29 namespace seqan3::detail
34 template <
typename derived_t,
typename edit_traits>
35 class edit_distance_unbanded_max_errors_policy :
41 static_assert(edit_traits::use_max_errors,
"This policy assumes that edit_traits::use_max_errors is true.");
49 edit_distance_unbanded_max_errors_policy() noexcept = default;
50 edit_distance_unbanded_max_errors_policy(edit_distance_unbanded_max_errors_policy const &) noexcept
52 edit_distance_unbanded_max_errors_policy(edit_distance_unbanded_max_errors_policy &&) noexcept
54 edit_distance_unbanded_max_errors_policy & operator=(edit_distance_unbanded_max_errors_policy const &) noexcept
56 edit_distance_unbanded_max_errors_policy & operator=(edit_distance_unbanded_max_errors_policy &&) noexcept
58 ~edit_distance_unbanded_max_errors_policy() noexcept = default;
61 using typename edit_traits::word_type;
62 using typename edit_traits::score_type;
69 score_type max_errors{255};
71 size_t last_block{0u};
73 word_type last_score_mask{};
81 void max_errors_init(
size_t block_count) noexcept
83 derived_t *
self =
static_cast<derived_t *
>(
this);
85 max_errors = -get<align_cfg::min_score>(self->config).score;
87 assert(max_errors >= score_type{0});
89 if (std::ranges::empty(self->query))
92 self->score_mask = 0u;
93 last_score_mask =
self->score_mask;
97 last_block = block_count - 1u;
98 last_score_mask =
self->score_mask;
103 size_t const local_max_errors = std::min<size_t>(max_errors,
std::ranges::size(self->query) - 1u);
104 self->score_mask = word_type{1u} << (local_max_errors %
self->word_size);
105 last_block =
std::min(local_max_errors / self->word_size, last_block);
106 self->_score = local_max_errors + 1u;
110 bool is_last_active_cell_within_last_row() const noexcept
112 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
113 return (self->score_mask == this->last_score_mask) && (this->last_block ==
self->vp.size() - 1u);
117 bool prev_last_active_cell() noexcept
119 derived_t *
self =
static_cast<derived_t *
>(
this);
120 self->score_mask >>= 1u;
121 if (self->score_mask != 0u)
124 if constexpr (edit_traits::is_global)
126 if (last_block == 0u)
132 self->score_mask = word_type{1u} << (edit_traits::word_size - 1u);
137 void next_last_active_cell() noexcept
139 derived_t *
self =
static_cast<derived_t *
>(
this);
140 self->score_mask <<= 1u;
141 if (self->score_mask)
144 self->score_mask = 1u;
151 bool update_last_active_cell() noexcept
153 derived_t *
self =
static_cast<derived_t *
>(
this);
155 while (!(self->_score <= max_errors))
157 self->advance_score(self->vn[last_block], self->vp[last_block], self->score_mask);
158 if (!prev_last_active_cell())
161 assert(edit_traits::is_global);
164 return !edit_traits::compute_matrix;
168 if (is_last_active_cell_within_last_row())
170 assert(self->_score <= max_errors);
172 if constexpr(edit_traits::is_semi_global)
173 self->update_best_score();
175 return self->on_hit();
179 next_last_active_cell();
180 self->advance_score(self->vp[last_block], self->vn[last_block], self->score_mask);
188 static size_t max_rows(word_type
const score_mask,
unsigned const last_block,
189 score_type
const score, score_type
const max_errors) noexcept
191 using score_matrix_type =
typename edit_traits::score_matrix_type;
192 return score_matrix_type::max_rows(score_mask,
202 template <
typename derived_t,
typename edit_traits>
203 class edit_distance_unbanded_global_policy :
209 static_assert(edit_traits::is_global || edit_traits::is_semi_global,
210 "This policy assumes that edit_traits::is_global or edit_traits::is_semi_global is true.");
218 edit_distance_unbanded_global_policy() noexcept = default;
219 edit_distance_unbanded_global_policy(edit_distance_unbanded_global_policy const &) noexcept
221 edit_distance_unbanded_global_policy(edit_distance_unbanded_global_policy &&) noexcept
223 edit_distance_unbanded_global_policy & operator=(edit_distance_unbanded_global_policy const &) noexcept
225 edit_distance_unbanded_global_policy & operator=(edit_distance_unbanded_global_policy &&) noexcept
227 ~edit_distance_unbanded_global_policy() noexcept = default;
231 using typename edit_traits::score_type;
241 score_type _best_score{};
249 void score_init() noexcept
251 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
252 _best_score =
self->_score;
256 bool is_valid() const noexcept
258 [[maybe_unused]] derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
263 if constexpr(edit_traits::use_max_errors)
264 return _best_score <=
self->max_errors;
272 alignment_coordinate invalid_coordinate() const noexcept
274 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
279 void update_best_score() noexcept
281 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
282 _best_score =
self->_score;
286 size_t end_positions_first() const noexcept
288 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
302 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
303 static_assert(edit_traits::compute_score,
"score() can only be computed if you specify the result type within "
304 "your alignment config.");
305 if (!self->is_valid())
313 alignment_coordinate end_positions() const noexcept
315 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
316 static_assert(edit_traits::compute_end_positions,
"end_positions() can only be computed if you specify the "
317 "result type within your alignment config.");
318 if (!self->is_valid())
319 return self->invalid_coordinate();
321 column_index_type
const first{
self->end_positions_first()};
323 return {first, second};
329 template <
typename derived_t,
typename edit_traits>
330 class edit_distance_unbanded_semi_global_policy :
331 public edit_distance_unbanded_global_policy<derived_t, edit_traits>
334 static_assert(edit_traits::is_semi_global,
"This policy assumes that edit_traits::is_semi_global is true.");
342 edit_distance_unbanded_semi_global_policy() noexcept = default;
343 edit_distance_unbanded_semi_global_policy(edit_distance_unbanded_semi_global_policy const &) noexcept
345 edit_distance_unbanded_semi_global_policy(edit_distance_unbanded_semi_global_policy &&) noexcept
347 edit_distance_unbanded_semi_global_policy & operator=(edit_distance_unbanded_semi_global_policy const &) noexcept
349 edit_distance_unbanded_semi_global_policy & operator=(edit_distance_unbanded_semi_global_policy &&) noexcept
351 ~edit_distance_unbanded_semi_global_policy() noexcept = default;
355 using base_t = edit_distance_unbanded_global_policy<derived_t, edit_traits>;
357 using database_iterator = typename edit_traits::database_iterator;
358 using base_t::_best_score;
372 database_iterator _best_score_col{};
380 void score_init() noexcept
382 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
383 base_t::score_init();
384 _best_score_col =
self->database_it_end;
388 void update_best_score() noexcept
390 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
392 if constexpr(edit_traits::use_max_errors)
394 assert(std::ranges::empty(self->query) || self->is_last_active_cell_within_last_row());
397 _best_score_col = (
self->_score <= _best_score) ? self->database_it : _best_score_col;
398 _best_score = (self->_score <= _best_score) ?
self->_score : _best_score;
402 size_t end_positions_first() const noexcept
404 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
406 size_t offset = std::ranges::empty(self->database) ? 0u : 1u;
407 return std::ranges::distance(std::ranges::begin(self->database), _best_score_col) +
offset;
415 template <
typename derived_t,
typename edit_traits>
416 class edit_distance_unbanded_score_matrix_policy :
422 static_assert(edit_traits::compute_score_matrix,
423 "This policy assumes that edit_traits::compute_score_matrix is true.");
431 edit_distance_unbanded_score_matrix_policy() noexcept = default;
432 edit_distance_unbanded_score_matrix_policy(edit_distance_unbanded_score_matrix_policy const &) noexcept
434 edit_distance_unbanded_score_matrix_policy(edit_distance_unbanded_score_matrix_policy &&) noexcept
436 edit_distance_unbanded_score_matrix_policy & operator=(edit_distance_unbanded_score_matrix_policy const &) noexcept
438 edit_distance_unbanded_score_matrix_policy & operator=(edit_distance_unbanded_score_matrix_policy &&) noexcept
440 ~edit_distance_unbanded_score_matrix_policy() noexcept = default;
443 using typename edit_traits::score_matrix_type;
450 score_matrix_type _score_matrix{};
465 void score_matrix_init()
467 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
482 score_matrix_type
const & score_matrix() const noexcept
484 static_assert(edit_traits::compute_score_matrix,
"score_matrix() can only be computed if you specify the "
485 "result type within your alignment config.");
486 return _score_matrix;
494 template <
typename derived_t,
typename edit_traits>
495 class 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 & operator=(edit_distance_unbanded_trace_matrix_policy const &) noexcept
517 edit_distance_unbanded_trace_matrix_policy & operator=(edit_distance_unbanded_trace_matrix_policy &&) noexcept
519 ~edit_distance_unbanded_trace_matrix_policy() noexcept = default;
522 using typename edit_traits::word_type;
523 using typename edit_traits::trace_matrix_type;
524 using typename edit_traits::alignment_result_type;
531 std::vector<word_type> hp{};
536 trace_matrix_type _trace_matrix{};
551 void trace_matrix_init(
size_t block_count)
553 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
558 hp.resize(block_count, 0u);
559 db.resize(block_count, 0u);
569 trace_matrix_type
const & trace_matrix() const noexcept
571 static_assert(edit_traits::compute_trace_matrix,
"trace_matrix() can only be computed if you specify the "
572 "result type within your alignment config.");
573 return _trace_matrix;
578 alignment_coordinate begin_positions() const noexcept
580 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
581 static_assert(edit_traits::compute_begin_positions,
"begin_positions() can only be computed if you specify the "
582 "result type within your alignment config.");
583 if (!self->is_valid())
584 return self->invalid_coordinate();
586 alignment_coordinate
const back =
self->end_positions();
587 auto trace_path =
self->trace_matrix().trace_path(
back);
589 std::ranges::advance(trace_path_it, std::ranges::end(trace_path));
590 matrix_coordinate coordinate = trace_path_it.coordinate();
591 return {column_index_type{coordinate.col}, row_index_type{coordinate.row}};
600 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
601 static_assert(edit_traits::compute_sequence_alignment,
"alignment() can only be computed if you specify the "
602 "result type within your alignment config.");
604 if (!self->is_valid())
605 return alignment_t{};
607 alignment_coordinate
const back =
self->end_positions();
608 aligned_sequence_builder builder{
self->database,
self->query};
609 auto trace_path =
self->trace_matrix().trace_path(
back);
610 return builder(trace_path).alignment;
618 template <
typename value_t>
619 class proxy_reference
625 proxy_reference() noexcept = default;
626 proxy_reference(proxy_reference const &) noexcept = default;
627 proxy_reference(proxy_reference &&) noexcept = default;
628 proxy_reference & operator=(proxy_reference const &) noexcept = default;
629 proxy_reference & operator=(proxy_reference &&) noexcept = default;
630 ~proxy_reference() = default;
633 proxy_reference(value_t & t) noexcept
634 : ptr(
std::addressof(t))
637 proxy_reference(value_t &&) =
delete;
640 template <
typename other_value_t>
642 requires std::convertible_to<other_value_t, value_t>
644 proxy_reference & operator=(other_value_t && u) noexcept
646 get() = std::forward<other_value_t>(u);
652 value_t &
get() const noexcept
654 assert(ptr !=
nullptr);
659 operator value_t & ()
const noexcept
666 value_t * ptr{
nullptr};
680 template <std::ranges::viewable_range database_t,
681 std::ranges::viewable_range query_t,
682 typename align_config_t,
683 typename edit_traits>
684 class edit_distance_unbanded :
687 public edit_distance_base<
688 edit_traits::use_max_errors,
689 edit_distance_unbanded_max_errors_policy,
691 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
692 public edit_distance_base<
693 edit_traits::is_global,
694 edit_distance_unbanded_global_policy,
696 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
697 public edit_distance_base<
698 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<
703 edit_traits::compute_score_matrix,
704 edit_distance_unbanded_score_matrix_policy,
706 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
707 public edit_distance_base<
708 edit_traits::compute_trace_matrix,
709 edit_distance_unbanded_trace_matrix_policy,
711 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>
715 using typename edit_traits::word_type;
716 using typename edit_traits::score_type;
717 using typename edit_traits::database_type;
718 using typename edit_traits::query_type;
719 using typename edit_traits::align_config_type;
720 using edit_traits::word_size;
724 template <
typename other_derived_t,
typename other_edit_traits>
725 friend class edit_distance_unbanded_max_errors_policy;
727 template <
typename other_derived_t,
typename other_edit_traits>
728 friend class edit_distance_unbanded_global_policy;
730 template <
typename other_derived_t,
typename other_edit_traits>
731 friend class edit_distance_unbanded_semi_global_policy;
733 template <
typename other_derived_t,
typename other_edit_traits>
734 friend class edit_distance_unbanded_score_matrix_policy;
736 template <
typename other_derived_t,
typename other_edit_traits>
737 friend class edit_distance_unbanded_trace_matrix_policy;
739 using typename edit_traits::database_iterator;
740 using typename edit_traits::query_alphabet_type;
741 using typename edit_traits::alignment_result_type;
742 using edit_traits::use_max_errors;
743 using edit_traits::is_semi_global;
744 using edit_traits::is_global;
745 using edit_traits::compute_score;
746 using edit_traits::compute_end_positions;
747 using edit_traits::compute_begin_positions;
748 using edit_traits::compute_sequence_alignment;
749 using edit_traits::compute_score_matrix;
750 using edit_traits::compute_trace_matrix;
751 using edit_traits::compute_matrix;
752 using typename edit_traits::score_matrix_type;
753 using typename edit_traits::trace_matrix_type;
760 align_config_t config;
763 static constexpr word_type hp0 = is_global ? 1u : 0u;
765 static constexpr word_type hn0 = 0u;
767 static constexpr word_type vp0 = ~word_type{0u};
769 static constexpr word_type vn0 = 0u;
779 word_type score_mask{0u};
793 database_iterator database_it{};
795 database_iterator database_it_end{};
798 struct compute_state_trace_matrix
801 proxy_reference<word_type> db{};
805 struct compute_state : enable_state_t<compute_trace_matrix, compute_state_trace_matrix>
819 proxy_reference<word_type> vp{};
821 proxy_reference<word_type> vn{};
823 word_type carry_d0{};
825 word_type carry_hp{hp0};
827 word_type carry_hn{};
833 if constexpr(!use_max_errors && compute_score_matrix)
834 this->_score_matrix.add_column(vp, vn);
836 if constexpr(!use_max_errors && compute_trace_matrix)
837 this->_trace_matrix.add_column(this->hp, this->db, vp);
839 if constexpr(use_max_errors && compute_matrix)
841 size_t max_rows = this->max_rows(score_mask, this->last_block, _score, this->max_errors);
842 if constexpr(compute_score_matrix)
843 this->_score_matrix.add_column(vp, vn, max_rows);
845 if constexpr(compute_trace_matrix)
846 this->_trace_matrix.add_column(this->hp, this->db, vp, max_rows);
855 edit_distance_unbanded() =
delete;
856 edit_distance_unbanded(edit_distance_unbanded
const &) =
default;
857 edit_distance_unbanded(edit_distance_unbanded &&) =
default;
858 edit_distance_unbanded & operator=(edit_distance_unbanded
const &) =
default;
859 edit_distance_unbanded & operator=(edit_distance_unbanded &&) =
default;
860 ~edit_distance_unbanded() =
default;
868 edit_distance_unbanded(database_t _database,
870 align_config_t _config,
871 edit_traits
const & SEQAN3_DOXYGEN_ONLY(_traits)) :
872 database{
std::
forward<database_t>(_database)},
874 config{
std::
forward<align_config_t>(_config)},
875 _score{static_cast<score_type>(
std::ranges::
size(query))},
876 database_it{ranges::
begin(database)},
877 database_it_end{ranges::
end(database)}
879 static constexpr
size_t alphabet_size_ = alphabet_size<query_alphabet_type>;
881 size_t const block_count = (
std::ranges::size(query) - 1u + word_size) / word_size;
882 score_mask = word_type{1u} << ((
std::ranges::size(query) - 1u + word_size) % word_size);
885 if constexpr(use_max_errors)
886 this->max_errors_init(block_count);
888 if constexpr(compute_score_matrix)
889 this->score_matrix_init();
891 if constexpr(compute_trace_matrix)
892 this->trace_matrix_init(block_count);
894 vp.resize(block_count, vp0);
895 vn.resize(block_count, vn0);
896 bit_masks.resize((alphabet_size_ + 1u) * block_count, 0u);
901 size_t const i = block_count *
seqan3::to_rank(query[j]) + j / word_size;
902 bit_masks[i] |= word_type{1u} << (j % word_size);
911 template <
bool with_carry>
912 static void compute_step(compute_state & state) noexcept
915 assert(state.carry_d0 <= 1u);
916 assert(state.carry_hp <= 1u);
917 assert(state.carry_hn <= 1u);
919 x = state.b | state.vn;
920 t = state.vp + (x & state.vp) + state.carry_d0;
922 state.d0 = (t ^ state.vp) | x;
923 state.hn = state.vp & state.d0;
924 state.hp = state.vn | ~(state.vp | state.d0);
926 if constexpr(with_carry)
927 state.carry_d0 = (state.carry_d0 != 0u) ? t <= state.vp : t < state.vp;
929 x = (state.hp << 1u) | state.carry_hp;
930 state.vn = x & state.d0;
931 state.vp = (state.hn << 1u) | ~(x | state.d0) | state.carry_hn;
933 if constexpr(with_carry)
935 state.carry_hp = state.hp >> (word_size - 1u);
936 state.carry_hn = state.hn >> (word_size - 1u);
941 template <
bool with_carry>
942 void compute_kernel(compute_state & state,
size_t const block_offset,
size_t const current_block) noexcept
944 state.vp = proxy_reference<word_type>{this->vp[current_block]};
945 state.vn = proxy_reference<word_type>{this->vn[current_block]};
946 if constexpr(compute_trace_matrix)
948 state.hp = proxy_reference<word_type>{this->hp[current_block]};
949 state.db = proxy_reference<word_type>{this->db[current_block]};
951 state.b = bit_masks[block_offset + current_block];
953 compute_step<with_carry>(state);
954 if constexpr(compute_trace_matrix)
955 state.db = ~(state.b ^ state.d0);
959 void advance_score(word_type P, word_type N, word_type mask) noexcept
961 if ((P & mask) != word_type{0u})
963 else if ((N & mask) != word_type{0u})
968 bool on_hit() noexcept
975 inline bool small_patterns();
978 inline bool large_patterns();
981 inline void compute_empty_query_sequence()
983 assert(std::ranges::empty(query));
985 bool abort_computation =
false;
987 for (; database_it != database_it_end; ++database_it)
989 if constexpr(is_global)
992 this->update_best_score();
995 if constexpr(use_max_errors)
996 abort_computation = on_hit();
999 if (abort_computation)
1008 if constexpr(use_max_errors && is_global && !compute_matrix)
1028 if (vp.size() == 0u)
1029 compute_empty_query_sequence();
1030 else if (vp.size() == 1u)
1035 if constexpr(is_global)
1036 this->update_best_score();
1044 template <
typename callback_t>
1045 void operator()([[maybe_unused]]
size_t const idx, callback_t && callback)
1047 using traits_type = alignment_configuration_traits<align_config_t>;
1048 using result_value_type =
typename alignment_result_value_type_accessor<alignment_result_type>::type;
1055 auto cached_end_positions = this->invalid_coordinate();
1056 auto cached_begin_positions = this->invalid_coordinate();
1058 if constexpr (compute_end_positions)
1059 cached_end_positions = this->end_positions();
1061 if constexpr (compute_begin_positions && !compute_sequence_alignment)
1063 static_assert(compute_end_positions,
"End positions required to compute the begin positions.");
1064 cached_begin_positions = this->begin_positions();
1070 result_value_type res_vt{};
1072 if constexpr (traits_type::output_sequence1_id)
1073 res_vt.sequence1_id = idx;
1075 if constexpr (traits_type::output_sequence2_id)
1076 res_vt.sequence2_id = idx;
1078 if constexpr (traits_type::compute_score)
1079 res_vt.score = this->score().value_or(matrix_inf<score_type>);
1081 if constexpr (traits_type::compute_sequence_alignment)
1083 if (this->is_valid())
1085 aligned_sequence_builder builder{this->database, this->query};
1086 auto trace_res = builder(this->trace_matrix().trace_path(cached_end_positions));
1087 res_vt.alignment =
std::move(trace_res.alignment);
1088 cached_begin_positions.first = trace_res.first_sequence_slice_positions.first;
1089 cached_begin_positions.second = trace_res.second_sequence_slice_positions.first;
1093 if constexpr (traits_type::compute_end_positions)
1094 res_vt.end_positions =
std::move(cached_end_positions);
1096 if constexpr (traits_type::compute_begin_positions)
1097 res_vt.begin_positions =
std::move(cached_begin_positions);
1099 callback(alignment_result_type{
std::move(res_vt)});
1103 template <
typename database_t,
typename query_t,
typename align_config_t,
typename traits_t>
1104 bool edit_distance_unbanded<database_t, query_t, align_config_t, traits_t>::small_patterns()
1106 bool abort_computation =
false;
1109 while (database_it != database_it_end)
1111 compute_state state{};
1112 size_t const block_offset =
seqan3::to_rank((query_alphabet_type) *database_it);
1114 compute_kernel<false>(state, block_offset, 0u);
1115 advance_score(state.hp, state.hn, score_mask);
1118 if constexpr(is_semi_global && !use_max_errors)
1119 this->update_best_score();
1122 if constexpr(use_max_errors)
1123 abort_computation = this->update_last_active_cell();
1127 if (abort_computation)
1134 template <
typename database_t,
typename query_t,
typename align_config_t,
typename traits_t>
1135 bool edit_distance_unbanded<database_t, query_t, align_config_t, traits_t>::large_patterns()
1137 bool abort_computation =
false;
1139 while (database_it != database_it_end)
1141 compute_state state{};
1142 size_t const block_offset = vp.size() *
seqan3::to_rank((query_alphabet_type) *database_it);
1144 size_t block_count = vp.size();
1145 if constexpr(use_max_errors)
1146 block_count = this->last_block + 1;
1149 for (
size_t current_block = 0u; current_block < block_count; current_block++)
1150 compute_kernel<true>(state, block_offset, current_block);
1152 advance_score(state.hp, state.hn, score_mask);
1155 if constexpr(is_semi_global && !use_max_errors)
1156 this->update_best_score();
1158 if constexpr(use_max_errors)
1161 bool additional_block = score_mask >> (word_size - 1u);
1162 bool reached_last_block = this->last_block + 1u == vp.size();
1164 if (reached_last_block)
1165 additional_block =
false;
1167 if (additional_block)
1169 size_t const current_block = this->last_block + 1u;
1171 vp[current_block] = vp0;
1172 vn[current_block] = vn0;
1173 compute_kernel<false>(state, block_offset, current_block);
1177 abort_computation = this->update_last_active_cell();
1183 if (abort_computation)
1196 template <
typename database_t,
typename query_t,
typename config_t,
typename traits_t>
1197 edit_distance_unbanded(database_t && database, query_t && query, config_t config, traits_t)
1198 -> edit_distance_unbanded<database_t, query_t, config_t, traits_t>;
Provides seqan3::detail::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: concept.hpp:146
@ 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.
typename decltype(detail::back(list_t{}))::type back
Return the last type from the type list.
Definition: traits.hpp:264
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:150
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:70
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:434
SeqAn specific customisations in the standard namespace.
Adaptations of concepts from the Ranges TS.