seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t > Class Template Reference

Implements the alignment recursion function for the alignment algorithm using affine gap costs with trace information. More...

#include <seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion.hpp>

Inheritance diagram for seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >:

Protected Types
using	affine_cell_type = affine_cell_proxy< std::pair< affine_score_tuple_t, affine_trace_tuple_t > >
	The affine cell type returned by the functions.
using	affine_score_tuple_t = std::tuple< score_type, score_type, score_type >
	The internal tuple storing the scores of an affine cell.
using	affine_trace_tuple_t = std::tuple< trace_type, trace_type, trace_type >
	The internal tuple storing the trace directions of an affine cell.
using	base_t = policy_affine_gap_recursion< alignment_configuration_t >
	The type of the base policy.
using	score_type = typename traits_type::score_type
	The configured score type.
using	trace_type = typename traits_type::trace_type
	The trace type to use.
using	traits_type = alignment_configuration_traits< alignment_configuration_t >
	The configuration traits type.
Protected Types inherited from seqan3::detail::policy_affine_gap_recursion< alignment_configuration_t >
using	affine_cell_type = affine_cell_proxy< affine_score_tuple_t >
	The affine cell type returned by the functions.
using	affine_score_tuple_t = std::tuple< score_type, score_type, score_type >
	The internal tuple storing the scores of an affine cell.
using	original_score_type = typename traits_type::original_score_type
	The configured original score type.
using	score_type = typename traits_type::score_type
	The configured score type.
using	traits_type = alignment_configuration_traits< alignment_configuration_t >
	The configuration traits type.

Protected Member Functions
template<typename affine_cell_t >
affine_cell_type	compute_inner_cell (score_type diagonal_score, affine_cell_t previous_cell, score_type const sequence_score) const noexcept
	Computes an inner cell of the alignment matrix.
template<typename affine_cell_t >
affine_cell_type	initialise_first_column_cell (affine_cell_t previous_cell) const noexcept
	Initialises a cell of the first alignment matrix column.
template<typename affine_cell_t >
affine_cell_type	initialise_first_row_cell (affine_cell_t previous_cell) const noexcept
	Initialises the first cell of a alignment matrix column.
affine_cell_type	initialise_origin_cell () const noexcept
	Initialises the first cell of the alignment matrix in the top left corner of the matrix.
Constructors, destructor and assignment
	policy_affine_gap_with_trace_recursion ()=default
	Defaulted.
	policy_affine_gap_with_trace_recursion (policy_affine_gap_with_trace_recursion const &)=default
	Defaulted.
	policy_affine_gap_with_trace_recursion (policy_affine_gap_with_trace_recursion &&)=default
	Defaulted.
policy_affine_gap_with_trace_recursion &	operator= (policy_affine_gap_with_trace_recursion const &)=default
	Defaulted.
policy_affine_gap_with_trace_recursion &	operator= (policy_affine_gap_with_trace_recursion &&)=default
	Defaulted.
	~policy_affine_gap_with_trace_recursion ()=default
	Defaulted.
	policy_affine_gap_with_trace_recursion (alignment_configuration_t const &config)
	Defaulted.
Protected Member Functions inherited from seqan3::detail::policy_affine_gap_recursion< alignment_configuration_t >
template<typename affine_cell_t >
affine_cell_type	compute_inner_cell (score_type diagonal_score, affine_cell_t previous_cell, score_type const sequence_score) const noexcept
	Computes an inner cell of the alignment matrix.
template<typename affine_cell_t >
affine_cell_type	initialise_first_column_cell (affine_cell_t previous_cell) const noexcept
	Initialises a cell of the first alignment matrix column.
template<typename affine_cell_t >
affine_cell_type	initialise_first_row_cell (affine_cell_t previous_cell) const noexcept
	Initialises the first cell of a alignment matrix column.
affine_cell_type	initialise_origin_cell () const noexcept
	Initialises the first cell of the alignment matrix in the top left corner of the matrix.
score_type	lowest_viable_score () const noexcept
	Returns the lowest viable score.
template<typename score_t > requires arithmetic<std::remove_cvref_t<score_t>>
constexpr auto	maybe_convert_to_simd (score_t &&score) const noexcept
	Converts the given score type to a simd vector if the alignment is executed in vectorised mode.
	policy_affine_gap_recursion ()=default
	Defaulted.
	policy_affine_gap_recursion (policy_affine_gap_recursion const &)=default
	Defaulted.
	policy_affine_gap_recursion (policy_affine_gap_recursion &&)=default
	Defaulted.
policy_affine_gap_recursion &	operator= (policy_affine_gap_recursion const &)=default
	Defaulted.
policy_affine_gap_recursion &	operator= (policy_affine_gap_recursion &&)=default
	Defaulted.
	~policy_affine_gap_recursion ()=default
	Defaulted.
	policy_affine_gap_recursion (alignment_configuration_t const &config)
	Construction and initialisation using the alignment configuration.

Protected Attributes
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.
score_type	gap_extension_score
	The score for a gap extension.
score_type	gap_open_score
	The score for a gap opening including the gap extension.
Protected Attributes inherited from seqan3::detail::policy_affine_gap_recursion< alignment_configuration_t >
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.
score_type	gap_extension_score {}
	The score for a gap extension.
score_type	gap_open_score {}
	The score for a gap opening including the gap extension.

Detailed Descriptionno-api

template<typename alignment_configuration_t>
class seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >

Implements the alignment recursion function for the alignment algorithm using affine gap costs with trace information.

Template Parameters

alignment_configuration_t

The type of the alignment configuration.

Implements the functions to initialise and compute the alignment matrix using the recursion formula for affine gaps. Other policies can inherit from this policy and overload the recursion functions, e.g. to change the initialisation of the alignment matrix.

Note

For more information, please refer to the original article for the alignment with affine gap cost function: GOTOH, Osamu. An improved algorithm for matching biological sequences. Journal of molecular biology, 1982, 162. Jg., Nr. 3, S. 705-708.

Constructor & Destructor Documentation

policy_affine_gap_with_trace_recursion() [no-api]

template<typename alignment_configuration_t >

seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >::policy_affine_gap_with_trace_recursion ( alignment_configuration_t const &  config )

no-apiinlineexplicitprotected

Defaulted.

Member Function Documentation

compute_inner_cell() [no-api]

template<typename alignment_configuration_t >

template<typename affine_cell_t >

affine_cell_type seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >::compute_inner_cell ( score_type  diagonal_score, affine_cell_t  previous_cell, score_type const  sequence_score  ) const

no-apiinlineprotectednoexcept

Computes an inner cell of the alignment matrix.

Template Parameters

affine_cell_t

The type of the affine cell; must be an instance of seqan3::detail::affine_cell_proxy.

Parameters

[in]	diagonal_score	The previous diagonal score, which corresponds to $M[i-1,j-1]$.
[in]	previous_cell	The predecessor cell corresponding to the values $V[i-1,j]$ and $H[i,j-1]$.
[in]	sequence_score	The score obtained from the scoring scheme for the current cell ( $\delta$).

Returns

The computed affine cell.

Computes the current cell according to following recursion formula:

• $H[i,j]=max\{M[i,j-1]+g_o,H[i,j-1]+g_e\}$
• $V[i,j]=max\{M[i-1,j]+g_o,V[i-1,j]+g_e\}$
• $M[i,j]=max\{M[i-1,j-1]+\delta ,H[i,j],V[i,j]\}$

initialise_first_column_cell() [no-api]

template<typename alignment_configuration_t >

template<typename affine_cell_t >

affine_cell_type seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >::initialise_first_column_cell ( affine_cell_t  previous_cell ) const

no-apiinlineprotectednoexcept

Initialises a cell of the first alignment matrix column.

Template Parameters

affine_cell_t

The type of the affine cell; must be an instance of seqan3::detail::affine_cell_proxy.

Parameters

[in]

previous_cell

The predecessor cell on the same column $M[i-1,0]$.

Returns

The computed affine cell.

Initialises a cell of the first alignment matrix column. The optimal score is the same as the vertical score which is equal to $V[i,0]=M[i,0]=g_o+g_e\ast i$. The horizontal score is initialised to $H[i,0]=V[i,0]+g_o$ to prohibit extending a gap in the horizontal matrix from $H[i,0]$.

initialise_first_row_cell() [no-api]

template<typename alignment_configuration_t >

template<typename affine_cell_t >

affine_cell_type seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >::initialise_first_row_cell ( affine_cell_t  previous_cell ) const

no-apiinlineprotectednoexcept

Initialises the first cell of a alignment matrix column.

Template Parameters

affine_cell_t

The type of the affine cell; must be an instance of seqan3::detail::affine_cell_proxy.

Parameters

[in]

previous_cell

The predecessor cell on the same row $M[0,j-1]$.

Returns

The computed affine cell.

Initialises the first cell of a alignment matrix column. The optimal score is the same as the horizontal score which is equal to $H[0,j]=M[0,j]=g_o+g_e\ast j$. The vertical score is initialised to $V[0,j]=H[0,j]+g_o$ to prohibit extending a gap in the vertical matrix from $V[0,j]$.

initialise_origin_cell() [no-api]

template<typename alignment_configuration_t >

affine_cell_type seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >::initialise_origin_cell ( ) const

no-apiinlineprotectednoexcept

Initialises the first cell of the alignment matrix in the top left corner of the matrix.

Returns

The computed affine cell.

Initialises the cell at the origin of the alignment matrix (top left corner of the matrix). The optimal score is initialised to 0, while the value of the horizontal and vertical matrix are initialised as: $V[0,0]=H[0,0]=g_o$.

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

• policy_affine_gap_with_trace_recursion.hpp