25namespace seqan3::detail
30template <
typename derived_t,
typename edit_traits>
31class edit_distance_unbanded_max_errors_policy :
37 static_assert(edit_traits::use_max_errors,
"This policy assumes that edit_traits::use_max_errors is true.");
45 edit_distance_unbanded_max_errors_policy() noexcept = default;
46 edit_distance_unbanded_max_errors_policy(edit_distance_unbanded_max_errors_policy const &) noexcept =
48 edit_distance_unbanded_max_errors_policy(edit_distance_unbanded_max_errors_policy &&) noexcept =
50 edit_distance_unbanded_max_errors_policy &
51 operator=(edit_distance_unbanded_max_errors_policy const &) noexcept = default;
52 edit_distance_unbanded_max_errors_policy &
53 operator=(edit_distance_unbanded_max_errors_policy &&) noexcept = default;
54 ~edit_distance_unbanded_max_errors_policy() noexcept = default;
58 using typename edit_traits::score_type;
59 using typename edit_traits::word_type;
66 score_type max_errors{255};
68 size_t last_block{0u};
70 word_type last_score_mask{};
78 void max_errors_init(
size_t block_count)
noexcept
80 derived_t * self =
static_cast<derived_t *
>(
this);
82 max_errors = -get<align_cfg::min_score>(self->config).score;
84 assert(max_errors >= score_type{0});
86 if (std::ranges::empty(self->query))
89 self->score_mask = 0u;
90 last_score_mask = self->score_mask;
94 last_block = block_count - 1u;
95 last_score_mask = self->score_mask;
100 size_t const local_max_errors = std::min<size_t>(max_errors, std::ranges::size(self->query) - 1u);
101 self->score_mask = word_type{1u} << (local_max_errors % self->word_size);
102 last_block =
std::min(local_max_errors / self->word_size, last_block);
103 self->_score = local_max_errors + 1u;
107 bool is_last_active_cell_within_last_row() const noexcept
109 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
110 return (self->score_mask == this->last_score_mask) && (this->last_block == self->vp.size() - 1u);
114 bool prev_last_active_cell() noexcept
116 derived_t * self =
static_cast<derived_t *
>(
this);
117 self->score_mask >>= 1u;
118 if (self->score_mask != 0u)
121 if constexpr (edit_traits::is_global)
123 if (last_block == 0u)
129 self->score_mask = word_type{1u} << (edit_traits::word_size - 1u);
134 void next_last_active_cell() noexcept
136 derived_t * self =
static_cast<derived_t *
>(
this);
137 self->score_mask <<= 1u;
138 if (self->score_mask)
141 self->score_mask = 1u;
148 bool update_last_active_cell() noexcept
150 derived_t * self =
static_cast<derived_t *
>(
this);
152 while (!(self->_score <= max_errors))
154 self->advance_score(self->vn[last_block], self->vp[last_block], self->score_mask);
155 if (!prev_last_active_cell())
158 assert(edit_traits::is_global);
161 return !edit_traits::compute_matrix;
165 if (is_last_active_cell_within_last_row())
167 assert(self->_score <= max_errors);
169 if constexpr (edit_traits::is_semi_global)
170 self->update_best_score();
172 return self->on_hit();
176 next_last_active_cell();
177 self->advance_score(self->vp[last_block], self->vn[last_block], self->score_mask);
185 static size_t max_rows(word_type
const score_mask,
186 unsigned const last_block,
187 score_type
const score,
188 score_type
const max_errors)
noexcept
190 using score_matrix_type =
typename edit_traits::score_matrix_type;
191 return score_matrix_type::max_rows(score_mask, last_block, score, max_errors);
198template <
typename derived_t,
typename edit_traits>
199class edit_distance_unbanded_global_policy :
205 static_assert(edit_traits::is_global || edit_traits::is_semi_global,
206 "This policy assumes that edit_traits::is_global or edit_traits::is_semi_global is true.");
214 edit_distance_unbanded_global_policy() noexcept = default;
215 edit_distance_unbanded_global_policy(edit_distance_unbanded_global_policy const &) noexcept =
217 edit_distance_unbanded_global_policy(edit_distance_unbanded_global_policy &&) noexcept = default;
218 edit_distance_unbanded_global_policy &
219 operator=(edit_distance_unbanded_global_policy const &) noexcept = default;
220 edit_distance_unbanded_global_policy &
221 operator=(edit_distance_unbanded_global_policy &&) noexcept = default;
222 ~edit_distance_unbanded_global_policy() noexcept = default;
227 using typename edit_traits::score_type;
237 score_type _best_score{};
245 void score_init() noexcept
247 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
248 _best_score = self->_score;
252 bool is_valid() const noexcept
254 [[maybe_unused]] derived_t
const * self =
static_cast<derived_t
const *
>(
this);
259 if constexpr (edit_traits::use_max_errors)
260 return _best_score <= self->max_errors;
268 seqan3::detail::advanceable_alignment_coordinate<> invalid_coordinate() const noexcept
270 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
271 return {column_index_type{std::ranges::size(self->database)}, row_index_type{std::ranges::size(self->query)}};
275 void update_best_score() noexcept
277 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
278 _best_score = self->_score;
282 size_t end_positions_first() const noexcept
284 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
285 return std::ranges::size(self->database);
298 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
299 static_assert(edit_traits::compute_score,
300 "score() can only be computed if you specify the result type within "
301 "your alignment config.");
302 if (!self->is_valid())
310 seqan3::detail::advanceable_alignment_coordinate<> end_positions() const noexcept
312 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
313 static_assert(edit_traits::compute_end_positions,
314 "end_positions() can only be computed if you specify the "
315 "result type within your alignment config.");
316 if (!self->is_valid())
317 return self->invalid_coordinate();
319 column_index_type
const first{self->end_positions_first()};
320 row_index_type
const second{std::ranges::size(self->query)};
321 return {first, second};
327template <
typename derived_t,
typename edit_traits>
328class edit_distance_unbanded_semi_global_policy :
public edit_distance_unbanded_global_policy<derived_t, edit_traits>
331 static_assert(edit_traits::is_semi_global,
"This policy assumes that edit_traits::is_semi_global is true.");
339 edit_distance_unbanded_semi_global_policy() noexcept = default;
340 edit_distance_unbanded_semi_global_policy(edit_distance_unbanded_semi_global_policy const &) noexcept =
342 edit_distance_unbanded_semi_global_policy(edit_distance_unbanded_semi_global_policy &&) noexcept =
344 edit_distance_unbanded_semi_global_policy &
345 operator=(edit_distance_unbanded_semi_global_policy const &) noexcept = default;
346 edit_distance_unbanded_semi_global_policy &
347 operator=(edit_distance_unbanded_semi_global_policy &&) noexcept = default;
348 ~edit_distance_unbanded_semi_global_policy() noexcept = default;
353 using base_t = edit_distance_unbanded_global_policy<derived_t, edit_traits>;
355 using database_iterator = typename edit_traits::database_iterator;
356 using base_t::_best_score;
370 database_iterator _best_score_col{};
378 void score_init() noexcept
380 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
381 base_t::score_init();
382 _best_score_col = self->database_it_end;
386 void update_best_score() noexcept
388 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
390 if constexpr (edit_traits::use_max_errors)
392 assert(std::ranges::empty(self->query) || self->is_last_active_cell_within_last_row());
395 _best_score_col = (self->_score <= _best_score) ? self->database_it : _best_score_col;
396 _best_score = (self->_score <= _best_score) ? self->_score : _best_score;
400 size_t end_positions_first() const noexcept
402 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
404 size_t offset = std::ranges::empty(self->database) ? 0u : 1u;
413template <
typename derived_t,
typename edit_traits>
414class edit_distance_unbanded_score_matrix_policy :
420 static_assert(edit_traits::compute_score_matrix,
421 "This policy assumes that edit_traits::compute_score_matrix is true.");
429 edit_distance_unbanded_score_matrix_policy() noexcept = default;
430 edit_distance_unbanded_score_matrix_policy(edit_distance_unbanded_score_matrix_policy const &) noexcept =
432 edit_distance_unbanded_score_matrix_policy(edit_distance_unbanded_score_matrix_policy &&) noexcept =
434 edit_distance_unbanded_score_matrix_policy &
435 operator=(edit_distance_unbanded_score_matrix_policy const &) noexcept = default;
436 edit_distance_unbanded_score_matrix_policy &
437 operator=(edit_distance_unbanded_score_matrix_policy &&) noexcept = default;
438 ~edit_distance_unbanded_score_matrix_policy() noexcept = default;
442 using typename edit_traits::score_matrix_type;
449 score_matrix_type _score_matrix{};
464 void score_matrix_init()
466 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
468 _score_matrix = score_matrix_type{std::ranges::size(self->query) + 1u};
469 _score_matrix.reserve(std::ranges::size(self->database) + 1u);
481 score_matrix_type
const & score_matrix() const noexcept
483 static_assert(edit_traits::compute_score_matrix,
484 "score_matrix() can only be computed if you specify the "
485 "result type within your alignment config.");
486 return _score_matrix;
494template <
typename derived_t,
typename edit_traits>
495class edit_distance_unbanded_trace_matrix_policy :
501 static_assert(edit_traits::compute_trace_matrix,
502 "This policy assumes that edit_traits::compute_trace_matrix is true.");
510 edit_distance_unbanded_trace_matrix_policy() noexcept = default;
511 edit_distance_unbanded_trace_matrix_policy(edit_distance_unbanded_trace_matrix_policy const &) noexcept =
513 edit_distance_unbanded_trace_matrix_policy(edit_distance_unbanded_trace_matrix_policy &&) noexcept =
515 edit_distance_unbanded_trace_matrix_policy &
516 operator=(edit_distance_unbanded_trace_matrix_policy const &) noexcept = default;
517 edit_distance_unbanded_trace_matrix_policy &
518 operator=(edit_distance_unbanded_trace_matrix_policy &&) noexcept = default;
519 ~edit_distance_unbanded_trace_matrix_policy() noexcept = default;
523 using typename edit_traits::alignment_result_type;
524 using typename edit_traits::trace_matrix_type;
525 using typename edit_traits::word_type;
532 std::vector<word_type> hp{};
537 trace_matrix_type _trace_matrix{};
552 void trace_matrix_init(
size_t block_count)
554 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
556 _trace_matrix = trace_matrix_type{std::ranges::size(self->query) + 1u};
557 _trace_matrix.
reserve(std::ranges::size(self->database) + 1u);
559 hp.resize(block_count, 0u);
560 db.resize(block_count, 0u);
570 trace_matrix_type
const & trace_matrix() const noexcept
572 static_assert(edit_traits::compute_trace_matrix,
573 "trace_matrix() can only be computed if you specify the "
574 "result type within your alignment config.");
575 return _trace_matrix;
580 seqan3::detail::advanceable_alignment_coordinate<> begin_positions() const noexcept
582 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
583 static_assert(edit_traits::compute_begin_positions,
584 "begin_positions() can only be computed if you specify the "
585 "result type within your alignment config.");
586 if (!self->is_valid())
587 return self->invalid_coordinate();
589 auto [first, second] = self->end_positions();
590 detail::matrix_coordinate
const end_positions{detail::row_index_type{second}, detail::column_index_type{first}};
591 auto trace_path = self->trace_matrix().trace_path(end_positions);
593 std::ranges::advance(trace_path_it, std::ranges::end(trace_path));
594 detail::matrix_coordinate
const begin_positions = trace_path_it.coordinate();
595 return {detail::column_index_type{begin_positions.col}, detail::row_index_type{begin_positions.row}};
604 derived_t
const * self =
static_cast<derived_t
const *
>(
this);
605 static_assert(edit_traits::compute_sequence_alignment,
606 "alignment() can only be computed if you specify the "
607 "result type within your alignment config.");
609 if (!self->is_valid())
610 return alignment_t{};
612 auto [first, second] = self->end_positions();
613 detail::matrix_coordinate
const end_positions{detail::row_index_type{second}, detail::column_index_type{first}};
614 aligned_sequence_builder builder{self->database, self->query};
615 auto trace_path = self->trace_matrix().trace_path(end_positions);
616 return builder(trace_path).alignment;
624template <
typename value_t>
631 proxy_reference() noexcept = default;
632 proxy_reference(proxy_reference const &) noexcept = default;
633 proxy_reference(proxy_reference &&) noexcept = default;
634 proxy_reference & operator=(proxy_reference const &) noexcept = default;
635 proxy_reference & operator=(proxy_reference &&) noexcept = default;
636 ~proxy_reference() = default;
639 proxy_reference(value_t & t) noexcept : ptr(
std::addressof(t))
642 proxy_reference(value_t &&) =
delete;
645 template <
typename other_value_t>
646 requires std::convertible_to<other_value_t, value_t>
647 proxy_reference & operator=(other_value_t && u)
noexcept
649 get() = std::forward<other_value_t>(u);
655 value_t &
get() const noexcept
657 assert(ptr !=
nullptr);
662 operator value_t &()
const noexcept
669 value_t * ptr{
nullptr};
683template <std::ranges::viewable_range database_t,
684 std::ranges::viewable_range query_t,
685 typename align_config_t,
686 typename edit_traits>
687class edit_distance_unbanded :
690 public edit_distance_base<edit_traits::use_max_errors,
691 edit_distance_unbanded_max_errors_policy,
693 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
694 public edit_distance_base<edit_traits::is_global,
695 edit_distance_unbanded_global_policy,
697 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
698 public edit_distance_base<edit_traits::is_semi_global,
699 edit_distance_unbanded_semi_global_policy,
701 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
702 public edit_distance_base<edit_traits::compute_score_matrix,
703 edit_distance_unbanded_score_matrix_policy,
705 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
706 public edit_distance_base<edit_traits::compute_trace_matrix,
707 edit_distance_unbanded_trace_matrix_policy,
709 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>
713 using edit_traits::word_size;
714 using typename edit_traits::align_config_type;
715 using typename edit_traits::database_type;
716 using typename edit_traits::query_type;
717 using typename edit_traits::score_type;
718 using typename edit_traits::word_type;
722 template <
typename other_derived_t,
typename other_edit_traits>
723 friend class edit_distance_unbanded_max_errors_policy;
725 template <
typename other_derived_t,
typename other_edit_traits>
726 friend class edit_distance_unbanded_global_policy;
728 template <
typename other_derived_t,
typename other_edit_traits>
729 friend class edit_distance_unbanded_semi_global_policy;
731 template <
typename other_derived_t,
typename other_edit_traits>
732 friend class edit_distance_unbanded_score_matrix_policy;
734 template <
typename other_derived_t,
typename other_edit_traits>
735 friend class edit_distance_unbanded_trace_matrix_policy;
737 using edit_traits::compute_begin_positions;
738 using edit_traits::compute_end_positions;
739 using edit_traits::compute_matrix;
740 using edit_traits::compute_score;
741 using edit_traits::compute_score_matrix;
742 using edit_traits::compute_sequence_alignment;
743 using edit_traits::compute_trace_matrix;
744 using edit_traits::is_global;
745 using edit_traits::is_semi_global;
746 using edit_traits::use_max_errors;
747 using typename edit_traits::alignment_result_type;
748 using typename edit_traits::database_iterator;
749 using typename edit_traits::query_alphabet_type;
750 using typename edit_traits::score_matrix_type;
751 using typename edit_traits::trace_matrix_type;
758 align_config_t config;
761 static constexpr word_type hp0 = is_global ? 1u : 0u;
763 static constexpr word_type hn0 = 0u;
765 static constexpr word_type vp0 = ~word_type{0u};
767 static constexpr word_type vn0 = 0u;
777 word_type score_mask{0u};
791 database_iterator database_it{};
793 database_iterator database_it_end{};
796 struct compute_state_trace_matrix
799 proxy_reference<word_type> db{};
803 struct compute_state : enable_state_t<edit_traits::compute_trace_matrix, compute_state_trace_matrix>
817 proxy_reference<word_type> vp{};
819 proxy_reference<word_type> vn{};
821 word_type carry_d0{};
823 word_type carry_hp{hp0};
825 word_type carry_hn{};
831 if constexpr (!use_max_errors && compute_score_matrix)
832 this->_score_matrix.add_column(vp, vn);
834 if constexpr (!use_max_errors && compute_trace_matrix)
835 this->_trace_matrix.add_column(this->hp, this->db, vp);
837 if constexpr (use_max_errors && compute_matrix)
839 size_t max_rows = this->max_rows(score_mask, this->last_block, _score, this->max_errors);
840 if constexpr (compute_score_matrix)
841 this->_score_matrix.add_column(vp, vn, max_rows);
843 if constexpr (compute_trace_matrix)
844 this->_trace_matrix.add_column(this->hp, this->db, vp, max_rows);
853 edit_distance_unbanded() =
delete;
854 edit_distance_unbanded(edit_distance_unbanded
const &) =
default;
855 edit_distance_unbanded(edit_distance_unbanded &&) =
default;
856 edit_distance_unbanded & operator=(edit_distance_unbanded
const &) =
default;
857 edit_distance_unbanded & operator=(edit_distance_unbanded &&) =
default;
858 ~edit_distance_unbanded() =
default;
866 edit_distance_unbanded(database_t _database,
868 align_config_t _config,
869 edit_traits
const & SEQAN3_DOXYGEN_ONLY(_traits)) :
870 database{
std::
forward<database_t>(_database)},
872 config{
std::
forward<align_config_t>(_config)},
873 _score{static_cast<score_type>(
std::ranges::
size(query))},
874 database_it{
std::ranges::
begin(database)},
875 database_it_end{
std::ranges::
end(database)}
877 static constexpr size_t alphabet_size_ = alphabet_size<query_alphabet_type>;
879 size_t const block_count = (std::ranges::size(query) - 1u + word_size) / word_size;
880 score_mask = word_type{1u} << ((std::ranges::size(query) - 1u + word_size) % word_size);
883 if constexpr (use_max_errors)
884 this->max_errors_init(block_count);
886 if constexpr (compute_score_matrix)
887 this->score_matrix_init();
889 if constexpr (compute_trace_matrix)
890 this->trace_matrix_init(block_count);
892 vp.resize(block_count, vp0);
893 vn.resize(block_count, vn0);
894 bit_masks.resize((alphabet_size_ + 1u) * block_count, 0u);
897 for (
size_t j = 0u; j < std::ranges::size(query); j++)
899 size_t const i = block_count *
seqan3::to_rank(query[j]) + j / word_size;
900 bit_masks[i] |= word_type{1u} << (j % word_size);
909 template <
bool with_carry>
910 static void compute_step(compute_state & state)
noexcept
913 assert(state.carry_d0 <= 1u);
914 assert(state.carry_hp <= 1u);
915 assert(state.carry_hn <= 1u);
917 x = state.b | state.vn;
918 t = state.vp + (x & state.vp) + state.carry_d0;
920 state.d0 = (t ^ state.vp) | x;
921 state.hn = state.vp & state.d0;
922 state.hp = state.vn | ~(state.vp | state.d0);
924 if constexpr (with_carry)
925 state.carry_d0 = (state.carry_d0 != 0u) ? t <= state.vp : t < state.vp;
927 x = (state.hp << 1u) | state.carry_hp;
928 state.vn = x & state.d0;
929 state.vp = (state.hn << 1u) | ~(x | state.d0) | state.carry_hn;
931 if constexpr (with_carry)
933 state.carry_hp = state.hp >> (word_size - 1u);
934 state.carry_hn = state.hn >> (word_size - 1u);
939 template <
bool with_carry>
940 void compute_kernel(compute_state & state,
size_t const block_offset,
size_t const current_block)
noexcept
942 state.vp = proxy_reference<word_type>{this->vp[current_block]};
943 state.vn = proxy_reference<word_type>{this->vn[current_block]};
944 if constexpr (compute_trace_matrix)
946 state.hp = proxy_reference<word_type>{this->hp[current_block]};
947 state.db = proxy_reference<word_type>{this->db[current_block]};
949 state.b = bit_masks[block_offset + current_block];
951 compute_step<with_carry>(state);
952 if constexpr (compute_trace_matrix)
953 state.db = ~(state.b ^ state.d0);
957 void advance_score(word_type P, word_type N, word_type mask)
noexcept
959 if ((P & mask) != word_type{0u})
961 else if ((N & mask) != word_type{0u})
966 bool on_hit() noexcept
973 inline bool small_patterns();
976 inline bool large_patterns();
979 inline void compute_empty_query_sequence()
981 assert(std::ranges::empty(query));
983 bool abort_computation =
false;
985 for (; database_it != database_it_end; ++database_it)
987 if constexpr (is_global)
990 this->update_best_score();
993 if constexpr (use_max_errors)
994 abort_computation = on_hit();
997 if (abort_computation)
1006 if constexpr (use_max_errors && is_global && !compute_matrix)
1018 size_t const max_length = std::ranges::size(query) + this->max_errors + 1u;
1019 size_t const haystack_length =
std::min(std::ranges::size(database), max_length);
1020 database_it_end -= std::ranges::size(database) - haystack_length;
1026 if (vp.size() == 0u)
1027 compute_empty_query_sequence();
1028 else if (vp.size() == 1u)
1033 if constexpr (is_global)
1034 this->update_best_score();
1042 template <
typename callback_t>
1043 void operator()([[maybe_unused]]
size_t const idx, callback_t && callback)
1045 using traits_type = alignment_configuration_traits<align_config_t>;
1046 using result_value_type =
typename alignment_result_value_type_accessor<alignment_result_type>::type;
1053 auto cached_end_positions = this->invalid_coordinate();
1054 auto cached_begin_positions = this->invalid_coordinate();
1056 if constexpr (compute_end_positions)
1057 cached_end_positions = this->end_positions();
1059 if constexpr (compute_begin_positions && !compute_sequence_alignment)
1061 static_assert(compute_end_positions,
"End positions required to compute the begin positions.");
1062 cached_begin_positions = this->begin_positions();
1068 result_value_type res_vt{};
1070 if constexpr (traits_type::output_sequence1_id)
1071 res_vt.sequence1_id = idx;
1073 if constexpr (traits_type::output_sequence2_id)
1074 res_vt.sequence2_id = idx;
1076 if constexpr (traits_type::compute_score)
1077 res_vt.score = this->score().value_or(matrix_inf<score_type>);
1079 if constexpr (traits_type::compute_sequence_alignment)
1081 if (this->is_valid())
1083 auto [first, second] = cached_end_positions;
1084 detail::matrix_coordinate
const end_positions{detail::row_index_type{second},
1085 detail::column_index_type{first}};
1087 aligned_sequence_builder builder{this->database, this->query};
1088 auto trace_res = builder(this->trace_matrix().trace_path(end_positions));
1089 res_vt.alignment = std::move(trace_res.alignment);
1090 cached_begin_positions.first = trace_res.first_sequence_slice_positions.first;
1091 cached_begin_positions.second = trace_res.second_sequence_slice_positions.first;
1095 if constexpr (traits_type::compute_end_positions)
1096 res_vt.end_positions = std::move(cached_end_positions);
1098 if constexpr (traits_type::compute_begin_positions)
1099 res_vt.begin_positions = std::move(cached_begin_positions);
1101 callback(alignment_result_type{std::move(res_vt)});
1105template <std::ranges::viewable_range database_t,
1106 std::ranges::viewable_range query_t,
1107 typename align_config_t,
1109bool edit_distance_unbanded<database_t, query_t, align_config_t, traits_t>::small_patterns()
1111 bool abort_computation =
false;
1114 while (database_it != database_it_end)
1116 compute_state state{};
1117 size_t const block_offset =
seqan3::to_rank((query_alphabet_type)*database_it);
1119 compute_kernel<false>(state, block_offset, 0u);
1120 advance_score(state.hp, state.hn, score_mask);
1123 if constexpr (is_semi_global && !use_max_errors)
1124 this->update_best_score();
1127 if constexpr (use_max_errors)
1128 abort_computation = this->update_last_active_cell();
1132 if (abort_computation)
1139template <std::ranges::viewable_range database_t,
1140 std::ranges::viewable_range query_t,
1141 typename align_config_t,
1143bool edit_distance_unbanded<database_t, query_t, align_config_t, traits_t>::large_patterns()
1145 bool abort_computation =
false;
1147 while (database_it != database_it_end)
1149 compute_state state{};
1150 size_t const block_offset = vp.size() *
seqan3::to_rank((query_alphabet_type)*database_it);
1152 size_t block_count = vp.size();
1153 if constexpr (use_max_errors)
1154 block_count = this->last_block + 1;
1157 for (
size_t current_block = 0u; current_block < block_count; current_block++)
1158 compute_kernel<true>(state, block_offset, current_block);
1160 advance_score(state.hp, state.hn, score_mask);
1163 if constexpr (is_semi_global && !use_max_errors)
1164 this->update_best_score();
1166 if constexpr (use_max_errors)
1169 bool additional_block = score_mask >> (word_size - 1u);
1170 bool reached_last_block = this->last_block + 1u == vp.size();
1172 if (reached_last_block)
1173 additional_block =
false;
1175 if (additional_block)
1177 size_t const current_block = this->last_block + 1u;
1179 vp[current_block] = vp0;
1180 vn[current_block] = vn0;
1181 compute_kernel<false>(state, block_offset, current_block);
1185 abort_computation = this->update_last_active_cell();
1191 if (abort_computation)
1204template <
typename database_t,
typename query_t,
typename config_t,
typename traits_t>
1205edit_distance_unbanded(database_t && database, query_t && query, config_t config, traits_t)
1206 -> edit_distance_unbanded<database_t, query_t, config_t, traits_t>;
Provides seqan3::detail::advanceable_alignment_coordinate.
Provides seqan3::alignment_result.
Provides seqan3::configuration and utility functions.
Forwards for seqan3::edit_distance_unbanded related types.
Provides seqan3::detail::edit_distance_score_matrix_full.
Provides seqan3::detail::edit_distance_trace_matrix_full.
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition alphabet/concept.hpp:152
@ alignment
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
constexpr size_t size
The size of a type pack.
Definition type_pack/traits.hpp:143
Provides seqan3::detail::matrix.
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:412
SeqAn specific customisations in the standard namespace.