seqan3::detail::affine_gap_init_policy< alignment_algorithm_t > Class Template Reference

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 Description

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()

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

inlineconstexprprivatenoexcept

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()

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

inlineconstexprprivatenoexcept

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()

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

inlineconstexprprivatenoexcept

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()

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

inlineconstexprprivatenoexcept

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