A two dimensional matrix used inside of alignment algorithms. More...

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

Inheritance diagram for seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >:

Classes
class	basic_iterator
	A two-dimensional matrix iterator. More...

Public Types
Associated types
using	value_type = typename storage_type::value_type
	The value type.

using	reference = typename storage_type::reference
	The reference type.

using	const_reference = typename storage_type::const_reference
	The const reference type.

using	pointer = typename storage_type::pointer
	The pointer type.

using	const_pointer = typename storage_type::const_pointer
	The pointer type.

using	difference_type = typename storage_type::difference_type
	The difference type.

using	size_type = typename storage_type::size_type
	The difference type.

using	iterator = basic_iterator< false >
	The iterator type.

using	const_iterator = basic_iterator< true >

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

constexpr const_reference	at (matrix_coordinate const &coordinate) const
	A reference to the entry of the matrix at the given coordinate.

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

constexpr const_pointer	data () const noexcept
	Returns a pointer to the data.

constexpr pointer	data () noexcept
	Returns a pointer to the data.

constexpr const_reference	operator[] (matrix_coordinate const &coordinate) const noexcept
	Returns a reference to the element at the given coordinate.

constexpr reference	operator[] (matrix_coordinate const &coordinate) noexcept
	Returns a reference to the element at the given coordinate.

void	resize (number_rows const row_dim, number_cols const col_dim)
	Resizes the underlying matrix storage to the given matrix dimensions.

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

Constructors, destructor and assignment
	two_dimensional_matrix ()=default
	Defaulted.

	two_dimensional_matrix (two_dimensional_matrix const &)=default
	Defaulted.

	two_dimensional_matrix (two_dimensional_matrix &&)=default
	Defaulted.

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

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

	~two_dimensional_matrix ()=default
	Defaulted.

	two_dimensional_matrix (number_rows const row_dim, number_cols const col_dim)
	Constructs the matrix by the given dimensions.

template<std::ranges::forward_range entries_t> requires (std::convertible_to<std::ranges::range_value_t<entries_t>, value_type>)
	two_dimensional_matrix (number_rows const row_dim, number_cols const col_dim, entries_t entries)
	Constructs the matrix by the given dimensions and initialises it with the given range.

	two_dimensional_matrix (number_rows const row_dim, number_cols const col_dim, storage_type entries)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<typename other_value_t , typename other_allocator_t , matrix_major_order other_order> requires std::assignable_from<other_value_t &, value_t &>
constexpr	two_dimensional_matrix (two_dimensional_matrix< other_value_t, other_allocator_t, other_order > const &matrix)
	Explicit construction from the other major-order.

Iterators
Provides iterators to move in two-dimensional space.
constexpr iterator	begin () noexcept
	Returns an iterator pointing to the first element of the matrix.

constexpr const_iterator	begin () const noexcept
	Returns an iterator pointing to the first element of the matrix.

constexpr const_iterator	cbegin () const noexcept
	Returns an iterator pointing to the first element of the matrix.

constexpr iterator	end () noexcept
	Returns an iterator pointing behind-the-end of the matrix.

constexpr const_iterator	end () const noexcept
	Returns an iterator pointing behind-the-end of the matrix.

constexpr const_iterator	cend () const noexcept
	Returns an iterator pointing behind-the-end of the matrix.

Private Types
Auxiliary types
using	storage_type = std::vector< value_t, allocator_t >

Private Attributes
size_type	col_dim
	The number of columns in the matrix.

size_type	row_dim
	The number of rows in the matrix.

storage_type	storage
	The matrix as a one-dimensional (flattened) vector of entries.

Detailed Description

template<typename value_t, typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>
class seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >

A two dimensional matrix used inside of alignment algorithms.

Template Parameters

value_t	The value type to store.
allocator_t	The allocator type used to allocate the storage; defaults to std::allocator.
order	The matrix-major-order; defaults to seqan3::detail::matrix_major_order::row.

This two dimensional matrix type is a base data structure for several alignment matrices. It can be customised over the value type, the allocator type and the major matrix order. The data is stored in a flat std::vector. Depending on the given order, the element access on the underlying buffer follows a row-major-order or a column-major-order. Accordingly, it is cache friendly and thus more efficient to access the data in the row-major-order row by row instead of column by column and vice versa for the column-major-order.

Member Typedef Documentation

◆ const_iterator

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

using seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::const_iterator = basic_iterator<true>

The const iterator type.

◆ storage_type

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

using seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::storage_type = std::vector<value_t, allocator_t>

private

The storage type.

Constructor & Destructor Documentation

◆ two_dimensional_matrix() [1/3]

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::two_dimensional_matrix	(	number_rows const	row_dim,
		number_cols const	col_dim
	)

inline

Constructs the matrix by the given dimensions.

Parameters

row_dim	The row dimension (number of rows).
col_dim	The column dimension (number of columns).

◆ two_dimensional_matrix() [2/3]

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

template<std::ranges::forward_range entries_t>
requires (std::convertible_to<std::ranges::range_value_t<entries_t>, value_type>)

seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::two_dimensional_matrix	(	number_rows const	row_dim,
		number_cols const	col_dim,
		entries_t	entries
	)

inline

Constructs the matrix by the given dimensions and initialises it with the given range.

Template Parameters

entries_t Range of values that are convertible to value_type; must model std::ranges::forward_range

Parameters

[in]	row_dim	The row dimension (number of rows).
[in]	col_dim	The column dimension (number of columns).
[in]	entries	A range used to fill the underlying matrix.

◆ two_dimensional_matrix() [3/3]

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

template<typename other_value_t , typename other_allocator_t , matrix_major_order other_order>
requires std::assignable_from<other_value_t &, value_t &>

constexpr seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::two_dimensional_matrix ( two_dimensional_matrix< other_value_t, other_allocator_t, other_order > const & matrix )

inlineexplicitconstexpr

Explicit construction from the other major-order.

Template Parameters

other_value_t	The target value type; must be assignable from `value_t`.
other_allocator_t	The allocator type used for the target matrix.
other_order	The other seqan3::detail::matrix_major_order.

Copies the matrix cell by cell, rearranging the stored elements in the internal memory to represent the converted major-order.

Consider the following matrix:

0 1 2 3 4 5 6 7 8 9 10 11

In row-major-order the data is stored in a flat vector in the following way: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11

Converting it to column-major-order will rearrange the elements: 0, 4, 8, 1, 5, 9, 2, 6, 10, 3, 7, 11

Note that the matrix is not transposed, so that the general layout as displayed above will remain the same. It only changes the matrix major order, i.e. data stored row wise is now stored column wise and vice versa.

Member Function Documentation

◆ at() [1/2]

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

constexpr reference seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::at ( matrix_coordinate const & coordinate )

inlineconstexpr

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

◆ at() [2/2]

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

constexpr const_reference seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::at ( matrix_coordinate const & coordinate ) const

inlineconstexpr

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

◆ begin()

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

constexpr const_iterator seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::begin ( ) const

inlineconstexprnoexcept

Returns an iterator pointing to the first element of the matrix.

◆ cbegin()

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

constexpr const_iterator seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::cbegin ( ) const

inlineconstexprnoexcept

Returns an iterator pointing to the first element of the matrix.

◆ cend()

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

constexpr const_iterator seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::cend ( ) const

inlineconstexprnoexcept

Returns an iterator pointing behind-the-end of the matrix.

◆ cols()

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

size_t seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::cols ( ) const

inlinenoexcept

The number of columns in the matrix.

◆ end()

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

constexpr const_iterator seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::end ( ) const

inlineconstexprnoexcept

Returns an iterator pointing behind-the-end of the matrix.

◆ operator[]() [1/2]

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

constexpr const_reference seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::operator[] ( matrix_coordinate const & coordinate ) const

inlineconstexprnoexcept

Returns a reference to the element at the given coordinate.

Parameters

[in] coordinate The two-dimensional coordinate to access.

◆ operator[]() [2/2]

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

constexpr reference seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::operator[] ( matrix_coordinate const & coordinate )

inlineconstexprnoexcept

Returns a reference to the element at the given coordinate.

Parameters

[in] coordinate The two-dimensional coordinate to access.

◆ resize()

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

void seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::resize	(	number_rows const	row_dim,
		number_cols const	col_dim
	)

inline

Resizes the underlying matrix storage to the given matrix dimensions.

Parameters

row_dim	The row dimension (row count).
col_dim	The column dimension (column count).

◆ rows()

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

size_t seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::rows ( ) const

inlinenoexcept

The number of rows in the matrix.

Member Data Documentation

◆ col_dim

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

size_type seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::col_dim

private

The number of columns in the matrix.

◆ row_dim

template<typename value_t , typename allocator_t = std::allocator<value_t>, matrix_major_order order = matrix_major_order::row>

size_type seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::row_dim

private

The number of rows in the matrix.

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

two_dimensional_matrix.hpp

Classes

Public Types

Public Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ storage_type

Constructor & Destructor Documentation

◆ two_dimensional_matrix() [1/3]

◆ two_dimensional_matrix() [2/3]

◆ two_dimensional_matrix() [3/3]

Member Function Documentation

◆ at() [1/2]

◆ at() [2/2]

◆ begin()

◆ cbegin()

◆ cend()

◆ cols()

◆ end()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ resize()

◆ rows()

Member Data Documentation

◆ col_dim

◆ row_dim