34template <
typename derived_t,
typename edit_traits>
41 static_assert(edit_traits::use_max_errors,
"This policy assumes that edit_traits::use_max_errors is true.");
86 max_errors = -get<align_cfg::min_score>(self->config).score;
90 if (std::ranges::empty(self->query))
93 self->score_mask = 0u;
105 self->score_mask =
word_type{1u} << (local_max_errors % self->word_size);
107 self->_score = local_max_errors + 1u;
114 return (self->score_mask == this->last_score_mask) && (this->
last_block == self->vp.size() - 1u);
121 self->score_mask >>= 1u;
122 if (self->score_mask != 0u)
125 if constexpr (edit_traits::is_global)
133 self->score_mask =
word_type{1u} << (edit_traits::word_size - 1u);
141 self->score_mask <<= 1u;
142 if (self->score_mask)
145 self->score_mask = 1u;
162 assert(edit_traits::is_global);
165 return !edit_traits::compute_matrix;
173 if constexpr(edit_traits::is_semi_global)
174 self->update_best_score();
176 return self->on_hit();
203template <
typename derived_t,
typename edit_traits>
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.");
265 if constexpr(edit_traits::use_max_errors)
266 return _best_score <= self->max_errors;
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())
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();
325 return {first, second};
331template <
typename derived_t,
typename edit_traits>
336 static_assert(edit_traits::is_semi_global,
"This policy assumes that edit_traits::is_semi_global is true.");
395 if constexpr(edit_traits::use_max_errors)
397 assert(std::ranges::empty(self->query) || self->is_last_active_cell_within_last_row());
409 size_t offset = std::ranges::empty(self->database) ? 0u : 1u;
418template <
typename derived_t,
typename edit_traits>
425 static_assert(edit_traits::compute_score_matrix,
426 "This policy assumes that edit_traits::compute_score_matrix is true.");
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.");
498template <
typename derived_t,
typename edit_traits>
505 static_assert(edit_traits::compute_trace_matrix,
506 "This policy assumes that edit_traits::compute_trace_matrix is true.");
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.");
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();
593 auto trace_path = self->trace_matrix().trace_path(end_positions);
594 auto trace_path_it = std::ranges::begin(trace_path);
595 std::ranges::advance(trace_path_it, std::ranges::end(trace_path));
596 detail::matrix_coordinate
const begin_positions = trace_path_it.coordinate();
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();
616 auto trace_path = self->trace_matrix().trace_path(end_positions);
617 return builder(trace_path).alignment;
625template <
typename value_t>
647 template <
typename other_value_t>
649 requires std::convertible_to<other_value_t, value_t>
653 get() = std::forward<other_value_t>(u);
659 value_t &
get() const noexcept
661 assert(
ptr !=
nullptr);
666 operator value_t & ()
const noexcept
687template <std::ranges::viewable_range database_t,
688 std::ranges::viewable_range query_t,
689 typename align_config_t,
690 typename edit_traits>
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>>,
700 edit_traits::is_global,
701 edit_distance_unbanded_global_policy,
703 edit_distance_unbanded<database_t, query_t, align_config_t, edit_traits>>,
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>>,
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>>,
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>
734 template <
typename other_derived_t,
typename other_edit_traits>
737 template <
typename other_derived_t,
typename other_edit_traits>
740 template <
typename other_derived_t,
typename other_edit_traits>
743 template <
typename other_derived_t,
typename other_edit_traits>
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;
877 align_config_t _config,
878 edit_traits
const & SEQAN3_DOXYGEN_ONLY(_traits)) :
880 query{
std::forward<query_t>(_query)},
881 config{
std::forward<align_config_t>(_config)},
886 static constexpr size_t alphabet_size_ = alphabet_size<query_alphabet_type>;
918 template <
bool with_carry>
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>
958 state.b =
bit_masks[block_offset + current_block];
960 compute_step<with_carry>(state);
962 state.db = ~(state.b ^ state.d0);
990 assert(std::ranges::empty(
query));
992 bool abort_computation =
false;
1003 abort_computation =
on_hit();
1006 if (abort_computation)
1037 else if (
vp.
size() == 1u)
1051 template <
typename callback_t>
1052 void operator()([[maybe_unused]]
size_t const idx, callback_t && callback)
1055 using result_value_type =
typename alignment_result_value_type_accessor<alignment_result_type>::type;
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)
1092 auto [first, second] = cached_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);
1114template <std::ranges::viewable_range database_t,
1115 std::ranges::viewable_range query_t,
1116 typename align_config_t,
1120 bool abort_computation =
false;
1123 while (database_it != database_it_end)
1128 compute_kernel<false>(state, block_offset, 0u);
1129 advance_score(state.hp, state.hn, score_mask);
1132 if constexpr(is_semi_global && !use_max_errors)
1133 this->update_best_score();
1136 if constexpr(use_max_errors)
1137 abort_computation = this->update_last_active_cell();
1141 if (abort_computation)
1148template <std::ranges::viewable_range database_t,
1149 std::ranges::viewable_range query_t,
1150 typename align_config_t,
1154 bool abort_computation =
false;
1156 while (database_it != database_it_end)
1161 size_t block_count = vp.size();
1162 if constexpr(use_max_errors)
1163 block_count = this->last_block + 1;
1166 for (
size_t current_block = 0u; current_block < block_count; current_block++)
1167 compute_kernel<true>(state, block_offset, current_block);
1169 advance_score(state.hp, state.hn, score_mask);
1172 if constexpr(is_semi_global && !use_max_errors)
1173 this->update_best_score();
1175 if constexpr(use_max_errors)
1178 bool additional_block = score_mask >> (word_size - 1u);
1179 bool reached_last_block = this->last_block + 1u == vp.size();
1181 if (reached_last_block)
1182 additional_block =
false;
1184 if (additional_block)
1186 size_t const current_block = this->last_block + 1u;
1188 vp[current_block] = vp0;
1189 vn[current_block] = vn0;
1190 compute_kernel<false>(state, block_offset, current_block);
1194 abort_computation = this->update_last_active_cell();
1200 if (abort_computation)
1213template <
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:66
Builds the alignment for a given pair of sequences and the respective trace.
Definition: aligned_sequence_builder.hpp:117
The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the score mat...
Definition: edit_distance_score_matrix_full.hpp:33
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:109
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:201
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:95
The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the trace mat...
Definition: edit_distance_trace_matrix_full.hpp:33
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:92
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:196
Only available when default_edit_distance_trait_type::is_global is true.
Definition: edit_distance_unbanded.hpp:208
bool is_valid() const noexcept
Returns true if the computation produced a valid alignment.
Definition: edit_distance_unbanded.hpp:258
friend derived_t
Befriends the derived type.
Definition: edit_distance_unbanded.hpp:211
size_t end_positions_first() const noexcept
Returns the first component of the end_positions.
Definition: edit_distance_unbanded.hpp:288
void update_best_score() noexcept
Update the current best known score if the current score is better.
Definition: edit_distance_unbanded.hpp:281
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:302
void score_init() noexcept
Initialises global policy.
Definition: edit_distance_unbanded.hpp:251
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:243
seqan3::detail::advanceable_alignment_coordinate invalid_coordinate() const noexcept
Returns an invalid_coordinate for this alignment.
Definition: edit_distance_unbanded.hpp:274
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:315
Only available when default_edit_distance_trait_type::use_max_errors is true.
Definition: edit_distance_unbanded.hpp:39
friend derived_t
Befriends the derived type.
Definition: edit_distance_unbanded.hpp:41
void next_last_active_cell() noexcept
Increment the last active cell position.
Definition: edit_distance_unbanded.hpp:138
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:111
bool update_last_active_cell() noexcept
Use the ukkonen trick and update the last active cell.
Definition: edit_distance_unbanded.hpp:152
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:189
word_type last_score_mask
A mask with a bit set on the position of the last row.
Definition: edit_distance_unbanded.hpp:74
score_type max_errors
Which score value is considered as a hit?
Definition: edit_distance_unbanded.hpp:70
bool prev_last_active_cell() noexcept
Decrement the last active cell position.
Definition: edit_distance_unbanded.hpp:118
void max_errors_init(size_t block_count) noexcept
Initialises max_errors policy.
Definition: edit_distance_unbanded.hpp:82
size_t last_block
The block containing the last active cell.
Definition: edit_distance_unbanded.hpp:72
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:423
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:486
edit_distance_unbanded_score_matrix_policy() noexcept=default
Defaulted.
friend derived_t
Befriends the derived type.
Definition: edit_distance_unbanded.hpp:426
score_matrix_type _score_matrix
The score matrix of the edit distance alignment.
Definition: edit_distance_unbanded.hpp:454
void score_matrix_init()
Initialises score-matrix policy.
Definition: edit_distance_unbanded.hpp:469
Only available when default_edit_distance_trait_type::is_semi_global is true.
Definition: edit_distance_unbanded.hpp:334
friend derived_t
Befriends the derived type.
Definition: edit_distance_unbanded.hpp:336
size_t end_positions_first() const noexcept
Returns the first component of the end_positions.
Definition: edit_distance_unbanded.hpp:405
void score_init() noexcept
Initialises semi-global policy.
Definition: edit_distance_unbanded.hpp:383
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:391
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:375
Only available when default_edit_distance_trait_type::compute_trace_matrix is true.
Definition: edit_distance_unbanded.hpp:503
std::vector< word_type > db
The machine word which stores if trace_directions::diagonal is true.
Definition: edit_distance_unbanded.hpp:538
void trace_matrix_init(size_t block_count)
Initialises trace-matrix policy.
Definition: edit_distance_unbanded.hpp:556
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:541
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:583
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:602
trace_matrix_type const & trace_matrix() const noexcept
Return the trace matrix of the alignment.
Definition: edit_distance_unbanded.hpp:574
friend derived_t
Befriends the derived type.
Definition: edit_distance_unbanded.hpp:506
std::vector< word_type > hp
The machine word which stores the positive horizontal differences.
Definition: edit_distance_unbanded.hpp:536
This calculates an alignment using the edit distance and without a band.
Definition: edit_distance_unbanded.hpp:720
database_iterator database_it
The current position in the database.
Definition: edit_distance_unbanded.hpp:800
void add_state()
Add a computation step.
Definition: edit_distance_unbanded.hpp:838
database_iterator database_it_end
The end position of the database.
Definition: edit_distance_unbanded.hpp:802
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:1118
edit_distance_unbanded(edit_distance_unbanded &&)=default
Defaulted.
void compute()
Compute the alignment.
Definition: edit_distance_unbanded.hpp:1012
void operator()(size_t const idx, callback_t &&callback)
Generic invocable interface.
Definition: edit_distance_unbanded.hpp:1052
word_type score_mask
The mask with a bit set at the position where the score change.
Definition: edit_distance_unbanded.hpp:786
void compute_empty_query_sequence()
Special case if query sequence is empty.
Definition: edit_distance_unbanded.hpp:988
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:765
edit_distance_unbanded & operator=(edit_distance_unbanded &&)=default
Defaulted.
database_t database
The horizontal/database sequence.
Definition: edit_distance_unbanded.hpp:763
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:919
bool large_patterns()
Pattern is larger than one machine word. Use overflow aware computation.
Definition: edit_distance_unbanded.hpp:1152
edit_distance_unbanded(database_t _database, query_t _query, align_config_t _config, edit_traits const &_traits)
Constructor.
Definition: edit_distance_unbanded.hpp:875
static constexpr word_type vp0
How to pre-initialise vp.
Definition: edit_distance_unbanded.hpp:774
static constexpr word_type vn0
How to pre-initialise vn.
Definition: edit_distance_unbanded.hpp:776
~edit_distance_unbanded()=default
Defaulted.
static constexpr word_type hp0
How to pre-initialise hp.
Definition: edit_distance_unbanded.hpp:770
static constexpr word_type hn0
How to pre-initialise hn.
Definition: edit_distance_unbanded.hpp:772
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:788
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:949
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:797
std::vector< word_type > vn
The machine word which stores the negative vertical differences.
Definition: edit_distance_unbanded.hpp:790
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:966
score_type _score
The score of the current column.
Definition: edit_distance_unbanded.hpp:779
align_config_t config
The configuration.
Definition: edit_distance_unbanded.hpp:767
bool on_hit() noexcept
Will be called if a hit was found (e.g., score <= max_errors).
Definition: edit_distance_unbanded.hpp:975
The same as value_t & but it is default constructible and is re-assignable.
Definition: edit_distance_unbanded.hpp:627
value_t * ptr
The stored reference.
Definition: edit_distance_unbanded.hpp:673
value_t & get() const noexcept
Get the stored reference.
Definition: edit_distance_unbanded.hpp:659
proxy_reference & operator=(other_value_t &&u) noexcept
Assign a value to the stored reference.
Definition: edit_distance_unbanded.hpp:651
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:37
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:154
@ 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.
The internal SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
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:131
SeqAn specific customisations in the standard namespace.
The <ranges> header from C++20's standard library.
A traits type for the alignment algorithm that exposes static information stored within the alignment...
Definition: type_traits.hpp:87
A strong type for designated initialisation of the column index of a matrix.
Definition: matrix_coordinate.hpp:34
typename alignment_traits_type::original_score_type score_type
The type of the score.
Definition: edit_distance_fwd.hpp:74
word_t word_type
The type of one machine word.
Definition: edit_distance_fwd.hpp:70
static constexpr bool is_global
Whether the alignment is a global alignment or not.
Definition: edit_distance_fwd.hpp:99
std::ranges::iterator_t< database_type > database_iterator
The type of an iterator of the database sequence.
Definition: edit_distance_fwd.hpp:85
static constexpr uint8_t word_size
The size of one machine word.
Definition: edit_distance_fwd.hpp:81
static constexpr bool compute_trace_matrix
Whether the alignment configuration indicates to compute and/or store the trace matrix.
Definition: edit_distance_fwd.hpp:113
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:95
static constexpr bool compute_score_matrix
Whether the alignment configuration indicates to compute and/or store the score matrix.
Definition: edit_distance_fwd.hpp:111
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:115
typename alignment_traits_type::alignment_result_type alignment_result_type
The alignment result type generated by the algorithm.
Definition: edit_distance_fwd.hpp:89
static constexpr bool compute_end_positions
Whether the alignment configuration indicates to compute and/or store the end positions.
Definition: edit_distance_fwd.hpp:108
typename alignment_result_value_type_accessor< alignment_result_type >::type result_value_type
The alignment result value type.
Definition: edit_distance_fwd.hpp:91
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:103
static constexpr bool compute_begin_positions
Whether the alignment configuration indicates to compute and/or store the begin positions.
Definition: edit_distance_fwd.hpp:105
The internal state needed to compute the trace matrix.
Definition: edit_distance_unbanded.hpp:806
proxy_reference< word_type > db
The machine word which stores if trace_directions::diagonal is true.
Definition: edit_distance_unbanded.hpp:808
The internal state needed to compute the alignment.
Definition: edit_distance_unbanded.hpp:813
word_type b
The machine word which stores wether the current character matches.
Definition: edit_distance_unbanded.hpp:818
word_type d0
The machine word which stores the diagonal differences.
Definition: edit_distance_unbanded.hpp:820
proxy_reference< word_type > vn
The machine word which stores the negative vertical differences.
Definition: edit_distance_unbanded.hpp:828
word_type carry_hp
The carry-bit of hp.
Definition: edit_distance_unbanded.hpp:832
proxy_reference< word_type > vp
The machine word which stores the positive vertical differences.
Definition: edit_distance_unbanded.hpp:826
word_type carry_d0
The carry-bit of d0.
Definition: edit_distance_unbanded.hpp:830
word_type hn
The machine word which stores the negative horizontal differences.
Definition: edit_distance_unbanded.hpp:824
word_type carry_hn
The carry-bit of hn.
Definition: edit_distance_unbanded.hpp:834
hp_type hp
The machine word which stores the positive horizontal differences.
Definition: edit_distance_unbanded.hpp:822
A strong type for designated initialisation of the row index of a matrix.
Definition: matrix_coordinate.hpp:65