The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the score matrix. More...

#include <seqan3/alignment/matrix/detail/edit_distance_score_matrix_full.hpp>

Classes
struct	column_type
	The state of one computation step. More...

struct	max_errors_state
	If use_max_errors is true store these additional state information in state_type. More...

struct	score_matrix_state
	This information is needed to infer the score matrix. More...

Public Types
using	reference = value_type
	The type of a reference to an entry in the matrix.

using	score_type = score_t
	The type of the score.

using	size_type = size_t
	The size type of the matrix.

using	value_type = std::conditional_t< use_max_errors, std::optional< score_type >, score_type >
	The type of an entry in the matrix.

using	word_type = word_t
	The type of one machine word.

Public Member Functions
reference	at (matrix_coordinate const &coordinate) const noexcept
	A reference to the entry of the matrix at the given coordinate.

size_t	cols () const noexcept
	The number of columns in the matrix.

void	reserve (size_t const new_capacity)
	Increase the capacity of the columns to a value that is greater or equal to `new_capacity`.

size_t	rows () const noexcept
	The number of rows in the matrix.

Static Public Member Functions
template<typename score_type >
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.

static score_type	score_delta_of_word (word_type const &vp, word_type const &vn) noexcept
	Computes delta score between `vp` and `vn`.

Static Public Attributes
static constexpr std::optional< score_type >	inf = std::nullopt
	A special score which represents infinity.

static constexpr auto	word_size = bits_of<word_type>
	The size of one machine word.

Protected Member Functions
void	add_column (std::vector< word_type > vp, std::vector< word_type > vn)
	Adds a column to the score matrix.

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.

Private Attributes
std::vector< column_type >	columns {}
	The columns of the score matrix.

size_t	rows_size {}
	The number of rows in the matrix.

Friends
template<std::ranges::viewable_range database_t, std::ranges::viewable_range query_t, typename align_config_t , typename edit_traits >
class	edit_distance_unbanded
	This friend allows the edit distance algorithm to fill the score matrix via add_column.

Constructors, destructor and assignment
template<typename derived_t , typename edit_traits >
class	edit_distance_unbanded_score_matrix_policy
	Allow seqan3::detail::edit_distance_unbanded_score_matrix_policy to access the private constructor.

	edit_distance_score_matrix_full ()=default
	Defaulted.

	edit_distance_score_matrix_full (edit_distance_score_matrix_full const &)=default
	Defaulted.

	edit_distance_score_matrix_full (edit_distance_score_matrix_full &&)=default
	Defaulted.

edit_distance_score_matrix_full &	operator= (edit_distance_score_matrix_full const &)=default
	Defaulted.

edit_distance_score_matrix_full &	operator= (edit_distance_score_matrix_full &&)=default
	Defaulted.

	~edit_distance_score_matrix_full ()=default
	Defaulted.

	edit_distance_score_matrix_full (size_t const rows_size)
	Construct the score_matrix by giving the number of rows within the matrix.

Detailed Description

template<typename word_t, typename score_t, bool is_semi_global, bool use_max_errors>
class seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >

The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the score matrix.

Template Parameters

word_t	The type of one machine word.
score_t	The type of the score.
is_semi_global	Whether the alignment is a semi-global alignment or not.
use_max_errors	When true the computation will use the ukkonen trick with the last active cell and bounds the error to config.max_errors.

Member Typedef Documentation

◆ reference

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

using seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::reference = value_type

The type of a reference to an entry in the matrix.

◆ score_type

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

using seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::score_type = score_t

The type of the score.

◆ size_type

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

using seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::size_type = size_t

The size type of the matrix.

◆ value_type

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

using seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::value_type = std::conditional_t<use_max_errors, std::optional<score_type>, score_type>

The type of an entry in the matrix.

◆ word_type

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

using seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::word_type = word_t

The type of one machine word.

Constructor & Destructor Documentation

◆ edit_distance_score_matrix_full()

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::edit_distance_score_matrix_full ( size_t const rows_size )

inlineprotected

Construct the score_matrix by giving the number of rows within the matrix.

Parameters

rows_size The number of rows in the matrix.

Member Function Documentation

◆ add_column() [1/2]

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

void seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::add_column	(	std::vector< word_type >	vp,
		std::vector< word_type >	vn
	)

inlineprotected

Adds a column to the score matrix.

Parameters

vp	The machine word which stores the positive vertical differences.
vn	The machine word which stores the negative vertical differences.

◆ add_column() [2/2]

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

void seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::add_column	(	std::vector< word_type >	vp,
		std::vector< word_type >	vn,
		size_t const	max_rows
	)

inlineprotected

Adds a column to the score matrix.

Parameters

vp	The machine word which stores the positive vertical differences.
vn	The machine word which stores the negative vertical differences.
max_rows	The number of max_rows within the current column. Computed by seqan3::detail::edit_distance_score_matrix_full::max_rows.

◆ at()

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

reference seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::at ( matrix_coordinate const & coordinate ) const

inlinenoexcept

A reference to the entry of the matrix at the given coordinate.

◆ cols()

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

size_t seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::cols ( ) const

inlinenoexcept

The number of columns in the matrix.

◆ max_rows()

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

template<typename score_type >

static size_t seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::max_rows	(	word_type const	score_mask,
		unsigned const	last_block,
		score_type const	score,
		score_type const	max_errors
	)

inlinestaticnoexcept

Computes the number of max rows in the current column.

Template Parameters

score_type The type of the score.

Parameters

score_mask	The mask with a bit set at the position where the score change.
last_block	The block containing the last active cell.
score	The score of the current column.
max_errors	Which score value is considered as a hit?

Returns: Number of max rows in the current column.

◆ reserve()

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

void seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::reserve ( size_t const new_capacity )

inline

Increase the capacity of the columns to a value that is greater or equal to new_capacity.

Parameters

new_capacity The new capacity.

Exception

Strong exception guarantee.

◆ rows()

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

size_t seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::rows ( ) const

inlinenoexcept

The number of rows in the matrix.

◆ score_delta_of_word()

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

static score_type seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::score_delta_of_word	(	word_type const &	vp,
		word_type const &	vn
	)

inlinestaticnoexcept

Computes delta score between vp and vn.

Parameters

vp	The machine word which stores the positive vertical differences.
vn	The machine word which stores the negative vertical differences.

Returns: Delta score.

Member Data Documentation

◆ rows_size

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

size_t seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::rows_size {}

private

The number of rows in the matrix.

◆ word_size

template<typename word_t , typename score_t , bool is_semi_global, bool use_max_errors>

constexpr auto seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >::word_size = bits_of<word_type>

staticconstexpr

The size of one machine word.

The documentation for this class was generated from the following file:

edit_distance_score_matrix_full.hpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Friends

Constructors, destructor and assignment

Detailed Description

Member Typedef Documentation

◆ reference

◆ score_type

◆ size_type

◆ value_type

◆ word_type

Constructor & Destructor Documentation

◆ edit_distance_score_matrix_full()

Member Function Documentation

◆ add_column() [1/2]

◆ add_column() [2/2]

◆ at()

◆ cols()

◆ max_rows()

◆ reserve()

Exception

◆ rows()

◆ score_delta_of_word()

Member Data Documentation

◆ rows_size

◆ word_size