An alignment score matrix storing only a single column for the computation. More...

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

Inheritance diagram for seqan3::detail::alignment_score_matrix_one_column< score_t >:

Public Types
Associated types
using	value_type = alignment_score_matrix_proxy< score_t >
	The proxy type of an alignment matrix.

using	reference = value_type
	Same as value type.

using	iterator = typename range_base_t::iterator
	The type of the iterator.

using	sentinel = typename range_base_t::sentinel
	The type of sentinel.

using	size_type = size_t
	The size type.

using	underlying_type = score_t
	The underlying type of the scores.

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

constexpr	alignment_score_matrix_one_column (alignment_score_matrix_one_column const &)=default
	Defaulted.

constexpr	alignment_score_matrix_one_column (alignment_score_matrix_one_column &&)=default
	Defaulted.

constexpr alignment_score_matrix_one_column &	operator= (alignment_score_matrix_one_column const &)=default
	Defaulted.

constexpr alignment_score_matrix_one_column &	operator= (alignment_score_matrix_one_column &&)=default
	Defaulted.

	~alignment_score_matrix_one_column ()=default
	Defaulted.

template<std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>
constexpr	alignment_score_matrix_one_column (first_sequence_t &&first, second_sequence_t &&second, score_t const initial_value=score_t{})
	Construction from two ranges.

Public Member Functions inherited from seqan3::detail::alignment_matrix_column_major_range_base< alignment_score_matrix_one_column< score_t > >
constexpr iterator	begin () noexcept
	Returns an iterator to the first column of the matrix.

constexpr iterator	begin () const noexcept=delete
	Deleted begin for const-qualified alignment matrix.

constexpr sentinel	end () noexcept
	Returns a sentinel marking the end of the matrix.

constexpr sentinel	end () const noexcept=delete
	Deleted end for const-qualified alignment matrix.

Protected Types
using	column_data_view_type = std::span< element_type >
	The view over the current alignment-column; must model std::ranges::view and std::ranges::input_range.

using	element_type = std::tuple< underlying_type, underlying_type >
	The actual element type.

Protected Types inherited from seqan3::detail::alignment_score_matrix_one_column_base< score_t >
using	allocator_type = aligned_allocator< element_type, sizeof(element_type)>
	The allocator type.

using	element_type = std::tuple< underlying_type, underlying_type >
	The actual element type.

using	pool_type = std::vector< element_type, allocator_type >
	The type of the underlying storage.

using	size_type = size_t
	The size type.

using	underlying_type = score_t
	The underlying type of the scores.

Protected Attributes
size_type	num_cols
	The number of columns.

Protected Attributes inherited from seqan3::detail::alignment_score_matrix_one_column_base< score_t >
std::array< underlying_type, 3 >	cache {}
	Internal cache for the last diagonal and vertical value during the alignment computation.

size_type	num_cols {}
	The number of columns.

size_type	num_rows {}
	The number of num_rows.

pool_type	pool {}
	The linearised memory pool storing only one column of the matrix.

Private Types
using	matrix_base_t = alignment_score_matrix_one_column_base< score_t >
	The base class for data storage.

using	range_base_t = alignment_matrix_column_major_range_base< alignment_score_matrix_one_column< score_t > >
	The base class for iterating over the matrix.

Private Member Functions
template<std::random_access_iterator iter_t>
constexpr void	after_column_iterator_increment (iter_t host_iter) noexcept
	Allows to perform additional steps after incrementing the alignment-column-iterator.

template<std::random_access_iterator iter_t>
constexpr void	before_column_iterator_increment (iter_t host_iter) noexcept
	Allows to perform additional steps before incrementing the alignment-column-iterator.

constexpr alignment_column_type	initialise_column (size_type const column_index) noexcept
	Returns the current alignment-column at the given `column_index`.

template<std::random_access_iterator iter_t>
constexpr value_type	make_proxy (iter_t host_iter) noexcept
	Creates the proxy value returned when dereferencing the alignment-column-iterator.

template<std::random_access_iterator iter_t>
constexpr void	on_column_iterator_creation (iter_t host_iter) noexcept
	Allows additional initialisations when calling begin on an alignment-column.

Private Attributes
friend	range_base_t
	Befriend the range base class.

Detailed Description

template<typename score_t>
class seqan3::detail::alignment_score_matrix_one_column< score_t >

An alignment score matrix storing only a single column for the computation.

Template Parameters

score_t The type of the score; must model either seqan3::arithmetic or seqan3::detail::simd_concept.

This implementation allocates only a single column for the alignment score matrix. The matrix allows access to the underlying values through a range based interface. An iterator over the score matrix iterates in column-major-order. Dereferencing an iterator returns a view over the current matrix column. The value type is seqan3::detail::alignment_score_matrix_proxy, which gives an unified access to the respective matrix cells as needed by the standard alignment algorithm. The matrix is modelled as std::ranges::input_range since the alignment algorithm iterates only once over the complete matrix to calculate the values.

Member Typedef Documentation

◆ column_data_view_type

template<typename score_t >

using seqan3::detail::alignment_score_matrix_one_column< score_t >::column_data_view_type = std::span<element_type>

protected

The view over the current alignment-column; must model std::ranges::view and std::ranges::input_range.

Note: This type must be defined by the derived type.

◆ iterator

template<typename score_t >

using seqan3::detail::alignment_score_matrix_one_column< score_t >::iterator = typename range_base_t::iterator

The type of the iterator.

◆ sentinel

template<typename score_t >

using seqan3::detail::alignment_score_matrix_one_column< score_t >::sentinel = typename range_base_t::sentinel

The type of sentinel.

◆ value_type

template<typename score_t >

using seqan3::detail::alignment_score_matrix_one_column< score_t >::value_type = alignment_score_matrix_proxy<score_t>

The proxy type of an alignment matrix.

Note: This type must be defined by the derived type.

Constructor & Destructor Documentation

◆ alignment_score_matrix_one_column()

template<typename score_t >

template<std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>

constexpr seqan3::detail::alignment_score_matrix_one_column< score_t >::alignment_score_matrix_one_column	(	first_sequence_t &&	first,
		second_sequence_t &&	second,
		score_t const	initial_value = `score_t{}`
	)

inlineconstexpr

Construction from two ranges.

Template Parameters

first_sequence_t	The first range type; must model std::ranges::forward_range.
second_sequence_t	The second range type; must model std::ranges::forward_range.

Parameters

[in]	first	The first range.
[in]	second	The second range.
[in]	initial_value	The value to initialise the matrix with. Default initialised if not specified.

Obtains only the sizes of the passed ranges in order to allocate the score matrix. Only one column is allocated.

Member Function Documentation

◆ after_column_iterator_increment()

template<typename score_t >

template<std::random_access_iterator iter_t>

constexpr void seqan3::detail::alignment_score_matrix_one_column< score_t >::after_column_iterator_increment ( iter_t host_iter )

inlineconstexprprivatenoexcept

Allows to perform additional steps after incrementing the alignment-column-iterator.

Template Parameters

iter_t The iterator type of the host iterator.

Parameters

[in] host_iter The wrapped iterator to the actual memory storage.

◆ before_column_iterator_increment()

template<typename score_t >

template<std::random_access_iterator iter_t>

constexpr void seqan3::detail::alignment_score_matrix_one_column< score_t >::before_column_iterator_increment ( iter_t host_iter )

inlineconstexprprivatenoexcept

Allows to perform additional steps before incrementing the alignment-column-iterator.

Template Parameters

iter_t The iterator type of the host iterator.

Parameters

[in] host_iter The wrapped iterator to the actual memory storage.

◆ initialise_column()

template<typename score_t >

constexpr alignment_column_type seqan3::detail::alignment_score_matrix_one_column< score_t >::initialise_column ( size_type const column_index )

inlineconstexprprivatenoexcept

Returns the current alignment-column at the given column_index.

Parameters

[in] column_index The current column position of the outer matrix iterator.

Returns: A view representing the current alignment-column (seqan3::detail::alignment_matrix_column_major_range_base::alignment_column_type)

Creates a new seqan3::detail::alignment_matrix_column_major_range_base::alignment_column_type initialised with the current column of the alignment matrix depending on the given column_index. The alignment_column_type stores a column view as defined by the derived class using the seqan3::detail::alignment_matrix_column_major_range_base::column_data_view_type type definition.

◆ make_proxy()

template<typename score_t >

template<std::random_access_iterator iter_t>

constexpr value_type seqan3::detail::alignment_score_matrix_one_column< score_t >::make_proxy ( iter_t host_iter )

inlineconstexprprivatenoexcept

Creates the proxy value returned when dereferencing the alignment-column-iterator.

Parameters

[in] host_iter The wrapped iterator to the actual memory storage.

Returns: A proxy for the current matrix position, which must be of type seqan3::detail::alignment_matrix_column_major_range_base::value_type.

◆ on_column_iterator_creation()

template<typename score_t >

template<std::random_access_iterator iter_t>

constexpr void seqan3::detail::alignment_score_matrix_one_column< score_t >::on_column_iterator_creation ( iter_t host_iter )

inlineconstexprprivatenoexcept

Allows additional initialisations when calling begin on an alignment-column.

Template Parameters

iter_t The iterator type of the host iterator.

Parameters

[in] host_iter The wrapped iterator to the actual memory storage.

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

alignment_score_matrix_one_column.hpp

Public Types

Public Member Functions

Protected Types

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ column_data_view_type

◆ iterator

◆ sentinel

◆ value_type

Constructor & Destructor Documentation

◆ alignment_score_matrix_one_column()

Member Function Documentation

◆ after_column_iterator_increment()

◆ before_column_iterator_increment()

◆ initialise_column()

◆ make_proxy()

◆ on_column_iterator_creation()