seqan3::detail::policy_alignment_matrix< traits_t, alignment_matrix_t > Class Template Reference

A policy that provides a common interface to acquire the correct alignment matrices. More...

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

Protected Types
using	matrix_index_type = typename traits_t::matrix_index_type
	The configured matrix index type to store the coordinates.
using	score_type = typename traits_t::score_type
	The configured score type.

Protected Member Functions
auto	acquire_matrices (size_t const sequence1_size, size_t const sequence2_size, score_type initial_score=score_type{}) const
	Acquires a new thread local alignment and index matrix for the given sequence sizes.
void	check_valid_band_configuration (size_t const sequence1_size, size_t const sequence2_size) const
	Checks whether the band is valid for the given sequence sizes.
Constructors, destructor and assignment
	policy_alignment_matrix ()=default
	Defaulted.
	policy_alignment_matrix (policy_alignment_matrix const &)=default
	Defaulted.
	policy_alignment_matrix (policy_alignment_matrix &&)=default
	Defaulted.
policy_alignment_matrix &	operator= (policy_alignment_matrix const &)=default
	Defaulted.
policy_alignment_matrix &	operator= (policy_alignment_matrix &&)=default
	Defaulted.
	~policy_alignment_matrix ()=default
	Defaulted.
template<typename alignment_configuration_t > requires (is_type_specialisation_of_v<alignment_configuration_t, configuration>)
	policy_alignment_matrix (alignment_configuration_t const &config)
	Constructs and initialises the algorithm using the alignment configuration.

Protected Attributes
bool	last_column_is_free {}
	A flag indicating whether the final gaps in the last column are free.
bool	last_row_is_free {}
	A flag indicating whether the final gaps in the last row are free.
int32_t	lower_diagonal {}
	The selected lower diagonal.
int32_t	upper_diagonal {}
	The selected upper diagonal.

Detailed Description

template<typename traits_t, typename alignment_matrix_t>
requires (is_type_specialisation_of_v<traits_t, alignment_configuration_traits> && requires (alignment_matrix_t & matrix, typename traits_t::score_type const initial_score) { { matrix.resize(column_index_type{size_t{}}, row_index_type{size_t{}}, initial_score) }; })
class seqan3::detail::policy_alignment_matrix< traits_t, alignment_matrix_t >

A policy that provides a common interface to acquire the correct alignment matrices.

Template Parameters

traits_t	The alignment configuration traits type; must be an instance of seqan3::detail::alignment_configuration_traits.
alignment_matrix_t	The type of the alignment matrix for this alignment configuration [see requirements below].

The alignment matrix must be a matrix type that is compatible with the configured alignment algorithm. It must offer a resize member function that takes a seqan3::detail::column_index_type and seqan3::detail::row_index_type and an additional parameter to initialise the allocated matrix memory.

Constructor & Destructor Documentation

policy_alignment_matrix()

template<typename traits_t , typename alignment_matrix_t >

template<typename alignment_configuration_t >
requires (is_type_specialisation_of_v<alignment_configuration_t, configuration>)

seqan3::detail::policy_alignment_matrix< traits_t, alignment_matrix_t >::policy_alignment_matrix ( alignment_configuration_t const &  config )

inlineprotected

Constructs and initialises the algorithm using the alignment configuration.

Template Parameters

alignment_configuration_t

The type of the alignment configuration; must be an instance of seqan3::configuration.

Parameters

[in]

config

The configuration passed into the algorithm.

Initialises the members for the lower and upper diagonal. These members are only used if the banded alignment is computed.

Exceptions

seqan3::invalid_alignment_configuration

if the given band settings are invalid.

Member Function Documentation

acquire_matrices()

template<typename traits_t , typename alignment_matrix_t >

auto seqan3::detail::policy_alignment_matrix< traits_t, alignment_matrix_t >::acquire_matrices ( size_t const  sequence1_size, size_t const  sequence2_size, score_type  initial_score = score_type{}  ) const

inlineprotected

Acquires a new thread local alignment and index matrix for the given sequence sizes.

Parameters

[in]	sequence1_size	The size of the first sequence.
[in]	sequence2_size	The size of the second sequence.
[in]	initial_score	The initial score used for the acquired alignment matrix.

Returns

A std::tuple storing lvalue references to the thread local alignment and index matrix.

Acquires a thread local alignment and index matrix. Initialises the matrices with the given sequence sizes and the initial score value. In the banded alignment, the alignment matrix is reduced to the column count times the band size.

Exception

Might throw std::bad_alloc if the requested matrix size exceeds the available memory or seqan3::invalid_alignment_configuration if the band does not allow a valid computation of the configured alignment.

Exceptions

std::bad_alloc

or seqan3::invalid_alignment_configuration

check_valid_band_configuration()

template<typename traits_t , typename alignment_matrix_t >

void seqan3::detail::policy_alignment_matrix< traits_t, alignment_matrix_t >::check_valid_band_configuration ( size_t const  sequence1_size, size_t const  sequence2_size  ) const

inlineprotected

Checks whether the band is valid for the given sequence sizes.

Parameters

[in]	sequence1_size	The size of the first sequence.
[in]	sequence2_size	The size of the second sequence.

Exceptions

seqan3::invalid_alignment_configuration

if the band is invalid for the given sequence sizes and the alignment configuration.

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

• policy_alignment_matrix.hpp