31template <
typename word_t,
typename score_t,
bool is_semi_global,
bool use_max_errors>
36 template <std::ranges::viewable_range database_t,
37 std::ranges::viewable_range query_t,
38 typename align_config_t,
54 template <
typename derived_t,
typename edit_traits>
69 static constexpr auto word_size = bits_of<word_type>;
107 template <
typename score_type>
109 unsigned const last_block,
115 return active_row + (score <= max_errors);
134 size_t col = coordinate.col;
135 size_t row = coordinate.row;
138 assert(col <
cols());
141 if constexpr (use_max_errors)
147 size_t current_row = 1u;
148 size_t word_idx = 0u;
153 if (
row >= current_row)
201 requires (!use_max_errors)
204 column.vp = std::move(vp);
205 column.vn = std::move(vn);
216 requires use_max_errors
219 column.vp = std::move(vp);
220 column.vn = std::move(vn);
Provides utility functions for bit twiddling.
The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the score mat...
Definition: edit_distance_score_matrix_full.hpp:33
score_t score_type
The type of the score.
Definition: edit_distance_score_matrix_full.hpp:72
size_t size_type
The size type of the matrix.
Definition: edit_distance_score_matrix_full.hpp:81
edit_distance_score_matrix_full & operator=(edit_distance_score_matrix_full &&)=default
Defaulted.
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:108
size_t rows_size
The number of rows in the matrix.
Definition: edit_distance_score_matrix_full.hpp:228
reference at(matrix_coordinate const &coordinate) const noexcept
A reference to the entry of the matrix at the given coordinate.
Definition: edit_distance_score_matrix_full.hpp:132
edit_distance_score_matrix_full(size_t const rows_size)
Construct the score_matrix by giving the number of rows within the matrix.
Definition: edit_distance_score_matrix_full.hpp:60
std::vector< column_type > columns
The columns of the score matrix.
Definition: edit_distance_score_matrix_full.hpp:230
static constexpr std::optional< score_type > inf
A special score which represents infinity.
Definition: edit_distance_score_matrix_full.hpp:84
edit_distance_score_matrix_full(edit_distance_score_matrix_full &&)=default
Defaulted.
size_t rows() const noexcept
The number of rows in the matrix.
Definition: edit_distance_score_matrix_full.hpp:163
static constexpr auto word_size
The size of one machine word.
Definition: edit_distance_score_matrix_full.hpp:69
void add_column(std::vector< word_type > vp, std::vector< word_type > vn, size_t const max_rows)
Adds a column to the score matrix.
Definition: edit_distance_score_matrix_full.hpp:215
size_t cols() const noexcept
The number of columns in the matrix.
Definition: edit_distance_score_matrix_full.hpp:169
std::conditional_t< use_max_errors, std::optional< score_type >, score_type > value_type
The type of an entry in the matrix.
Definition: edit_distance_score_matrix_full.hpp:75
word_t word_type
The type of one machine word.
Definition: edit_distance_score_matrix_full.hpp:66
edit_distance_score_matrix_full(edit_distance_score_matrix_full const &)=default
Defaulted.
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:94
edit_distance_score_matrix_full & operator=(edit_distance_score_matrix_full const &)=default
Defaulted.
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:200
static score_type score_delta_of_word(word_type const &vp, word_type const &vn) noexcept
Computes delta score between vp and vn.
Definition: edit_distance_score_matrix_full.hpp:123
edit_distance_score_matrix_full()=default
Defaulted.
~edit_distance_score_matrix_full()=default
Defaulted.
Only available when default_edit_distance_trait_type::compute_score_matrix is true.
Definition: edit_distance_unbanded.hpp:421
This calculates an alignment using the edit distance and without a band.
Definition: edit_distance_unbanded.hpp:714
Implementation of a masked alphabet to be used for tuple composites..
Definition: mask.hpp:38
Forwards for seqan3::edit_distance_unbanded related types.
@ column
The corresponding alignment coordinate will be incrementable/decrementable in the column index.
@ row
The corresponding alignment coordinate will be incrementable/decrementable in the row index.
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
The internal SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
The state of one computation step.
Definition: edit_distance_score_matrix_full.hpp:194
If use_max_errors is true store these additional state information in state_type.
Definition: edit_distance_score_matrix_full.hpp:177
size_t max_rows
The number of max_rows within the current column. Computed by seqan3::detail::edit_distance_score_mat...
Definition: edit_distance_score_matrix_full.hpp:180
This information is needed to infer the score matrix.
Definition: edit_distance_score_matrix_full.hpp:185
std::vector< word_type > vn
The machine word which stores the negative vertical differences.
Definition: edit_distance_score_matrix_full.hpp:189
std::vector< word_type > vp
The machine word which stores the positive vertical differences.
Definition: edit_distance_score_matrix_full.hpp:187