A matrix over coordinates. More...

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

Inheritance diagram for seqan3::detail::coordinate_matrix< index_t >:

Classes
struct	convert_to_matrix_coordinate
	A function object that converts a column index and a row index to a seqan3::detail::matrix_coordinate. More...

class	iterator
	The iterator for the seqan3::detail::coordinate_matrix. More...

Public Member Functions
Constructors, destructor and assignment
	coordinate_matrix ()=default
	Defaulted.

	coordinate_matrix (coordinate_matrix const &)=default
	Defaulted.

	coordinate_matrix (coordinate_matrix &&)=default
	Defaulted.

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

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

	~coordinate_matrix ()=default
	Defaulted.

template<std::integral column_index_t, std::integral row_index_t>
void	resize (column_index_type< column_index_t > const column_count, row_index_type< row_index_t > const row_count) noexcept
	Resets the coordinate matrix with the given end column index and end row index representing the new dimensions of the matrix.

Iterators
iterator	begin () const noexcept
	Returns the iterator pointing to the first column of the matrix.

iterator	end () const noexcept
	Returns the iterator pointing to the end column of the matrix.

Private Types
template<typename simd_index_t >
using	lazy_scalar_type_t = typename simd_traits< simd_index_t >::scalar_type
	Type alias for the scalar type defined by the seqan3::simd::simd_traits type.

using	size_type = lazy_conditional_t< simd_concept< index_t >, lazy< lazy_scalar_type_t, index_t >, index_t >
	The internal size type which depends on `index_t` being a simd vector or a scalar type.

Private Attributes
size_type	column_count {}
	The number of columns (corresponds to the size of one row).

size_type	row_count {}
	The number od rows (corresponds to the size of one column).

Detailed Description

template<typename index_t>
requires (std::integral<index_t> || simd_index<index_t>)
class seqan3::detail::coordinate_matrix< index_t >

A matrix over coordinates.

Template Parameters

index_t The underlying matrix index type; must mode std::integral or seqan3::simd::simd_index.

This matrix emulates a two-dimensional index, such that each cell inside of the alignment matrix can be located through a unique coordinate (=index). In the alignment algorithm this matrix is paired with the alignment matrix to form an indexed alignment matrix.

This matrix is cheap as it stores only the dimensions of the matrix and does not allocate any memory for the coordinates. It uses the seqan3::detail::matrix_coordinate_iterator to iterate over the columns of this virtual matrix. When the seqan3::detail::coordinate_matrix::matrix_coordinate_iterator is dereferenced it returns an on-the-fly constructed range (prvalue) representing the current indexed column. The reference type of this range is seqan3::detail::matrix_coordinate.

Simd mode

If the index_t is a simd vector the matrix implements a vectorised coordinate matrix instead. In this case the matrix uses a seqan3::detail::coordinate_matrix::matrix_coordinate_simd_iterator to iterate over the vectorised matrix. When the seqan3::detail::coordinate_matrix::matrix_coordinate_iterator is dereferenced it returns an on-the-fly constructed range (prvalue) representing the current simd coordinate column. The reference type of this range is seqan3::detail::simd_matrix_coordinate.

Member Function Documentation

◆ resize()

template<typename index_t >

template<std::integral column_index_t, std::integral row_index_t>

void seqan3::detail::coordinate_matrix< index_t >::resize	(	column_index_type< column_index_t > const	column_count,
		row_index_type< row_index_t > const	row_count
	)

inlinenoexcept

Resets the coordinate matrix with the given end column index and end row index representing the new dimensions of the matrix.

Template Parameters

column_index_t	The size type for the column count; must model std:integral.
row_index_t	The size type for the row count; must model std:integral.

Parameters

[in]	column_count	The number of columns (corresponds to the size of one row).
[in]	row_count	The number od rows (corresponds to the size of one column).

Complexity

Constant

Exception

noexcept

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

coordinate_matrix.hpp

Classes

Public Member Functions