The CRTP-policy that implements the initialisation of the dynamic programming matrix with affine gaps. More...

#include <seqan3/alignment/pairwise/policy/affine_gap_init_policy.hpp>

Private Member Functions
template<typename score_t , typename value_t >
constexpr auto	convert_to_simd_maybe (value_t const value) const noexcept
	Converts the given value into a simd vector or just returns the value if alignment is not executed in vectorised mode.

template<typename cell_t , typename score_t >
constexpr auto	init_column_cell (cell_t &&column_cell, alignment_algorithm_state< score_t > &state) const noexcept
	Initialises a cell in the first column of the dynamic programming matrix.

template<typename cell_t , typename score_t >
constexpr auto	init_origin_cell (cell_t &&origin_cell, alignment_algorithm_state< score_t > &state) const noexcept
	Initialises the first cell of the dynamic programming matrix.

template<typename cell_t , typename score_t >
constexpr auto	init_row_cell (cell_t &&row_cell, alignment_algorithm_state< score_t > &state) const noexcept
	Initialises a cell in the first row of the dynamic programming matrix.

Constructors, destructor and assignment
Defaulted all standard constructor.
constexpr	affine_gap_init_policy () noexcept=default
	Defaulted.

constexpr	affine_gap_init_policy (affine_gap_init_policy const &) noexcept=default
	Defaulted.

constexpr	affine_gap_init_policy (affine_gap_init_policy &&) noexcept=default
	Defaulted.

constexpr affine_gap_init_policy &	operator= (affine_gap_init_policy const &) noexcept=default
	Defaulted.

constexpr affine_gap_init_policy &	operator= (affine_gap_init_policy &&) noexcept=default
	Defaulted.

	~affine_gap_init_policy () noexcept=default
	Defaulted.

template<typename config_t >
	affine_gap_init_policy (config_t const &config)
	Initialises the policy with the configuration.

Private Attributes
friend	alignment_algorithm_t
	Befriends the derived class to grant it access to the private members.

bool	first_column_is_free {}
	Initialisation state of the first column of the alignment.

bool	first_row_is_free {}
	Initialisation state of the first row of the alignment.

Detailed Descriptionno-api

template<typename alignment_algorithm_t>
class seqan3::detail::affine_gap_init_policy< alignment_algorithm_t >

The CRTP-policy that implements the initialisation of the dynamic programming matrix with affine gaps.

Template Parameters

alignment_algorithm_t	The derived type (seqan3::detail::alignment_algorithm) to be augmented with this CRTP-policy.
traits_type	The traits type to determine the initialisation rules of the dynamic programming matrix. Defaults to seqan3::detail::default_affine_init_traits.

Remarks: The template parameters of this CRTP-policy are selected in the seqan3::detail::alignment_configurator::select_gap_init_policy when selecting the alignment for the given configuration.

Member Function Documentation

◆ convert_to_simd_maybe() [no-api]

template<typename alignment_algorithm_t >

template<typename score_t , typename value_t >

constexpr auto seqan3::detail::affine_gap_init_policy< alignment_algorithm_t >::convert_to_simd_maybe ( value_t const value ) const

no-apiinlineconstexprprivatenoexcept

Converts the given value into a simd vector or just returns the value if alignment is not executed in vectorised mode.

Template Parameters

score_t	The type of the score; must model either seqan3::simd::simd_concept or seqan3::arithmetic.
value_t	The value type to convert; must model seqan3::arithmetic.

Parameters

[in] value The value to possibly convert.

Returns: A simd vector filled with the given value or the value itself if the alignment is not executed in vectorised mode.

◆ init_column_cell() [no-api]

template<typename alignment_algorithm_t >

template<typename cell_t , typename score_t >

constexpr auto seqan3::detail::affine_gap_init_policy< alignment_algorithm_t >::init_column_cell	(	cell_t &&	column_cell,
		alignment_algorithm_state< score_t > &	state
	)		const

no-apiinlineconstexprprivatenoexcept

Initialises a cell in the first column of the dynamic programming matrix.

Template Parameters

cell_t	The underlying cell type.
score_t	The score type used inside of the alignment algorithm.

Parameters

[in,out]	column_cell	A cell of the first row of the dynamic programming matrix.
[in,out]	state	The state with gap information and the current alignment optimum.

cell_t is the result type of dereferencing the zipped iterator over the respective alignment score matrix and the alignment trace matrix used inside of the seqan3::detail::alignment_matrix_policy. The first parameter stored in the zipped tuple is the seqan3::detail::alignment_score_matrix_proxy and the second value is the seqan3::detail::alignment_trace_matrix_proxy.

◆ init_origin_cell() [no-api]

template<typename alignment_algorithm_t >

template<typename cell_t , typename score_t >

constexpr auto seqan3::detail::affine_gap_init_policy< alignment_algorithm_t >::init_origin_cell	(	cell_t &&	origin_cell,
		alignment_algorithm_state< score_t > &	state
	)		const

no-apiinlineconstexprprivatenoexcept

Initialises the first cell of the dynamic programming matrix.

Template Parameters

cell_t	The underlying cell type.
score_t	The score type used inside of the alignment algorithm.

Parameters

[in,out]	origin_cell	The first cell of the dynamic programming matrix.
[in,out]	state	The state with gap information and the current alignment optimum.

cell_t is the result type of dereferencing the zipped iterator over the respective alignment score matrix and the alignment trace matrix used inside of the seqan3::detail::alignment_matrix_policy. The first parameter stored in the zipped tuple is the seqan3::detail::alignment_score_matrix_proxy and the second value is the seqan3::detail::alignment_trace_matrix_proxy.

◆ init_row_cell() [no-api]

template<typename alignment_algorithm_t >

template<typename cell_t , typename score_t >

constexpr auto seqan3::detail::affine_gap_init_policy< alignment_algorithm_t >::init_row_cell	(	cell_t &&	row_cell,
		alignment_algorithm_state< score_t > &	state
	)		const

no-apiinlineconstexprprivatenoexcept

Initialises a cell in the first row of the dynamic programming matrix.

Template Parameters

cell_t	The underlying cell type.
score_t	The score type used inside of the alignment algorithm.

Parameters

[in,out]	row_cell	A cell of the first row of the dynamic programming matrix.
[in,out]	state	The state with gap information and the current alignment optimum.

cell_t is the result type of dereferencing the zipped iterator over the respective alignment score matrix and the alignment trace matrix used inside of the seqan3::detail::alignment_matrix_policy. The first parameter stored in the zipped tuple is the seqan3::detail::alignment_score_matrix_proxy and the second value is the seqan3::detail::alignment_trace_matrix_proxy.

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

affine_gap_init_policy.hpp

Private Member Functions

Private Attributes

Detailed Descriptionno-api

Member Function Documentation

◆ convert_to_simd_maybe() [no-api]

◆ init_column_cell() [no-api]

◆ init_origin_cell() [no-api]

◆ init_row_cell() [no-api]