29namespace seqan3::detail
34template <
typename derived_t,
typename edit_traits>
35class 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;
62 using typename edit_traits::word_type;
63 using typename edit_traits::score_type;
70 score_type max_errors{255};
72 size_t last_block{0u};
74 word_type last_score_mask{};
82 void max_errors_init(
size_t block_count)
noexcept
84 derived_t *
self =
static_cast<derived_t *
>(
this);
86 max_errors = -get<align_cfg::min_score>(self->config).score;
88 assert(max_errors >= score_type{0});
90 if (std::ranges::empty(self->query))
93 self->score_mask = 0u;
94 last_score_mask =
self->score_mask;
98 last_block = block_count - 1u;
99 last_score_mask =
self->score_mask;
104 size_t const local_max_errors = std::min<size_t>(max_errors,
std::ranges::size(self->query) - 1u);
105 self->score_mask = word_type{1u} << (local_max_errors %
self->word_size);
106 last_block =
std::min(local_max_errors / self->word_size, last_block);
107 self->_score = local_max_errors + 1u;
111 bool is_last_active_cell_within_last_row() const noexcept
113 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
114 return (self->score_mask == this->last_score_mask) && (this->last_block ==
self->vp.size() - 1u);
118 bool prev_last_active_cell() noexcept
120 derived_t *
self =
static_cast<derived_t *
>(
this);
121 self->score_mask >>= 1u;
122 if (self->score_mask != 0u)
125 if constexpr (edit_traits::is_global)
127 if (last_block == 0u)
133 self->score_mask = word_type{1u} << (edit_traits::word_size - 1u);
138 void next_last_active_cell() noexcept
140 derived_t *
self =
static_cast<derived_t *
>(
this);
141 self->score_mask <<= 1u;
142 if (self->score_mask)
145 self->score_mask = 1u;
152 bool update_last_active_cell() noexcept
154 derived_t *
self =
static_cast<derived_t *
>(
this);
156 while (!(self->_score <= max_errors))
158 self->advance_score(self->vn[last_block], self->vp[last_block], self->score_mask);
159 if (!prev_last_active_cell())
162 assert(edit_traits::is_global);
165 return !edit_traits::compute_matrix;
169 if (is_last_active_cell_within_last_row())
171 assert(self->_score <= max_errors);
173 if constexpr(edit_traits::is_semi_global)
174 self->update_best_score();
176 return self->on_hit();
180 next_last_active_cell();
181 self->advance_score(self->vp[last_block], self->vn[last_block], self->score_mask);
189 static size_t max_rows(word_type
const score_mask,
unsigned const last_block,
190 score_type
const score, score_type
const max_errors)
noexcept
192 using score_matrix_type =
typename edit_traits::score_matrix_type;
193 return score_matrix_type::max_rows(score_mask,
203template <
typename derived_t,
typename edit_traits>
204class edit_distance_unbanded_global_policy :
210 static_assert(edit_traits::is_global || edit_traits::is_semi_global,
211 "This policy assumes that edit_traits::is_global or edit_traits::is_semi_global is true.");
219 edit_distance_unbanded_global_policy() noexcept = default;
220 edit_distance_unbanded_global_policy(edit_distance_unbanded_global_policy const &) noexcept
222 edit_distance_unbanded_global_policy(edit_distance_unbanded_global_policy &&) noexcept
224 edit_distance_unbanded_global_policy & operator=(edit_distance_unbanded_global_policy const &) noexcept
226 edit_distance_unbanded_global_policy & operator=(edit_distance_unbanded_global_policy &&) noexcept
228 ~edit_distance_unbanded_global_policy() noexcept = default;
233 using typename edit_traits::score_type;
243 score_type _best_score{};
251 void score_init() noexcept
253 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
254 _best_score =
self->_score;
258 bool is_valid() const noexcept
260 [[maybe_unused]] derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
265 if constexpr(edit_traits::use_max_errors)
266 return _best_score <= self->max_errors;
274 seqan3::detail::advanceable_alignment_coordinate<> invalid_coordinate() const noexcept
276 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
281 void update_best_score() noexcept
283 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
284 _best_score =
self->_score;
288 size_t end_positions_first() const noexcept
290 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
304 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
305 static_assert(edit_traits::compute_score,
"score() can only be computed if you specify the result type within "
306 "your alignment config.");
307 if (!self->is_valid())
315 seqan3::detail::advanceable_alignment_coordinate<> end_positions() const noexcept
317 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
318 static_assert(edit_traits::compute_end_positions,
"end_positions() can only be computed if you specify the "
319 "result type within your alignment config.");
320 if (!self->is_valid())
321 return self->invalid_coordinate();
323 column_index_type
const first{
self->end_positions_first()};
325 return {first, second};
331template <
typename derived_t,
typename edit_traits>
332class edit_distance_unbanded_semi_global_policy :
333 public edit_distance_unbanded_global_policy<derived_t, edit_traits>
336 static_assert(edit_traits::is_semi_global,
"This policy assumes that edit_traits::is_semi_global is true.");
344 edit_distance_unbanded_semi_global_policy() noexcept = default;
345 edit_distance_unbanded_semi_global_policy(edit_distance_unbanded_semi_global_policy const &) noexcept
347 edit_distance_unbanded_semi_global_policy(edit_distance_unbanded_semi_global_policy &&) noexcept
349 edit_distance_unbanded_semi_global_policy & operator=(edit_distance_unbanded_semi_global_policy const &) noexcept
351 edit_distance_unbanded_semi_global_policy & operator=(edit_distance_unbanded_semi_global_policy &&) noexcept
353 ~edit_distance_unbanded_semi_global_policy() noexcept = default;
358 using base_t = edit_distance_unbanded_global_policy<derived_t, edit_traits>;
360 using database_iterator = typename edit_traits::database_iterator;
361 using base_t::_best_score;
375 database_iterator _best_score_col{};
383 void score_init() noexcept
385 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
386 base_t::score_init();
387 _best_score_col =
self->database_it_end;
391 void update_best_score() noexcept
393 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
395 if constexpr(edit_traits::use_max_errors)
397 assert(std::ranges::empty(self->query) || self->is_last_active_cell_within_last_row());
400 _best_score_col = (
self->_score <= _best_score) ? self->database_it : _best_score_col;
401 _best_score = (self->_score <= _best_score) ?
self->_score : _best_score;
405 size_t end_positions_first() const noexcept
407 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
409 size_t offset = std::ranges::empty(self->database) ? 0u : 1u;
410 return std::ranges::distance(std::ranges::begin(self->database), _best_score_col) +
offset;
418template <
typename derived_t,
typename edit_traits>
419class edit_distance_unbanded_score_matrix_policy :
425 static_assert(edit_traits::compute_score_matrix,
426 "This policy assumes that edit_traits::compute_score_matrix is true.");
434 edit_distance_unbanded_score_matrix_policy() noexcept = default;
435 edit_distance_unbanded_score_matrix_policy(edit_distance_unbanded_score_matrix_policy const &) noexcept
437 edit_distance_unbanded_score_matrix_policy(edit_distance_unbanded_score_matrix_policy &&) noexcept
439 edit_distance_unbanded_score_matrix_policy & operator=(edit_distance_unbanded_score_matrix_policy const &) noexcept
441 edit_distance_unbanded_score_matrix_policy & operator=(edit_distance_unbanded_score_matrix_policy &&) noexcept
443 ~edit_distance_unbanded_score_matrix_policy() noexcept = default;
447 using typename edit_traits::score_matrix_type;
454 score_matrix_type _score_matrix{};
469 void score_matrix_init()
471 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
486 score_matrix_type
const & score_matrix() const noexcept
488 static_assert(edit_traits::compute_score_matrix,
"score_matrix() can only be computed if you specify the "
489 "result type within your alignment config.");
490 return _score_matrix;
498template <
typename derived_t,
typename edit_traits>
499class edit_distance_unbanded_trace_matrix_policy :
505 static_assert(edit_traits::compute_trace_matrix,
506 "This policy assumes that edit_traits::compute_trace_matrix is true.");
514 edit_distance_unbanded_trace_matrix_policy() noexcept = default;
515 edit_distance_unbanded_trace_matrix_policy(edit_distance_unbanded_trace_matrix_policy const &) noexcept
517 edit_distance_unbanded_trace_matrix_policy(edit_distance_unbanded_trace_matrix_policy &&) noexcept
519 edit_distance_unbanded_trace_matrix_policy & operator=(edit_distance_unbanded_trace_matrix_policy const &) noexcept
521 edit_distance_unbanded_trace_matrix_policy & operator=(edit_distance_unbanded_trace_matrix_policy &&) noexcept
523 ~edit_distance_unbanded_trace_matrix_policy() noexcept = default;
527 using typename edit_traits::word_type;
528 using typename edit_traits::trace_matrix_type;
529 using typename edit_traits::alignment_result_type;
536 std::vector<word_type> hp{};
541 trace_matrix_type _trace_matrix{};
556 void trace_matrix_init(
size_t block_count)
558 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
563 hp.resize(block_count, 0u);
564 db.resize(block_count, 0u);
574 trace_matrix_type
const & trace_matrix() const noexcept
576 static_assert(edit_traits::compute_trace_matrix,
"trace_matrix() can only be computed if you specify the "
577 "result type within your alignment config.");
578 return _trace_matrix;
583 seqan3::detail::advanceable_alignment_coordinate<> begin_positions() const noexcept
585 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
586 static_assert(edit_traits::compute_begin_positions,
"begin_positions() can only be computed if you specify the "
587 "result type within your alignment config.");
588 if (!self->is_valid())
589 return self->invalid_coordinate();
591 auto [first, second] =
self->end_positions();
592 detail::matrix_coordinate
const end_positions{detail::row_index_type{second}, detail::column_index_type{first}};
593 auto trace_path =
self->trace_matrix().trace_path(end_positions);
595 std::ranges::advance(trace_path_it, std::ranges::end(trace_path));
596 detail::matrix_coordinate
const begin_positions = trace_path_it.coordinate();
597 return {detail::column_index_type{begin_positions.col}, detail::row_index_type{begin_positions.row}};
606 derived_t
const *
self =
static_cast<derived_t
const *
>(
this);
607 static_assert(edit_traits::compute_sequence_alignment,
"alignment() can only be computed if you specify the "
608 "result type within your alignment config.");
610 if (!self->is_valid())
611 return alignment_t{};
613 auto [first, second] =
self->end_positions();
614 detail::matrix_coordinate
const end_positions{detail::row_index_type{second}, detail::column_index_type{first}};
615 aligned_sequence_builder builder{
self->database,
self->query};
616 auto trace_path =
self->trace_matrix().trace_path(end_positions);
617 return builder(trace_path).alignment;
625template <
typename value_t>
632 proxy_reference() noexcept = default;
633 proxy_reference(proxy_reference const &) noexcept = default;
634 proxy_reference(proxy_reference &&) noexcept = default;
635 proxy_reference & operator=(proxy_reference const &) noexcept = default;
636 proxy_reference & operator=(proxy_reference &&) noexcept = default;
637 ~proxy_reference() = default;
640 proxy_reference(value_t & t) noexcept
641 : ptr(
std::addressof(t))
644 proxy_reference(value_t &&) =
delete;
647 template <
typename other_value_t>
649 requires std::convertible_to<other_value_t, value_t>
651 proxy_reference & operator=(other_value_t && u)
noexcept
653 get() = std::forward<other_value_t>(u);
659 value_t &
get() const noexcept
661 assert(ptr !=
nullptr);
666 operator value_t & ()
const noexcept
673 value_t * ptr{
nullptr};
687template <std::ranges::viewable_range database_t,
688 std::ranges::viewable_range query_t,
689 typename align_config_t,
690 typename edit_traits>
691class edit_distance_unbanded :
694 public edit_distance_base<
695 edit_traits::use_max_errors,
696 edit_distance_unbanded_max_errors_policy,
698 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
699 public edit_distance_base<
700 edit_traits::is_global,
701 edit_distance_unbanded_global_policy,
703 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
704 public edit_distance_base<
705 edit_traits::is_semi_global,
706 edit_distance_unbanded_semi_global_policy,
708 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
709 public edit_distance_base<
710 edit_traits::compute_score_matrix,
711 edit_distance_unbanded_score_matrix_policy,
713 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
714 public edit_distance_base<
715 edit_traits::compute_trace_matrix,
716 edit_distance_unbanded_trace_matrix_policy,
718 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>
722 using typename edit_traits::word_type;
723 using typename edit_traits::score_type;
724 using typename edit_traits::database_type;
725 using typename edit_traits::query_type;
726 using typename edit_traits::align_config_type;
727 using edit_traits::word_size;
731 template <
typename other_derived_t,
typename other_edit_traits>
732 friend class edit_distance_unbanded_max_errors_policy;
734 template <
typename other_derived_t,
typename other_edit_traits>
735 friend class edit_distance_unbanded_global_policy;
737 template <
typename other_derived_t,
typename other_edit_traits>
738 friend class edit_distance_unbanded_semi_global_policy;
740 template <
typename other_derived_t,
typename other_edit_traits>
741 friend class edit_distance_unbanded_score_matrix_policy;
743 template <
typename other_derived_t,
typename other_edit_traits>
744 friend class edit_distance_unbanded_trace_matrix_policy;
746 using typename edit_traits::database_iterator;
747 using typename edit_traits::query_alphabet_type;
748 using typename edit_traits::alignment_result_type;
749 using edit_traits::use_max_errors;
750 using edit_traits::is_semi_global;
751 using edit_traits::is_global;
752 using edit_traits::compute_score;
753 using edit_traits::compute_end_positions;
754 using edit_traits::compute_begin_positions;
755 using edit_traits::compute_sequence_alignment;
756 using edit_traits::compute_score_matrix;
757 using edit_traits::compute_trace_matrix;
758 using edit_traits::compute_matrix;
759 using typename edit_traits::score_matrix_type;
760 using typename edit_traits::trace_matrix_type;
767 align_config_t config;
770 static constexpr word_type hp0 = is_global ? 1u : 0u;
772 static constexpr word_type hn0 = 0u;
774 static constexpr word_type vp0 = ~word_type{0u};
776 static constexpr word_type vn0 = 0u;
786 word_type score_mask{0u};
800 database_iterator database_it{};
802 database_iterator database_it_end{};
805 struct compute_state_trace_matrix
808 proxy_reference<word_type> db{};
812 struct compute_state : enable_state_t<edit_traits::compute_trace_matrix, compute_state_trace_matrix>
826 proxy_reference<word_type> vp{};
828 proxy_reference<word_type> vn{};
830 word_type carry_d0{};
832 word_type carry_hp{hp0};
834 word_type carry_hn{};
840 if constexpr(!use_max_errors && compute_score_matrix)
841 this->_score_matrix.add_column(vp, vn);
843 if constexpr(!use_max_errors && compute_trace_matrix)
844 this->_trace_matrix.add_column(this->hp, this->db, vp);
846 if constexpr(use_max_errors && compute_matrix)
848 size_t max_rows = this->max_rows(score_mask, this->last_block, _score, this->max_errors);
849 if constexpr(compute_score_matrix)
850 this->_score_matrix.add_column(vp, vn, max_rows);
852 if constexpr(compute_trace_matrix)
853 this->_trace_matrix.add_column(this->hp, this->db, vp, max_rows);
862 edit_distance_unbanded() =
delete;
863 edit_distance_unbanded(edit_distance_unbanded
const &) =
default;
864 edit_distance_unbanded(edit_distance_unbanded &&) =
default;
865 edit_distance_unbanded & operator=(edit_distance_unbanded
const &) =
default;
866 edit_distance_unbanded & operator=(edit_distance_unbanded &&) =
default;
867 ~edit_distance_unbanded() =
default;
875 edit_distance_unbanded(database_t _database,
877 align_config_t _config,
878 edit_traits
const & SEQAN3_DOXYGEN_ONLY(_traits)) :
879 database{
std::
forward<database_t>(_database)},
881 config{
std::
forward<align_config_t>(_config)},
882 _score{static_cast<score_type>(
std::ranges::
size(query))},
883 database_it{ranges::
begin(database)},
884 database_it_end{ranges::
end(database)}
886 static constexpr size_t alphabet_size_ = alphabet_size<query_alphabet_type>;
888 size_t const block_count = (
std::ranges::size(query) - 1u + word_size) / word_size;
889 score_mask = word_type{1u} << ((
std::ranges::size(query) - 1u + word_size) % word_size);
892 if constexpr(use_max_errors)
893 this->max_errors_init(block_count);
895 if constexpr(compute_score_matrix)
896 this->score_matrix_init();
898 if constexpr(compute_trace_matrix)
899 this->trace_matrix_init(block_count);
901 vp.resize(block_count, vp0);
902 vn.resize(block_count, vn0);
903 bit_masks.resize((alphabet_size_ + 1u) * block_count, 0u);
908 size_t const i = block_count *
seqan3::to_rank(query[j]) + j / word_size;
909 bit_masks[i] |= word_type{1u} << (j % word_size);
918 template <
bool with_carry>
919 static void compute_step(compute_state & state)
noexcept
922 assert(state.carry_d0 <= 1u);
923 assert(state.carry_hp <= 1u);
924 assert(state.carry_hn <= 1u);
926 x = state.b | state.vn;
927 t = state.vp + (x & state.vp) + state.carry_d0;
929 state.d0 = (t ^ state.vp) | x;
930 state.hn = state.vp & state.d0;
931 state.hp = state.vn | ~(state.vp | state.d0);
933 if constexpr(with_carry)
934 state.carry_d0 = (state.carry_d0 != 0u) ? t <= state.vp : t < state.vp;
936 x = (state.hp << 1u) | state.carry_hp;
937 state.vn = x & state.d0;
938 state.vp = (state.hn << 1u) | ~(x | state.d0) | state.carry_hn;
940 if constexpr(with_carry)
942 state.carry_hp = state.hp >> (word_size - 1u);
943 state.carry_hn = state.hn >> (word_size - 1u);
948 template <
bool with_carry>
949 void compute_kernel(compute_state & state,
size_t const block_offset,
size_t const current_block)
noexcept
951 state.vp = proxy_reference<word_type>{this->vp[current_block]};
952 state.vn = proxy_reference<word_type>{this->vn[current_block]};
953 if constexpr(compute_trace_matrix)
955 state.hp = proxy_reference<word_type>{this->hp[current_block]};
956 state.db = proxy_reference<word_type>{this->db[current_block]};
958 state.b = bit_masks[block_offset + current_block];
960 compute_step<with_carry>(state);
961 if constexpr(compute_trace_matrix)
962 state.db = ~(state.b ^ state.d0);
966 void advance_score(word_type P, word_type N, word_type mask)
noexcept
968 if ((P & mask) != word_type{0u})
970 else if ((N & mask) != word_type{0u})
975 bool on_hit() noexcept
982 inline bool small_patterns();
985 inline bool large_patterns();
988 inline void compute_empty_query_sequence()
990 assert(std::ranges::empty(query));
992 bool abort_computation =
false;
994 for (; database_it != database_it_end; ++database_it)
996 if constexpr(is_global)
999 this->update_best_score();
1002 if constexpr(use_max_errors)
1003 abort_computation = on_hit();
1006 if (abort_computation)
1015 if constexpr(use_max_errors && is_global && !compute_matrix)
1035 if (vp.size() == 0u)
1036 compute_empty_query_sequence();
1037 else if (vp.size() == 1u)
1042 if constexpr(is_global)
1043 this->update_best_score();
1051 template <
typename callback_t>
1052 void operator()([[maybe_unused]]
size_t const idx, callback_t && callback)
1054 using traits_type = alignment_configuration_traits<align_config_t>;
1055 using result_value_type =
typename alignment_result_value_type_accessor<alignment_result_type>::type;
1062 auto cached_end_positions = this->invalid_coordinate();
1063 auto cached_begin_positions = this->invalid_coordinate();
1065 if constexpr (compute_end_positions)
1066 cached_end_positions = this->end_positions();
1068 if constexpr (compute_begin_positions && !compute_sequence_alignment)
1070 static_assert(compute_end_positions,
"End positions required to compute the begin positions.");
1071 cached_begin_positions = this->begin_positions();
1077 result_value_type res_vt{};
1079 if constexpr (traits_type::output_sequence1_id)
1080 res_vt.sequence1_id = idx;
1082 if constexpr (traits_type::output_sequence2_id)
1083 res_vt.sequence2_id = idx;
1085 if constexpr (traits_type::compute_score)
1086 res_vt.score = this->score().value_or(matrix_inf<score_type>);
1088 if constexpr (traits_type::compute_sequence_alignment)
1090 if (this->is_valid())
1092 auto [first, second] = cached_end_positions;
1093 detail::matrix_coordinate
const end_positions{detail::row_index_type{second},
1094 detail::column_index_type{first}};
1096 aligned_sequence_builder builder{this->database, this->query};
1097 auto trace_res = builder(this->trace_matrix().trace_path(end_positions));
1098 res_vt.alignment = std::move(trace_res.alignment);
1099 cached_begin_positions.first = trace_res.first_sequence_slice_positions.first;
1100 cached_begin_positions.second = trace_res.second_sequence_slice_positions.first;
1104 if constexpr (traits_type::compute_end_positions)
1105 res_vt.end_positions = std::move(cached_end_positions);
1107 if constexpr (traits_type::compute_begin_positions)
1108 res_vt.begin_positions = std::move(cached_begin_positions);
1110 callback(alignment_result_type{std::move(res_vt)});
1114template <
typename database_t,
typename query_t,
typename align_config_t,
typename traits_t>
1115bool edit_distance_unbanded<database_t, query_t, align_config_t, traits_t>::small_patterns()
1117 bool abort_computation =
false;
1120 while (database_it != database_it_end)
1122 compute_state state{};
1123 size_t const block_offset =
seqan3::to_rank((query_alphabet_type) *database_it);
1125 compute_kernel<false>(state, block_offset, 0u);
1126 advance_score(state.hp, state.hn, score_mask);
1129 if constexpr(is_semi_global && !use_max_errors)
1130 this->update_best_score();
1133 if constexpr(use_max_errors)
1134 abort_computation = this->update_last_active_cell();
1138 if (abort_computation)
1145template <
typename database_t,
typename query_t,
typename align_config_t,
typename traits_t>
1146bool edit_distance_unbanded<database_t, query_t, align_config_t, traits_t>::large_patterns()
1148 bool abort_computation =
false;
1150 while (database_it != database_it_end)
1152 compute_state state{};
1153 size_t const block_offset = vp.size() *
seqan3::to_rank((query_alphabet_type) *database_it);
1155 size_t block_count = vp.size();
1156 if constexpr(use_max_errors)
1157 block_count = this->last_block + 1;
1160 for (
size_t current_block = 0u; current_block < block_count; current_block++)
1161 compute_kernel<true>(state, block_offset, current_block);
1163 advance_score(state.hp, state.hn, score_mask);
1166 if constexpr(is_semi_global && !use_max_errors)
1167 this->update_best_score();
1169 if constexpr(use_max_errors)
1172 bool additional_block = score_mask >> (word_size - 1u);
1173 bool reached_last_block = this->last_block + 1u == vp.size();
1175 if (reached_last_block)
1176 additional_block =
false;
1178 if (additional_block)
1180 size_t const current_block = this->last_block + 1u;
1182 vp[current_block] = vp0;
1183 vn[current_block] = vn0;
1184 compute_kernel<false>(state, block_offset, current_block);
1188 abort_computation = this->update_last_active_cell();
1194 if (abort_computation)
1207template <
typename database_t,
typename query_t,
typename config_t,
typename traits_t>
1208edit_distance_unbanded(database_t && database, query_t && query, config_t config, traits_t)
1209 -> 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: concept.hpp:155
@ 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: traits.hpp:151
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:429
SeqAn specific customisations in the standard namespace.
The <ranges> header from C++20's standard library.