seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t > Class Template Reference

Implements the tracker to store the global optimum for a particular alignment computation. More...

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

Inheritance diagram for seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >:

Protected Types
using	matrix_coordinate_type = typename traits_type::matrix_coordinate_type
	The matrix coordinate type that is used to locate a cell inside of the alignment matrix.
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 cell_t >
void	invoke_comparator (cell_t &&cell, matrix_coordinate_type coordinate) noexcept
	Handles the invocation of the optimum comparator and updater.
void	reset_optimum () noexcept
	Resets the optimum such that a new alignment can be computed.
template<typename cell_t >
decltype(auto)	track_cell (cell_t &&cell, matrix_coordinate_type coordinate) noexcept
	Tracks any cell within the alignment matrix.
template<typename cell_t >
decltype(auto)	track_final_cell (cell_t &&cell, matrix_coordinate_type coordinate) noexcept
	Tracks the final cell of the alignment matrix.
template<typename cell_t >
decltype(auto)	track_last_column_cell (cell_t &&cell, matrix_coordinate_type coordinate) noexcept
	Tracks the last cell of a column within the alignment matrix.
template<typename cell_t >
decltype(auto)	track_last_row_cell (cell_t &&cell, matrix_coordinate_type coordinate) noexcept
	Tracks the last cell of a row within the alignment matrix.
Constructors, destructor and assignment
	policy_optimum_tracker ()=default
	Defaulted.
	policy_optimum_tracker (policy_optimum_tracker const &)=default
	Defaulted.
	policy_optimum_tracker (policy_optimum_tracker &&)=default
	Defaulted.
policy_optimum_tracker &	operator= (policy_optimum_tracker const &)=default
	Defaulted.
policy_optimum_tracker &	operator= (policy_optimum_tracker &&)=default
	Defaulted.
	~policy_optimum_tracker ()=default
	Defaulted.
	policy_optimum_tracker (alignment_configuration_t const &config)
	Construction and initialisation using the alignment configuration.

Protected Attributes
optimum_updater_t	compare_and_set_optimum {}
	The function object to compare and exchange the optimum.
matrix_coordinate_type	optimal_coordinate {}
	The matrix coordinate of the tracked optimum.
score_type	optimal_score {}
	The tracked score of the global optimum.
bool	test_every_cell {false}
	Whether every cell of the alignment matrix shall be tracked.
bool	test_last_column_cell {false}
	Whether cells of the last column shall be tracked.
bool	test_last_row_cell {false}
	Whether cells of the last row shall be tracked.

Detailed Description

template<typename alignment_configuration_t, std::semiregular optimum_updater_t>
requires is_type_specialisation_of_v<alignment_configuration_t, configuration> && std::invocable< optimum_updater_t, typename alignment_configuration_traits<alignment_configuration_t>::score_type &, typename alignment_configuration_traits<alignment_configuration_t>::matrix_coordinate_type &, typename alignment_configuration_traits<alignment_configuration_t>::score_type, typename alignment_configuration_traits<alignment_configuration_t>::matrix_coordinate_type>
class seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >

Implements the tracker to store the global optimum for a particular alignment computation.

Template Parameters

alignment_configuration_t	The type of the alignment configuration; must be a type specialisation of seqan3::configuration.
optimum_updater_t	The type of the optimum update operation, which compares and updates the alignment optimum with the current cell; must model std::semiregular.

Implements the interface to track the alignment optimum. It updates the currently stored optimum using the optimum update operation. The optimum update operation is stored inside of the class and can have a state. The optimum updater must be invokable with a reference to the optimal score and coordinate and the score and coordinate of the current cell. Special methods are offered to track any cell (for example when computing the local alignment), the last cell of a column or a row (for example when using free-end gaps), or the final cell of the entire matrix (for example in the standard global alignment). The optimum needs to be reset in between alignment computations in order to ensure that the correct result is tracked.

Constructor & Destructor Documentation

policy_optimum_tracker()

template<typename alignment_configuration_t , std::semiregular optimum_updater_t>

seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >::policy_optimum_tracker ( alignment_configuration_t const &  config )

inlineprotected

Construction and initialisation using the alignment configuration.

Parameters

[in]

config

The alignment configuration (not used in this context).

Reads the state of seqan3::align_cfg::method_global and enables the tracking of the last row or column if requested. Otherwise, only the last cell will be tracked.

Member Function Documentation

invoke_comparator()

template<typename alignment_configuration_t , std::semiregular optimum_updater_t>

template<typename cell_t >

void seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >::invoke_comparator ( cell_t &&  cell, matrix_coordinate_type  coordinate  )

inlineprotectednoexcept

Handles the invocation of the optimum comparator and updater.

Template Parameters

cell_t

The cell type of the alignment matrix; must have a member function best_score().

Parameters

[in]	cell	The current cell to be tracked.
[in]	coordinate	The matrix coordinate of the current cell.

Forwards the score and coordinate pair as a tuple and invokes the compare and set operation with the so far best score/coordinate pair and the current score/coordinate pair.

track_cell()

template<typename alignment_configuration_t , std::semiregular optimum_updater_t>

template<typename cell_t >

decltype(auto) seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >::track_cell ( cell_t &&  cell, matrix_coordinate_type  coordinate  )

inlineprotectednoexcept

Tracks any cell within the alignment matrix.

Template Parameters

cell_t

The cell type of the alignment matrix; must have a member function best_score().

Parameters

[in]	cell	The current cell to be tracked.
[in]	coordinate	The matrix coordinate of the current cell.

Returns

The forwarded cell.

A call to this function only tracks the optimal score of the given cell if the configuration of the alignment algorithm requires it, for example when a local alignment shall be computed.

track_final_cell()

template<typename alignment_configuration_t , std::semiregular optimum_updater_t>

template<typename cell_t >

decltype(auto) seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >::track_final_cell ( cell_t &&  cell, matrix_coordinate_type  coordinate  )

inlineprotectednoexcept

Tracks the final cell of the alignment matrix.

Template Parameters

cell_t

The cell type of the alignment matrix; must have a member function best_score().

Parameters

[in]	cell	The current cell to be tracked.
[in]	coordinate	The matrix coordinate of the current cell.

Returns

The forwarded cell.

A call to this function only tracks the optimal score of the given cell if the configuration of the alignment algorithm requires it, for example when a global alignment shall be computed.

track_last_column_cell()

template<typename alignment_configuration_t , std::semiregular optimum_updater_t>

template<typename cell_t >

decltype(auto) seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >::track_last_column_cell ( cell_t &&  cell, matrix_coordinate_type  coordinate  )

inlineprotectednoexcept

Tracks the last cell of a column within the alignment matrix.

Template Parameters

cell_t

The cell type of the alignment matrix; must have a member function best_score().

Parameters

[in]	cell	The current cell to be tracked.
[in]	coordinate	The matrix coordinate of the current cell.

Returns

The forwarded cell.

A call to this function only tracks the optimal score of the given cell if the configuration of the alignment algorithm requires it, for example when a semi-global alignment shall be computed.

track_last_row_cell()

template<typename alignment_configuration_t , std::semiregular optimum_updater_t>

template<typename cell_t >

decltype(auto) seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >::track_last_row_cell ( cell_t &&  cell, matrix_coordinate_type  coordinate  )

inlineprotectednoexcept

Tracks the last cell of a row within the alignment matrix.

Template Parameters

cell_t

The cell type of the alignment matrix; must have a member function best_score().

Parameters

[in]	cell	The current cell to be tracked.
[in]	coordinate	The matrix coordinate of the current cell.

Returns

The forwarded cell.

A call to this function only tracks the optimal score of the given cell if the configuration of the alignment algorithm requires it, for example when a semi-global alignment shall be computed.

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

• policy_optimum_tracker.hpp