;
210 this->initialise_find_optimum_policy(sequence1_range,
212 this->scoring_scheme.padding_match_score());
215 auto simd_sequences1 = convert_batch_of_sequences_to_simd_vector(sequence1_range);
216 auto simd_sequences2 = convert_batch_of_sequences_to_simd_vector(sequence2_range);
218 max_size_in_collection =
std::pair{simd_sequences1.size(), simd_sequences2.size()};
220 this->alignment_state.reset_optimum();
222 compute_matrix(simd_sequences1, simd_sequences2);
224 make_alignment_result(indexed_sequence_pairs, callback);
242 template <
typename sequence_range_t>
243 constexpr
auto convert_batch_of_sequences_to_simd_vector(sequence_range_t & sequences)
245 assert(
static_cast<size_t>(std::ranges::distance(sequences)) <= traits_t::alignments_per_vector);
247 using simd_score_t =
typename traits_t::score_type;
249 std::vector<simd_score_t, aligned_allocator<simd_score_t,
alignof(simd_score_t)>> simd_sequence{};
251 for (
auto && simd_vector_chunk : sequences | views::to_simd<simd_score_t>(this->scoring_scheme.padding_symbol))
252 for (
auto && simd_vector : simd_vector_chunk)
255 return simd_sequence;
275 template <std::ranges::forward_range sequence1_t,
276 std::ranges::forward_range sequence2_t,
278 constexpr
void compute_single_pair(
size_t const idx,
279 sequence1_t && sequence1,
280 sequence2_t && sequence2,
281 callback_t & callback)
283 assert(cfg_ptr !=
nullptr);
285 if constexpr (traits_t::is_debug)
286 initialise_debug_matrices(sequence1, sequence2);
289 this->alignment_state.reset_optimum();
291 if constexpr (traits_t::is_banded)
295 auto const & band = get<align_cfg::band_fixed_size>(*cfg_ptr);
296 check_valid_band_parameter(sequence1, sequence2, band);
297 auto && [subsequence1, subsequence2] = this->slice_sequences(sequence1, sequence2, band);
299 compute_matrix(subsequence1, subsequence2, band);
300 make_alignment_result(idx, subsequence1, subsequence2, callback);
304 compute_matrix(sequence1, sequence2);
305 make_alignment_result(idx, sequence1, sequence2, callback);
325 template <
typename sequence1_t,
typename sequence2_t>
326 constexpr
void check_valid_band_parameter(sequence1_t && sequence1,
327 sequence2_t && sequence2,
328 align_cfg::band_fixed_size
const & band)
330 static_assert(config_t::template exists<align_cfg::band_fixed_size>(),
331 "The band configuration is required for the banded alignment algorithm.");
334 static_assert(std::is_signed_v<diff_type>,
"Only signed types can be used to test the band parameters.");
336 if (
static_cast<diff_type
>(band.lower_diagonal) > std::ranges::distance(sequence1))
338 throw invalid_alignment_configuration
340 "Invalid band error: The lower diagonal excludes the whole alignment matrix."
344 if (
static_cast<diff_type
>(band.upper_diagonal) < -std::ranges::distance(sequence2))
346 throw invalid_alignment_configuration
348 "Invalid band error: The upper diagonal excludes the whole alignment matrix."
365 template <
typename sequence1_t,
typename sequence2_t>
366 constexpr
void initialise_debug_matrices(sequence1_t & sequence1, sequence2_t & sequence2)
368 size_t rows = std::ranges::distance(sequence2) + 1;
369 size_t cols = std::ranges::distance(sequence1) + 1;
371 score_debug_matrix = score_debug_matrix_t{number_rows{rows}, number_cols{cols}};
372 trace_debug_matrix = trace_debug_matrix_t{number_rows{rows}, number_cols{cols}};
382 template <
typename sequence1_t,
typename sequence2_t>
383 void compute_matrix(sequence1_t & sequence1, sequence2_t & sequence2)
385 requires (!traits_t::is_banded)
392 this->allocate_matrix(sequence1, sequence2);
393 initialise_first_alignment_column(sequence2);
399 for (
auto const & alphabet1 : sequence1)
401 compute_alignment_column<true>(this->scoring_scheme_profile_column(alphabet1), sequence2);
402 finalise_last_cell_in_column(
true);
409 finalise_alignment();
413 template <
typename sequence1_t,
typename sequence2_t>
414 void compute_matrix(sequence1_t & sequence1, sequence2_t & sequence2, align_cfg::band_fixed_size
const & band)
416 requires traits_t::is_banded
424 this->allocate_matrix(sequence1, sequence2, band, this->alignment_state);
425 using row_index_t = std::ranges::range_difference_t<sequence2_t>;
426 row_index_t last_row_index = this->score_matrix.band_row_index;
427 initialise_first_alignment_column(
std::views::take(sequence2, last_row_index));
433 row_index_t sequence2_size = std::ranges::distance(sequence2);
434 for (
auto const & seq1_value :
std::views::take(sequence1, this->score_matrix.band_col_index))
436 compute_alignment_column<true>(seq1_value,
std::views::take(sequence2, ++last_row_index));
438 finalise_last_cell_in_column(last_row_index >= sequence2_size);
445 size_t first_row_index = 0;
446 for (
auto const & seq1_value :
std::views::drop(sequence1, this->score_matrix.band_col_index))
449 compute_alignment_column<false>(seq1_value, sequence2 |
views::slice(first_row_index++, ++last_row_index));
451 finalise_last_cell_in_column(last_row_index >= sequence2_size);
458 finalise_alignment();
473 template <
typename sequence2_t>
474 auto initialise_first_alignment_column(sequence2_t && sequence2)
477 alignment_column = this->current_alignment_column();
478 assert(!alignment_column.empty());
481 alignment_column_it = alignment_column.begin();
482 this->init_origin_cell(*alignment_column_it, this->alignment_state);
485 for (
auto it = std::ranges::begin(sequence2); it != std::ranges::end(sequence2); ++it)
486 this->init_column_cell(*++alignment_column_it, this->alignment_state);
489 bool at_last_row =
true;
490 if constexpr (traits_t::is_banded)
491 at_last_row =
static_cast<size_t>(this->score_matrix.band_row_index) == this->score_matrix.num_rows - 1;
493 finalise_last_cell_in_column(at_last_row);
511 template <
bool initialise_first_cell,
typename sequence1_value_t,
typename sequence2_t>
512 void compute_alignment_column(sequence1_value_t
const & seq1_value, sequence2_t && sequence2)
514 this->next_alignment_column();
515 alignment_column = this->current_alignment_column();
516 alignment_column_it = alignment_column.begin();
520 if constexpr (initialise_first_cell)
522 this->init_row_cell(*alignment_column_it, this->alignment_state);
526 this->compute_first_band_cell(*alignment_column_it,
527 this->alignment_state,
528 this->scoring_scheme.score(seq1_value, *seq2_it));
532 for (; seq2_it != std::ranges::end(sequence2); ++seq2_it)
533 this->compute_cell(*++alignment_column_it,
534 this->alignment_state,
535 this->scoring_scheme.score(seq1_value, *seq2_it));
548 constexpr
void finalise_last_cell_in_column(
bool const at_last_row) noexcept
551 this->check_score_of_last_row_cell(*alignment_column_it, this->alignment_state);
553 if constexpr (traits_t::is_debug)
554 dump_alignment_column();
558 constexpr
void finalise_alignment() noexcept
564 this->check_score_of_cells_in_last_column(alignment_column, this->alignment_state);
565 this->check_score_of_last_cell(*alignment_column_it, this->alignment_state);
594 template <
typename index_t,
typename sequence1_t,
typename sequence2_t,
typename callback_t>
596 requires (!traits_t::is_vectorised)
598 constexpr
void make_alignment_result([[maybe_unused]] index_t
const idx,
599 [[maybe_unused]] sequence1_t & sequence1,
600 [[maybe_unused]] sequence2_t & sequence2,
601 callback_t & callback)
603 using result_value_t =
typename alignment_result_value_type_accessor<alignment_result_t>::type;
609 static_assert(seqan3::detail::alignment_configuration_traits<config_t>::has_output_configuration,
610 "The configuration must contain at least one align_cfg::output_* element.");
612 result_value_t res{};
614 if constexpr (traits_t::output_sequence1_id)
615 res.sequence1_id = idx;
617 if constexpr (traits_t::output_sequence2_id)
618 res.sequence2_id = idx;
621 if constexpr (traits_t::compute_score)
622 res.score = this->alignment_state.optimum.score;
624 if constexpr (traits_t::compute_end_positions)
626 using alignment_coordinate_t = detail::advanceable_alignment_coordinate<>;
627 res.end_positions = alignment_coordinate_t{column_index_type{this->alignment_state.optimum.column_index},
628 row_index_type{this->alignment_state.optimum.row_index}};
630 if constexpr (traits_t::is_banded)
631 res.end_positions.second += res.end_positions.first - this->trace_matrix.band_col_index;
634 if constexpr (traits_t::compute_begin_positions)
637 aligned_sequence_builder builder{sequence1, sequence2};
639 detail::matrix_coordinate
const optimum_coordinate
641 detail::row_index_type{this->alignment_state.optimum.row_index},
642 detail::column_index_type{this->alignment_state.optimum.column_index}
644 auto trace_res = builder(this->trace_matrix.trace_path(optimum_coordinate));
645 res.begin_positions.first = trace_res.first_sequence_slice_positions.first;
646 res.begin_positions.second = trace_res.second_sequence_slice_positions.first;
648 if constexpr (traits_t::compute_sequence_alignment)
649 res.alignment =
std::move(trace_res.alignment);
653 if constexpr (traits_t::is_debug)
655 res.score_debug_matrix =
std::move(score_debug_matrix);
656 if constexpr (traits_t::compute_sequence_alignment)
657 res.trace_debug_matrix =
std::move(trace_debug_matrix);
688 template <
typename indexed_sequence_pair_range_t,
typename callback_t>
690 requires traits_t::is_vectorised
692 constexpr
auto make_alignment_result(indexed_sequence_pair_range_t && index_sequence_pairs,
693 callback_t & callback)
695 using result_value_t =
typename alignment_result_value_type_accessor<alignment_result_t>::type;
697 size_t simd_index = 0;
698 for (
auto && [sequence_pairs, alignment_index] : index_sequence_pairs)
700 (void) sequence_pairs;
701 result_value_t res{};
703 if constexpr (traits_t::output_sequence1_id)
704 res.sequence1_id = alignment_index;
706 if constexpr (traits_t::output_sequence2_id)
707 res.sequence2_id = alignment_index;
709 if constexpr (traits_t::compute_score)
710 res.score = this->alignment_state.optimum.score[simd_index];
712 if constexpr (traits_t::compute_end_positions)
714 res.end_positions.first = this->alignment_state.optimum.column_index[simd_index];
715 res.end_positions.second = this->alignment_state.optimum.row_index[simd_index];
731 void dump_alignment_column()
735 auto column = this->current_alignment_column();
737 auto coord = get<1>(column.front()).coordinate;
738 if constexpr (traits_t::is_banded)
739 coord.second += coord.first - this->score_matrix.band_col_index;
747 return get<0>(tpl).current;
748 }), score_debug_matrix.begin() +
offset);
751 if constexpr (traits_t::compute_sequence_alignment)
753 auto trace_matrix_it = trace_debug_matrix.begin() +
offset;
757 return get<1>(tpl).current;
758 }), trace_debug_matrix.begin() +
offset);
765 alignment_column_t alignment_column{};
767 alignment_column_iterator_t alignment_column_it{};
769 score_debug_matrix_t score_debug_matrix{};
771 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::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 get
A view calling get on each element in a range.
Definition: elements.hpp:114
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition: slice.hpp:189
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:74
Provides C++20 additions to the <iterator> header.
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
Adaptations of concepts from the Ranges TS.
[DEPRECATED] Provides seqan3::views::take.
Provides seqan3::detail::to_simd view.
Provides the declaration of seqan3::detail::trace_directions.
Provides seqan3::aligned_allocator.
Provides seqan3::simd::simd_concept.
Provides seqan3::simd::simd_type.
Provides seqan3::simd::simd_traits.