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...>>...
81 using traits_t = alignment_configuration_traits<config_t>;
93 template <
typename alignment_algorithm_t = alignment_algorithm>
94 static auto _alignment_column_t() ->
decltype(std::declval<alignment_algorithm_t>().current_alignment_column());
97 using alignment_column_t =
decltype(_alignment_column_t());
99 using alignment_column_iterator_t = std::ranges::iterator_t<alignment_column_t>;
101 using alignment_result_t =
typename traits_t::alignment_result_type;
103 static_assert(!std::same_as<alignment_result_t, empty_type>,
"Alignment result type was not configured.");
106 using score_debug_matrix_t =
108 two_dimensional_matrix<std::optional<typename traits_t::original_score_type>,
110 matrix_major_order::column>,
113 using trace_debug_matrix_t =
115 two_dimensional_matrix<std::optional<trace_directions>,
117 matrix_major_order::column>,
124 constexpr alignment_algorithm() =
default;
125 constexpr alignment_algorithm(alignment_algorithm
const &) =
default;
126 constexpr alignment_algorithm(alignment_algorithm &&) =
default;
127 constexpr alignment_algorithm & operator=(alignment_algorithm
const &) =
default;
128 constexpr alignment_algorithm & operator=(alignment_algorithm &&) =
default;
129 ~alignment_algorithm() =
default;
139 explicit constexpr alignment_algorithm(config_t
const & cfg) :
140 invoke_deferred_crtp_base<algorithm_policies_t, alignment_algorithm<config_t, algorithm_policies_t...>>{cfg}...,
141 cfg_ptr{std::make_shared<config_t>(cfg)}
143 this->scoring_scheme = seqan3::get<align_cfg::scoring_scheme>(*cfg_ptr).scheme;
144 this->initialise_alignment_state(*cfg_ptr);
193 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
194 requires (!traits_t::is_vectorised) && std::invocable<callback_t, alignment_result_t>
195 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
199 for (
auto && [sequence_pair, idx] : indexed_sequence_pairs)
200 compute_single_pair(idx, get<0>(sequence_pair), get<1>(sequence_pair), callback);
204 template <indexed_sequence_pair_range indexed_sequence_pairs_t,
typename callback_t>
205 requires traits_t::is_vectorised && std::invocable<callback_t, alignment_result_t>
206 void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
208 assert(cfg_ptr !=
nullptr);
210 static_assert(simd_concept<typename traits_t::score_type>,
"Expected simd score type.");
211 static_assert(simd_concept<typename traits_t::trace_type>,
"Expected simd trace type.");
214 auto sequence1_range = indexed_sequence_pairs | views::elements<0> | views::elements<0>;
215 auto sequence2_range = indexed_sequence_pairs | views::elements<0> | views::elements<1>;
218 this->initialise_find_optimum_policy(sequence1_range,
220 this->scoring_scheme.padding_match_score());
223 auto simd_sequences1 = convert_batch_of_sequences_to_simd_vector(sequence1_range);
224 auto simd_sequences2 = convert_batch_of_sequences_to_simd_vector(sequence2_range);
226 max_size_in_collection =
std::pair{simd_sequences1.size(), simd_sequences2.size()};
228 this->alignment_state.reset_optimum();
230 compute_matrix(simd_sequences1, simd_sequences2);
232 make_alignment_result(indexed_sequence_pairs, callback);
250 template <
typename sequence_range_t>
251 constexpr auto convert_batch_of_sequences_to_simd_vector(sequence_range_t & sequences)
253 assert(
static_cast<size_t>(std::ranges::distance(sequences)) <= traits_t::alignments_per_vector);
255 using simd_score_t =
typename traits_t::score_type;
257 std::vector<simd_score_t, aligned_allocator<simd_score_t,
alignof(simd_score_t)>> simd_sequence{};
259 for (
auto && simd_vector_chunk : sequences | views::to_simd<simd_score_t>(this->scoring_scheme.padding_symbol))
260 for (
auto && simd_vector : simd_vector_chunk)
261 simd_sequence.
push_back(std::move(simd_vector));
263 return simd_sequence;
283 template <std::ranges::forward_range sequence1_t, std::ranges::forward_range sequence2_t,
typename callback_t>
285 compute_single_pair(
size_t const idx, sequence1_t && sequence1, sequence2_t && sequence2, callback_t & callback)
287 assert(cfg_ptr !=
nullptr);
289 if constexpr (traits_t::is_debug)
290 initialise_debug_matrices(sequence1, sequence2);
293 this->alignment_state.reset_optimum();
295 if constexpr (traits_t::is_banded)
299 auto const & band = get<align_cfg::band_fixed_size>(*cfg_ptr);
300 check_valid_band_parameter(sequence1, sequence2, band);
301 auto && [subsequence1, subsequence2] = this->slice_sequences(sequence1, sequence2, band);
303 compute_matrix(subsequence1, subsequence2, band);
304 make_alignment_result(idx, subsequence1, subsequence2, callback);
308 compute_matrix(sequence1, sequence2);
309 make_alignment_result(idx, sequence1, sequence2, callback);
329 template <
typename sequence1_t,
typename sequence2_t>
330 constexpr void check_valid_band_parameter(sequence1_t && sequence1,
331 sequence2_t && sequence2,
332 align_cfg::band_fixed_size
const & band)
334 static_assert(config_t::template exists<align_cfg::band_fixed_size>(),
335 "The band configuration is required for the banded alignment algorithm.");
338 static_assert(std::is_signed_v<diff_type>,
"Only signed types can be used to test the band parameters.");
340 if (
static_cast<diff_type
>(band.lower_diagonal) > std::ranges::distance(sequence1))
342 throw invalid_alignment_configuration{
343 "Invalid band error: The lower diagonal excludes the whole alignment matrix."};
346 if (
static_cast<diff_type
>(band.upper_diagonal) < -std::ranges::distance(sequence2))
348 throw invalid_alignment_configuration{
349 "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)
384 requires (!traits_t::is_banded)
390 this->allocate_matrix(sequence1, sequence2);
391 initialise_first_alignment_column(sequence2);
397 for (
auto const & alphabet1 : sequence1)
399 compute_alignment_column<true>(this->scoring_scheme_profile_column(alphabet1), sequence2);
400 finalise_last_cell_in_column(
true);
407 finalise_alignment();
411 template <
typename sequence1_t,
typename sequence2_t>
412 void compute_matrix(sequence1_t & sequence1, sequence2_t & sequence2, align_cfg::band_fixed_size
const & band)
413 requires (traits_t::is_banded)
420 this->allocate_matrix(sequence1, sequence2, band, this->alignment_state);
421 using row_index_t = std::ranges::range_difference_t<sequence2_t>;
422 row_index_t last_row_index = this->score_matrix.band_row_index;
423 initialise_first_alignment_column(
std::views::take(sequence2, last_row_index));
429 row_index_t sequence2_size = std::ranges::distance(sequence2);
430 for (
auto const & seq1_value :
std::views::take(sequence1, this->score_matrix.band_col_index))
432 compute_alignment_column<true>(seq1_value,
std::views::take(sequence2, ++last_row_index));
434 finalise_last_cell_in_column(last_row_index >= sequence2_size);
441 size_t first_row_index = 0;
442 for (
auto const & seq1_value :
std::views::drop(sequence1, this->score_matrix.band_col_index))
445 compute_alignment_column<false>(seq1_value, sequence2 |
views::slice(first_row_index++, ++last_row_index));
447 finalise_last_cell_in_column(last_row_index >= sequence2_size);
454 finalise_alignment();
469 template <
typename sequence2_t>
470 auto initialise_first_alignment_column(sequence2_t && sequence2)
473 alignment_column = this->current_alignment_column();
474 assert(!alignment_column.empty());
477 alignment_column_it = alignment_column.begin();
478 this->init_origin_cell(*alignment_column_it, this->alignment_state);
481 for (
auto it =
std::ranges::begin(sequence2); it != std::ranges::end(sequence2); ++it)
482 this->init_column_cell(*++alignment_column_it, this->alignment_state);
485 bool at_last_row =
true;
486 if constexpr (traits_t::is_banded)
487 at_last_row =
static_cast<size_t>(this->score_matrix.band_row_index) == this->score_matrix.num_rows - 1;
489 finalise_last_cell_in_column(at_last_row);
507 template <
bool initialise_first_cell,
typename sequence1_value_t,
typename sequence2_t>
508 void compute_alignment_column(sequence1_value_t
const & seq1_value, sequence2_t && sequence2)
510 this->next_alignment_column();
511 alignment_column = this->current_alignment_column();
512 alignment_column_it = alignment_column.begin();
516 if constexpr (initialise_first_cell)
518 this->init_row_cell(*alignment_column_it, this->alignment_state);
522 this->compute_first_band_cell(*alignment_column_it,
523 this->alignment_state,
524 this->scoring_scheme.score(seq1_value, *seq2_it));
528 for (; seq2_it != std::ranges::end(sequence2); ++seq2_it)
529 this->compute_cell(*++alignment_column_it,
530 this->alignment_state,
531 this->scoring_scheme.score(seq1_value, *seq2_it));
544 constexpr void finalise_last_cell_in_column(
bool const at_last_row)
noexcept
547 this->check_score_of_last_row_cell(*alignment_column_it, this->alignment_state);
549 if constexpr (traits_t::is_debug)
550 dump_alignment_column();
554 constexpr void finalise_alignment() noexcept
560 this->check_score_of_cells_in_last_column(alignment_column, this->alignment_state);
561 this->check_score_of_last_cell(*alignment_column_it, this->alignment_state);
590 template <
typename index_t,
typename sequence1_t,
typename sequence2_t,
typename callback_t>
591 requires (!traits_t::is_vectorised)
592 constexpr void make_alignment_result([[maybe_unused]] index_t
const idx,
593 [[maybe_unused]] sequence1_t & sequence1,
594 [[maybe_unused]] sequence2_t & sequence2,
595 callback_t & callback)
597 using result_value_t =
typename alignment_result_value_type_accessor<alignment_result_t>::type;
603 static_assert(seqan3::detail::alignment_configuration_traits<config_t>::has_output_configuration,
604 "The configuration must contain at least one align_cfg::output_* element.");
606 result_value_t res{};
608 if constexpr (traits_t::output_sequence1_id)
609 res.sequence1_id = idx;
611 if constexpr (traits_t::output_sequence2_id)
612 res.sequence2_id = idx;
615 if constexpr (traits_t::compute_score)
616 res.score = this->alignment_state.optimum.score;
618 if constexpr (traits_t::compute_end_positions)
620 using alignment_coordinate_t = detail::advanceable_alignment_coordinate<>;
621 res.end_positions = alignment_coordinate_t{column_index_type{this->alignment_state.optimum.column_index},
622 row_index_type{this->alignment_state.optimum.row_index}};
624 if constexpr (traits_t::is_banded)
625 res.end_positions.second += res.end_positions.first - this->trace_matrix.band_col_index;
628 if constexpr (traits_t::compute_begin_positions)
631 aligned_sequence_builder builder{sequence1, sequence2};
633 detail::matrix_coordinate
const optimum_coordinate{
634 detail::row_index_type{this->alignment_state.optimum.row_index},
635 detail::column_index_type{this->alignment_state.optimum.column_index}};
636 auto trace_res = builder(this->trace_matrix.trace_path(optimum_coordinate));
637 res.begin_positions.first = trace_res.first_sequence_slice_positions.first;
638 res.begin_positions.second = trace_res.second_sequence_slice_positions.first;
640 if constexpr (traits_t::compute_sequence_alignment)
641 res.alignment = std::move(trace_res.alignment);
645 if constexpr (traits_t::is_debug)
647 res.score_debug_matrix = std::move(score_debug_matrix);
648 if constexpr (traits_t::compute_sequence_alignment)
649 res.trace_debug_matrix = std::move(trace_debug_matrix);
652 callback(std::move(res));
680 template <
typename indexed_sequence_pair_range_t,
typename callback_t>
681 requires traits_t::is_vectorised
682 constexpr auto make_alignment_result(indexed_sequence_pair_range_t && index_sequence_pairs, callback_t & callback)
684 using result_value_t =
typename alignment_result_value_type_accessor<alignment_result_t>::type;
686 size_t simd_index = 0;
687 for (
auto && [sequence_pairs, alignment_index] : index_sequence_pairs)
689 (void)sequence_pairs;
690 result_value_t res{};
692 if constexpr (traits_t::output_sequence1_id)
693 res.sequence1_id = alignment_index;
695 if constexpr (traits_t::output_sequence2_id)
696 res.sequence2_id = alignment_index;
698 if constexpr (traits_t::compute_score)
699 res.score = this->alignment_state.optimum.score[simd_index];
701 if constexpr (traits_t::compute_end_positions)
703 res.end_positions.first = this->alignment_state.optimum.column_index[simd_index];
704 res.end_positions.second = this->alignment_state.optimum.row_index[simd_index];
707 callback(std::move(res));
720 void dump_alignment_column()
724 auto column = this->current_alignment_column();
726 auto coord = get<1>(column.front()).coordinate;
727 if constexpr (traits_t::is_banded)
728 coord.second += coord.first - this->score_matrix.band_col_index;
730 matrix_offset offset{row_index_type{
static_cast<std::ptrdiff_t>(coord.second)},
738 return get<0>(tpl).current;
740 score_debug_matrix.begin() +
offset);
743 if constexpr (traits_t::compute_sequence_alignment)
745 auto trace_matrix_it = trace_debug_matrix.begin() +
offset;
751 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::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:377
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:395
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:470
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition: slice.hpp:178
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:415
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.