19 #include <type_traits>
41 namespace seqan3::detail
77 template <
typename config_t,
typename ...algorithm_policies_t>
78 class alignment_algorithm :
79 public invoke_deferred_crtp_base<algorithm_policies_t, alignment_algorithm<config_t, algorithm_policies_t...>>...
84 using traits_t = alignment_configuration_traits<config_t>;
86 using alignment_column_t = decltype(std::declval<alignment_algorithm>().current_alignment_column());
88 using alignment_column_iterator_t = std::ranges::iterator_t<alignment_column_t>;
90 using alignment_result_t =
typename traits_t::alignment_result_type;
92 static_assert(!std::same_as<alignment_result_t, empty_type>,
"Alignment result type was not configured.");
95 using score_debug_matrix_t =
97 two_dimensional_matrix<std::optional<typename traits_t::original_score_type>,
99 matrix_major_order::column>,
102 using trace_debug_matrix_t =
104 two_dimensional_matrix<std::optional<trace_directions>,
106 matrix_major_order::column>,
113 constexpr alignment_algorithm() =
default;
114 constexpr alignment_algorithm(alignment_algorithm
const &) =
default;
115 constexpr alignment_algorithm(alignment_algorithm &&) =
default;
116 constexpr alignment_algorithm & operator=(alignment_algorithm
const &) =
default;
117 constexpr alignment_algorithm & operator=(alignment_algorithm &&) =
default;
118 ~alignment_algorithm() =
default;
128 explicit constexpr alignment_algorithm(config_t
const & cfg) :
129 invoke_deferred_crtp_base<algorithm_policies_t, alignment_algorithm<config_t, algorithm_policies_t...>>{cfg}...,
130 cfg_ptr{std::make_shared<config_t>(cfg)}
132 this->scoring_scheme = seqan3::get<align_cfg::scoring_scheme>(*cfg_ptr).scheme;
133 this->initialise_alignment_state(*cfg_ptr);
182 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
184 requires (!traits_t::is_vectorised) && std::invocable<callback_t, alignment_result_t>
186 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
190 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
191 compute_single_pair(idx, get<0>(sequence_pair), get<1>(sequence_pair), callback);
195 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
197 requires traits_t::is_vectorised && std::invocable<callback_t, alignment_result_t>
199 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
201 assert(cfg_ptr !=
nullptr);
203 static_assert(simd_concept<typename traits_t::score_type>,
"Expected simd score type.");
204 static_assert(simd_concept<typename traits_t::trace_type>,
"Expected simd trace type.");
207 auto sequence1_range = indexed_sequence_pairs | views::elements<0> | views::elements<0>;
208 auto sequence2_range = indexed_sequence_pairs | views::elements<0> | views::elements<1>;
211 this->initialise_find_optimum_policy(sequence1_range,
213 this->scoring_scheme.padding_match_score());
216 auto simd_sequences1 = convert_batch_of_sequences_to_simd_vector(sequence1_range);
217 auto simd_sequences2 = convert_batch_of_sequences_to_simd_vector(sequence2_range);
219 max_size_in_collection =
std::pair{simd_sequences1.size(), simd_sequences2.size()};
221 this->alignment_state.reset_optimum();
223 compute_matrix(simd_sequences1, simd_sequences2);
225 make_alignment_result(indexed_sequence_pairs, callback);
243 template <
typename sequence_range_t>
244 constexpr
auto convert_batch_of_sequences_to_simd_vector(sequence_range_t & sequences)
246 assert(
static_cast<size_t>(std::ranges::distance(sequences)) <= traits_t::alignments_per_vector);
248 using simd_score_t =
typename traits_t::score_type;
250 std::vector<simd_score_t, aligned_allocator<simd_score_t,
alignof(simd_score_t)>> simd_sequence{};
252 for (
auto && simd_vector_chunk : sequences | views::to_simd<simd_score_t>(this->scoring_scheme.padding_symbol))
253 for (
auto && simd_vector : simd_vector_chunk)
256 return simd_sequence;
276 template <std::ranges::forward_range sequence1_t,
277 std::ranges::forward_range sequence2_t,
279 constexpr
void compute_single_pair(
size_t const idx,
280 sequence1_t && sequence1,
281 sequence2_t && sequence2,
282 callback_t & callback)
284 assert(cfg_ptr !=
nullptr);
286 if constexpr (traits_t::is_debug)
287 initialise_debug_matrices(sequence1, sequence2);
290 this->alignment_state.reset_optimum();
292 if constexpr (traits_t::is_banded)
296 auto const & band = get<align_cfg::band_fixed_size>(*cfg_ptr);
297 check_valid_band_parameter(sequence1, sequence2, band);
298 auto && [subsequence1, subsequence2] = this->slice_sequences(sequence1, sequence2, band);
300 compute_matrix(subsequence1, subsequence2, band);
301 make_alignment_result(idx, subsequence1, subsequence2, callback);
305 compute_matrix(sequence1, sequence2);
306 make_alignment_result(idx, sequence1, sequence2, callback);
326 template <
typename sequence1_t,
typename sequence2_t>
327 constexpr
void check_valid_band_parameter(sequence1_t && sequence1,
328 sequence2_t && sequence2,
329 align_cfg::band_fixed_size
const & band)
331 static_assert(config_t::template exists<align_cfg::band_fixed_size>(),
332 "The band configuration is required for the banded alignment algorithm.");
335 static_assert(std::is_signed_v<diff_type>,
"Only signed types can be used to test the band parameters.");
337 if (
static_cast<diff_type
>(band.lower_diagonal) > std::ranges::distance(sequence1))
339 throw invalid_alignment_configuration
341 "Invalid band error: The lower diagonal excludes the whole alignment matrix."
345 if (
static_cast<diff_type
>(band.upper_diagonal) < -std::ranges::distance(sequence2))
347 throw invalid_alignment_configuration
349 "Invalid band error: The upper diagonal excludes the whole alignment matrix."
366 template <
typename sequence1_t,
typename sequence2_t>
367 constexpr
void initialise_debug_matrices(sequence1_t & sequence1, sequence2_t & sequence2)
369 size_t rows = std::ranges::distance(sequence2) + 1;
370 size_t cols = std::ranges::distance(sequence1) + 1;
372 score_debug_matrix = score_debug_matrix_t{number_rows{rows}, number_cols{cols}};
373 trace_debug_matrix = trace_debug_matrix_t{number_rows{rows}, number_cols{cols}};
383 template <
typename sequence1_t,
typename sequence2_t>
384 void compute_matrix(sequence1_t & sequence1, sequence2_t & sequence2)
386 requires (!traits_t::is_banded)
393 this->allocate_matrix(sequence1, sequence2);
394 initialise_first_alignment_column(sequence2);
400 for (
auto const & alphabet1 : sequence1)
402 compute_alignment_column<true>(this->scoring_scheme_profile_column(alphabet1), sequence2);
403 finalise_last_cell_in_column(
true);
410 finalise_alignment();
414 template <
typename sequence1_t,
typename sequence2_t>
415 void compute_matrix(sequence1_t & sequence1, sequence2_t & sequence2, align_cfg::band_fixed_size
const & band)
417 requires traits_t::is_banded
425 this->allocate_matrix(sequence1, sequence2, band, this->alignment_state);
426 size_t last_row_index = this->score_matrix.band_row_index;
427 initialise_first_alignment_column(sequence2 |
views::take(last_row_index));
433 size_t sequence2_size = std::ranges::distance(sequence2);
434 for (
auto const & seq1_value : sequence1 |
views::take(this->score_matrix.band_col_index))
436 compute_alignment_column<true>(seq1_value, sequence2 |
views::take(++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 : sequence1 |
std::views::drop(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 res.end_positions = alignment_coordinate{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};
637 auto optimum_coordinate = alignment_coordinate{column_index_type{this->alignment_state.optimum.column_index},
638 row_index_type{this->alignment_state.optimum.row_index}};
639 auto trace_res = builder(this->trace_matrix.trace_path(optimum_coordinate));
640 res.begin_positions.first = trace_res.first_sequence_slice_positions.first;
641 res.begin_positions.second = trace_res.second_sequence_slice_positions.first;
643 if constexpr (traits_t::compute_sequence_alignment)
644 res.alignment =
std::move(trace_res.alignment);
648 if constexpr (traits_t::is_debug)
650 res.score_debug_matrix =
std::move(score_debug_matrix);
651 if constexpr (traits_t::compute_sequence_alignment)
652 res.trace_debug_matrix =
std::move(trace_debug_matrix);
683 template <
typename indexed_sequence_pair_range_t,
typename callback_t>
685 requires traits_t::is_vectorised
687 constexpr
auto make_alignment_result(indexed_sequence_pair_range_t && index_sequence_pairs,
688 callback_t & callback)
690 using result_value_t =
typename alignment_result_value_type_accessor<alignment_result_t>::type;
692 size_t simd_index = 0;
693 for (
auto && [sequence_pairs, alignment_index] : index_sequence_pairs)
695 (void) sequence_pairs;
696 result_value_t res{};
698 if constexpr (traits_t::output_sequence1_id)
699 res.sequence1_id = alignment_index;
701 if constexpr (traits_t::output_sequence2_id)
702 res.sequence2_id = alignment_index;
704 if constexpr (traits_t::compute_score)
705 res.score = this->alignment_state.optimum.score[simd_index];
707 if constexpr (traits_t::compute_end_positions)
709 res.end_positions.first = this->alignment_state.optimum.column_index[simd_index];
710 res.end_positions.second = this->alignment_state.optimum.row_index[simd_index];
726 void dump_alignment_column()
730 auto column = this->current_alignment_column();
732 auto coord = get<1>(column.front()).coordinate;
733 if constexpr (traits_t::is_banded)
734 coord.second += coord.first - this->score_matrix.band_col_index;
742 return get<0>(tpl).current;
743 }), score_debug_matrix.begin() +
offset);
746 if constexpr (traits_t::compute_sequence_alignment)
748 auto trace_matrix_it = trace_debug_matrix.begin() +
offset;
752 return get<1>(tpl).current;
753 }), trace_debug_matrix.begin() +
offset);
760 alignment_column_t alignment_column{};
762 alignment_column_iterator_t alignment_column_it{};
764 score_debug_matrix_t score_debug_matrix{};
766 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::drop.
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{}))::second_type drop
Return a seqan3::type_list of the types in the input type list, except the first n.
Definition: traits.hpp:351
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:434
constexpr auto get
A view calling get on each element in a range.
Definition: get.hpp:26
constexpr auto take
A view adaptor that returns the first size elements from the underlying range (or less if the underly...
Definition: take.hpp:611
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition: slice.hpp:191
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:70
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:434
Adaptations of concepts from the Ranges TS.
Provides seqan3::views::take.
Provides seqan3::detail::to_simd view.
Provides the declaration of seqan3::detail::trace_directions.
Provides seqan3::simd::simd_concept.
Provides seqan3::simd::simd_type.
Provides seqan3::simd::simd_traits.