30template <
typename derived_t,
typename edit_traits>
37 static_assert(edit_traits::use_max_errors,
"This policy assumes that edit_traits::use_max_errors is true.");
82 max_errors = -get<align_cfg::min_score>(self->config).score;
86 if (std::ranges::empty(self->query))
89 self->score_mask = 0u;
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);
103 self->_score = local_max_errors + 1u;
110 return (self->score_mask == this->last_score_mask) && (this->
last_block == self->vp.size() - 1u);
117 self->score_mask >>= 1u;
118 if (self->score_mask != 0u)
121 if constexpr (edit_traits::is_global)
129 self->score_mask =
word_type{1u} << (edit_traits::word_size - 1u);
137 self->score_mask <<= 1u;
138 if (self->score_mask)
141 self->score_mask = 1u;
158 assert(edit_traits::is_global);
161 return !edit_traits::compute_matrix;
169 if constexpr (edit_traits::is_semi_global)
170 self->update_best_score();
172 return self->on_hit();
198template <
typename derived_t,
typename edit_traits>
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.");
259 if constexpr (edit_traits::use_max_errors)
260 return _best_score <= self->max_errors;
285 return std::ranges::size(self->database);
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())
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();
321 return {first, second};
327template <
typename derived_t,
typename edit_traits>
331 static_assert(edit_traits::is_semi_global,
"This policy assumes that edit_traits::is_semi_global is true.");
390 if constexpr (edit_traits::use_max_errors)
392 assert(std::ranges::empty(self->query) || self->is_last_active_cell_within_last_row());
404 size_t offset = std::ranges::empty(self->database) ? 0u : 1u;
413template <
typename derived_t,
typename edit_traits>
420 static_assert(edit_traits::compute_score_matrix,
421 "This policy assumes that edit_traits::compute_score_matrix is true.");
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.");
494template <
typename derived_t,
typename edit_traits>
501 static_assert(edit_traits::compute_trace_matrix,
502 "This policy assumes that edit_traits::compute_trace_matrix is true.");
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.");
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();
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();
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();
615 auto trace_path = self->trace_matrix().trace_path(end_positions);
616 return builder(trace_path).alignment;
624template <
typename value_t>
645 template <
typename other_value_t>
646 requires std::convertible_to<other_value_t, value_t>
649 get() = std::forward<other_value_t>(u);
655 value_t &
get() const noexcept
657 assert(
ptr !=
nullptr);
662 operator value_t &()
const noexcept
683template <std::ranges::viewable_range database_t,
684 std::ranges::viewable_range query_t,
685 typename align_config_t,
686 typename edit_traits>
691 edit_distance_unbanded_max_errors_policy,
693 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
695 edit_distance_unbanded_global_policy,
697 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
699 edit_distance_unbanded_semi_global_policy,
701 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
703 edit_distance_unbanded_score_matrix_policy,
705 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
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>
725 template <
typename other_derived_t,
typename other_edit_traits>
728 template <
typename other_derived_t,
typename other_edit_traits>
731 template <
typename other_derived_t,
typename other_edit_traits>
734 template <
typename other_derived_t,
typename other_edit_traits>
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;
868 align_config_t _config,
869 edit_traits
const & SEQAN3_DOXYGEN_ONLY(_traits)) :
871 query{
std::forward<query_t>(_query)},
872 config{
std::forward<align_config_t>(_config)},
877 static constexpr size_t alphabet_size_ = alphabet_size<query_alphabet_type>;
897 for (
size_t j = 0u; j < std::ranges::size(
query); j++)
909 template <
bool with_carry>
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>
949 state.b =
bit_masks[block_offset + current_block];
951 compute_step<with_carry>(state);
953 state.db = ~(state.b ^ state.d0);
981 assert(std::ranges::empty(
query));
983 bool abort_computation =
false;
994 abort_computation =
on_hit();
997 if (abort_computation)
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);
1028 else if (
vp.
size() == 1u)
1042 template <
typename callback_t>
1043 void operator()([[maybe_unused]]
size_t const idx, callback_t && callback)
1046 using result_value_type =
typename alignment_result_value_type_accessor<alignment_result_type>::type;
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)
1083 auto [first, second] = cached_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);
1105template <std::ranges::viewable_range database_t,
1106 std::ranges::viewable_range query_t,
1107 typename align_config_t,
1111 bool abort_computation =
false;
1114 while (database_it != database_it_end)
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,
1145 bool abort_computation =
false;
1147 while (database_it != database_it_end)
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>
Provides seqan3::detail::advanceable_alignment_coordinate.
Provides seqan3::alignment_result.
Implements an internal alignment coordinate that can be used as an argument to the std::ranges::iota_...
Definition advanceable_alignment_coordinate.hpp:63
Builds the alignment for a given pair of sequences and the respective trace.
Definition aligned_sequence_builder.hpp:114
The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the score mat...
Definition edit_distance_score_matrix_full.hpp:30
static size_t max_rows(word_type const score_mask, unsigned const last_block, score_type const score, score_type const max_errors) noexcept
Computes the number of max rows in the current column.
Definition edit_distance_score_matrix_full.hpp:105
void reserve(size_t const new_capacity)
Increase the capacity of the columns to a value that is greater or equal to new_capacity.
Definition edit_distance_score_matrix_full.hpp:91
void add_column(std::vector< word_type > vp, std::vector< word_type > vn)
Adds a column to the score matrix.
Definition edit_distance_score_matrix_full.hpp:197
The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the trace mat...
Definition edit_distance_trace_matrix_full.hpp:30
void reserve(size_t const new_capacity)
Increase the capacity of the columns to a value that's greater or equal to new_capacity.
Definition edit_distance_trace_matrix_full.hpp:88
void add_column(std::vector< word_type > left, std::vector< word_type > diagonal, std::vector< word_type > up)
Adds a column to the trace matrix.
Definition edit_distance_trace_matrix_full.hpp:190
Only available when default_edit_distance_trait_type::is_global is true.
Definition edit_distance_unbanded.hpp:203
bool is_valid() const noexcept
Returns true if the computation produced a valid alignment.
Definition edit_distance_unbanded.hpp:252
friend derived_t
Befriends the derived type.
Definition edit_distance_unbanded.hpp:209
size_t end_positions_first() const noexcept
Returns the first component of the end_positions.
Definition edit_distance_unbanded.hpp:282
void update_best_score() noexcept
Update the current best known score if the current score is better.
Definition edit_distance_unbanded.hpp:275
std::optional< score_type > score() const noexcept
Return the score of the alignment. Only available if default_edit_distance_trait_type::compute_score ...
Definition edit_distance_unbanded.hpp:296
void score_init() noexcept
Initialises global policy.
Definition edit_distance_unbanded.hpp:245
score_type _best_score
The best score of the alignment in the last row (if is_semi_global = true) or the last entry in the s...
Definition edit_distance_unbanded.hpp:237
seqan3::detail::advanceable_alignment_coordinate invalid_coordinate() const noexcept
Returns an invalid_coordinate for this alignment.
Definition edit_distance_unbanded.hpp:268
edit_distance_unbanded_global_policy() noexcept=default
Defaulted.
seqan3::detail::advanceable_alignment_coordinate end_positions() const noexcept
Return the end position of the alignment Only available if default_edit_distance_trait_type::compute_...
Definition edit_distance_unbanded.hpp:310
Only available when default_edit_distance_trait_type::use_max_errors is true.
Definition edit_distance_unbanded.hpp:35
friend derived_t
Befriends the derived type.
Definition edit_distance_unbanded.hpp:40
void next_last_active_cell() noexcept
Increment the last active cell position.
Definition edit_distance_unbanded.hpp:134
bool is_last_active_cell_within_last_row() const noexcept
Returns true if the current active cell is within the last row.
Definition edit_distance_unbanded.hpp:107
bool update_last_active_cell() noexcept
Use the ukkonen trick and update the last active cell.
Definition edit_distance_unbanded.hpp:148
static size_t max_rows(word_type const score_mask, unsigned const last_block, score_type const score, score_type const max_errors) noexcept
Computes the number of max rows in the current column.
Definition edit_distance_unbanded.hpp:185
word_type last_score_mask
A mask with a bit set on the position of the last row.
Definition edit_distance_unbanded.hpp:70
score_type max_errors
Which score value is considered as a hit?
Definition edit_distance_unbanded.hpp:66
bool prev_last_active_cell() noexcept
Decrement the last active cell position.
Definition edit_distance_unbanded.hpp:114
void max_errors_init(size_t block_count) noexcept
Initialises max_errors policy.
Definition edit_distance_unbanded.hpp:78
size_t last_block
The block containing the last active cell.
Definition edit_distance_unbanded.hpp:68
edit_distance_unbanded_max_errors_policy() noexcept=default
Defaulted.
Only available when default_edit_distance_trait_type::compute_score_matrix is true.
Definition edit_distance_unbanded.hpp:418
score_matrix_type const & score_matrix() const noexcept
Return the score matrix of the alignment. Only available if default_edit_distance_trait_type::compute...
Definition edit_distance_unbanded.hpp:481
edit_distance_unbanded_score_matrix_policy() noexcept=default
Defaulted.
friend derived_t
Befriends the derived type.
Definition edit_distance_unbanded.hpp:424
score_matrix_type _score_matrix
The score matrix of the edit distance alignment.
Definition edit_distance_unbanded.hpp:449
void score_matrix_init()
Initialises score-matrix policy.
Definition edit_distance_unbanded.hpp:464
Only available when default_edit_distance_trait_type::is_semi_global is true.
Definition edit_distance_unbanded.hpp:329
friend derived_t
Befriends the derived type.
Definition edit_distance_unbanded.hpp:334
size_t end_positions_first() const noexcept
Returns the first component of the end_positions.
Definition edit_distance_unbanded.hpp:400
void score_init() noexcept
Initialises semi-global policy.
Definition edit_distance_unbanded.hpp:378
edit_distance_unbanded_semi_global_policy() noexcept=default
Defaulted.
void update_best_score() noexcept
Update the current best known score if the current score is better.
Definition edit_distance_unbanded.hpp:386
database_iterator _best_score_col
In which column the best score of the alignment is located. Will only be tracked if is_semi_global is...
Definition edit_distance_unbanded.hpp:370
Only available when default_edit_distance_trait_type::compute_trace_matrix is true.
Definition edit_distance_unbanded.hpp:499
std::vector< word_type > db
The machine word which stores if trace_directions::diagonal is true.
Definition edit_distance_unbanded.hpp:534
void trace_matrix_init(size_t block_count)
Initialises trace-matrix policy.
Definition edit_distance_unbanded.hpp:552
edit_distance_unbanded_trace_matrix_policy() noexcept=default
Defaulted.
trace_matrix_type _trace_matrix
The trace matrix of the edit distance alignment.
Definition edit_distance_unbanded.hpp:537
seqan3::detail::advanceable_alignment_coordinate begin_positions() const noexcept
Return the begin position of the alignment. Only available if default_edit_distance_trait_type::compu...
Definition edit_distance_unbanded.hpp:580
auto alignment() const noexcept
Return the alignment, i.e. the actual base pair matching. Only available if default_edit_distance_tra...
Definition edit_distance_unbanded.hpp:600
trace_matrix_type const & trace_matrix() const noexcept
Return the trace matrix of the alignment.
Definition edit_distance_unbanded.hpp:570
friend derived_t
Befriends the derived type.
Definition edit_distance_unbanded.hpp:505
std::vector< word_type > hp
The machine word which stores the positive horizontal differences.
Definition edit_distance_unbanded.hpp:532
This calculates an alignment using the edit distance and without a band.
Definition edit_distance_unbanded.hpp:711
database_iterator database_it
The current position in the database.
Definition edit_distance_unbanded.hpp:791
void add_state()
Add a computation step.
Definition edit_distance_unbanded.hpp:829
database_iterator database_it_end
The end position of the database.
Definition edit_distance_unbanded.hpp:793
bool small_patterns()
Pattern is small enough that it fits into one machine word. Use faster computation with less overhead...
Definition edit_distance_unbanded.hpp:1109
edit_distance_unbanded(edit_distance_unbanded &&)=default
Defaulted.
void compute()
Compute the alignment.
Definition edit_distance_unbanded.hpp:1003
void operator()(size_t const idx, callback_t &&callback)
Generic invocable interface.
Definition edit_distance_unbanded.hpp:1043
word_type score_mask
The mask with a bit set at the position where the score change.
Definition edit_distance_unbanded.hpp:777
void compute_empty_query_sequence()
Special case if query sequence is empty.
Definition edit_distance_unbanded.hpp:979
edit_distance_unbanded()=delete
The class template parameter may resolve to an lvalue reference which prohibits default constructibil...
query_t query
The vertical/query sequence.
Definition edit_distance_unbanded.hpp:756
edit_distance_unbanded & operator=(edit_distance_unbanded &&)=default
Defaulted.
database_t database
The horizontal/database sequence.
Definition edit_distance_unbanded.hpp:754
edit_distance_unbanded(database_t &&database, query_t &&query, config_t config, traits_t) -> edit_distance_unbanded< database_t, query_t, config_t, traits_t >
Deduce the type from the provided arguments.
static void compute_step(compute_state &state) noexcept
A single compute step in the current column.
Definition edit_distance_unbanded.hpp:910
bool large_patterns()
Pattern is larger than one machine word. Use overflow aware computation.
Definition edit_distance_unbanded.hpp:1143
edit_distance_unbanded(database_t _database, query_t _query, align_config_t _config, edit_traits const &_traits)
Constructor.
Definition edit_distance_unbanded.hpp:866
static constexpr word_type vp0
How to pre-initialise vp.
Definition edit_distance_unbanded.hpp:765
static constexpr word_type vn0
How to pre-initialise vn.
Definition edit_distance_unbanded.hpp:767
~edit_distance_unbanded()=default
Defaulted.
static constexpr word_type hp0
How to pre-initialise hp.
Definition edit_distance_unbanded.hpp:761
static constexpr word_type hn0
How to pre-initialise hn.
Definition edit_distance_unbanded.hpp:763
edit_distance_unbanded(edit_distance_unbanded const &)=default
Defaulted.
std::vector< word_type > vp
The machine word which stores the positive vertical differences.
Definition edit_distance_unbanded.hpp:779
void compute_kernel(compute_state &state, size_t const block_offset, size_t const current_block) noexcept
A single compute step in the current column at a given position.
Definition edit_distance_unbanded.hpp:940
std::vector< word_type > bit_masks
The machine words which translate a letter of the query into a bit mask.
Definition edit_distance_unbanded.hpp:788
std::vector< word_type > vn
The machine word which stores the negative vertical differences.
Definition edit_distance_unbanded.hpp:781
edit_distance_unbanded & operator=(edit_distance_unbanded const &)=default
Defaulted.
void advance_score(word_type P, word_type N, word_type mask) noexcept
Increase or decrease the score.
Definition edit_distance_unbanded.hpp:957
score_type _score
The score of the current column.
Definition edit_distance_unbanded.hpp:770
align_config_t config
The configuration.
Definition edit_distance_unbanded.hpp:758
bool on_hit() noexcept
Will be called if a hit was found (e.g., score <= max_errors).
Definition edit_distance_unbanded.hpp:966
The same as value_t & but it is default constructible and is re-assignable.
Definition edit_distance_unbanded.hpp:626
value_t * ptr
The stored reference.
Definition edit_distance_unbanded.hpp:669
value_t & get() const noexcept
Get the stored reference.
Definition edit_distance_unbanded.hpp:655
proxy_reference & operator=(other_value_t &&u) noexcept
Assign a value to the stored reference.
Definition edit_distance_unbanded.hpp:647
proxy_reference(value_t &&)=delete
Deleted.
proxy_reference() noexcept=default
Defaulted.
Implementation of a masked alphabet to be used for tuple composites.
Definition mask.hpp:35
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
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
Provides seqan3::detail::matrix.
The internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
invoke_deferred_crtp_base< deferred_crtp_base< selector< enable_policy, policy_t, empty_state >::template select, edit_traits >, derived_t > edit_distance_base
A base class for edit_distance_unbanded.
Definition edit_distance_fwd.hpp:124
SeqAn specific customisations in the standard namespace.
A traits type for the alignment algorithm that exposes static information stored within the alignment...
Definition alignment/pairwise/detail/type_traits.hpp:80
A strong type for designated initialisation of the column index of a matrix.
Definition matrix_coordinate.hpp:29
typename alignment_traits_type::original_score_type score_type
The type of the score.
Definition edit_distance_fwd.hpp:71
word_t word_type
The type of one machine word.
Definition edit_distance_fwd.hpp:67
static constexpr bool is_global
Whether the alignment is a global alignment or not.
Definition edit_distance_fwd.hpp:96
std::ranges::iterator_t< database_type > database_iterator
The type of an iterator of the database sequence.
Definition edit_distance_fwd.hpp:82
static constexpr uint8_t word_size
The size of one machine word.
Definition edit_distance_fwd.hpp:78
static constexpr bool compute_trace_matrix
Whether the alignment configuration indicates to compute and/or store the trace matrix.
Definition edit_distance_fwd.hpp:110
static constexpr bool use_max_errors
When true the computation will use the ukkonen trick with the last active cell and bounds the error t...
Definition edit_distance_fwd.hpp:92
static constexpr bool compute_score_matrix
Whether the alignment configuration indicates to compute and/or store the score matrix.
Definition edit_distance_fwd.hpp:108
static constexpr bool compute_matrix
Whether the alignment configuration indicates to compute and/or store the score or trace matrix.
Definition edit_distance_fwd.hpp:112
typename alignment_traits_type::alignment_result_type alignment_result_type
The alignment result type generated by the algorithm.
Definition edit_distance_fwd.hpp:86
static constexpr bool compute_end_positions
Whether the alignment configuration indicates to compute and/or store the end positions.
Definition edit_distance_fwd.hpp:105
typename alignment_result_value_type_accessor< alignment_result_type >::type result_value_type
The alignment result value type.
Definition edit_distance_fwd.hpp:88
static constexpr bool compute_sequence_alignment
Whether the alignment configuration indicates to compute and/or store the alignment of the sequences.
Definition edit_distance_fwd.hpp:100
static constexpr bool compute_begin_positions
Whether the alignment configuration indicates to compute and/or store the begin positions.
Definition edit_distance_fwd.hpp:102
The internal state needed to compute the trace matrix.
Definition edit_distance_unbanded.hpp:797
proxy_reference< word_type > db
The machine word which stores if trace_directions::diagonal is true.
Definition edit_distance_unbanded.hpp:799
The internal state needed to compute the alignment.
Definition edit_distance_unbanded.hpp:804
word_type b
The machine word which stores wether the current character matches.
Definition edit_distance_unbanded.hpp:809
word_type d0
The machine word which stores the diagonal differences.
Definition edit_distance_unbanded.hpp:811
proxy_reference< word_type > vn
The machine word which stores the negative vertical differences.
Definition edit_distance_unbanded.hpp:819
word_type carry_hp
The carry-bit of hp.
Definition edit_distance_unbanded.hpp:823
proxy_reference< word_type > vp
The machine word which stores the positive vertical differences.
Definition edit_distance_unbanded.hpp:817
word_type carry_d0
The carry-bit of d0.
Definition edit_distance_unbanded.hpp:821
word_type hn
The machine word which stores the negative horizontal differences.
Definition edit_distance_unbanded.hpp:815
word_type carry_hn
The carry-bit of hn.
Definition edit_distance_unbanded.hpp:825
hp_type hp
The machine word which stores the positive horizontal differences.
Definition edit_distance_unbanded.hpp:813
A strong type for designated initialisation of the row index of a matrix.
Definition matrix_coordinate.hpp:58