The CRTP-policy to determine the optimum of the dynamic programming matrix. More...

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

Protected Member Functions
template<typename cell_t , typename score_t >
constexpr void	check_and_update (cell_t const &cell, alignment_algorithm_state< score_t > &state) const noexcept
	Tests if the score in the current cell is greater than the current alignment optimum.

template<typename cell_t , typename score_t >
constexpr void	check_score_of_cell (cell_t const &current_cell, alignment_algorithm_state< score_t > &state) const noexcept
	Checks if a given cell is a new optimum in the alignment.

template<typename alignment_column_t , typename score_t >
constexpr void	check_score_of_cells_in_last_column (alignment_column_t &&last_column, alignment_algorithm_state< score_t > &state) const noexcept
	Checks all cells of the last alignment column for a new alignment optimum.

template<typename cell_t , typename score_t >
constexpr void	check_score_of_last_cell (cell_t const &last_cell, alignment_algorithm_state< score_t > &state) const noexcept
	Checks if the last cell of the alignment matrix is a new optimum in the alignment.

template<typename cell_t , typename score_t >
constexpr void	check_score_of_last_row_cell (cell_t const &last_row_cell, alignment_algorithm_state< score_t > &state) const noexcept
	Checks if a cell in the last row of the alignment matrix is a new optimum in the alignment.

Private Member Functions
Constructors, destructor and assignment
constexpr	find_optimum_policy ()=default
	Defaulted.

constexpr	find_optimum_policy (find_optimum_policy const &)=default
	Defaulted.

constexpr	find_optimum_policy (find_optimum_policy &&)=default
	Defaulted.

constexpr find_optimum_policy &	operator= (find_optimum_policy const &)=default
	Defaulted.

constexpr find_optimum_policy &	operator= (find_optimum_policy &&)=default
	Defaulted.

	~find_optimum_policy ()=default
	Defaulted.

template<typename configuration_t >
	find_optimum_policy (configuration_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	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.

Friends
template<typename other_alignment_algorithm_t >
class	affine_gap_init_policy
	Allow seqan3::detail::affine_gap_init_policy to access check_score.

template<typename other_alignment_algorithm_t , typename score_t , typename is_local_t >
class	affine_gap_policy
	Allow seqan3::detail::affine_gap_policy to access check_score.

template<typename other_alignment_algorithm_t , simd_concept score_t, typename is_local_t >
class	simd_affine_gap_policy

Detailed Description

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

The CRTP-policy to determine the optimum of the dynamic programming matrix.

Template Parameters

alignment_algorithm_t The derived type (seqan3::detail::alignment_algorithm) to be augmented with this CRTP-policy.

This class determines the matrix wide optimum. The search space can be further refined using the traits_type which configures the search space of the alignment matrix.

Member Function Documentation

◆ check_and_update()

template<typename alignment_algorithm_t >

template<typename cell_t , typename score_t >

constexpr void seqan3::detail::find_optimum_policy< alignment_algorithm_t >::check_and_update	(	cell_t const &	cell,
		alignment_algorithm_state< score_t > &	state
	)		const

inlineconstexprprotectednoexcept

Tests if the score in the current cell is greater than the current alignment optimum.

Template Parameters

cell_t	The type of the alignment matrix cell. The cell type corresponds to the value type of the range returned by seqan3::detail::alignment_matrix_policy::current_alignment_column.
score_t	The alignment algorithm score type.

Parameters

[in]	cell	The current cell to get the score and the coordinate from.
[in,out]	state	The state with the current optimum to update.

◆ check_score_of_cell()

template<typename alignment_algorithm_t >

template<typename cell_t , typename score_t >

constexpr void seqan3::detail::find_optimum_policy< alignment_algorithm_t >::check_score_of_cell	(	cell_t const &	current_cell,
		alignment_algorithm_state< score_t > &	state
	)		const

inlineconstexprprotectednoexcept

Checks if a given cell is a new optimum in the alignment.

Template Parameters

cell_t	The type of the alignment matrix cell.
score_t	The type of the score.

Parameters

[in]	current_cell	The currently computed alignment matrix cell.
[in,out]	state	The state with the current optimum to update.

This function resolves to a "NO-OP" function if the trait for searching every cell is set to std::false_type.

◆ check_score_of_cells_in_last_column()

template<typename alignment_algorithm_t >

template<typename alignment_column_t , typename score_t >

constexpr void seqan3::detail::find_optimum_policy< alignment_algorithm_t >::check_score_of_cells_in_last_column	(	alignment_column_t &&	last_column,
		alignment_algorithm_state< score_t > &	state
	)		const

inlineconstexprprotectednoexcept

Checks all cells of the last alignment column for a new alignment optimum.

Template Parameters

alignment_column_t	The type of an alignment column.
score_t	The type of the optimal score.

Parameters

[in]	last_column	The last column of the alignment matrix.
[in,out]	state	The state with the current optimum to update.

This function resolves to a "NO-OP" function if the trait for searching the last column is set to std::false_type or if the trait for searching every cell is set to std::true_type.

◆ check_score_of_last_cell()

template<typename alignment_algorithm_t >

template<typename cell_t , typename score_t >

constexpr void seqan3::detail::find_optimum_policy< alignment_algorithm_t >::check_score_of_last_cell	(	cell_t const &	last_cell,
		alignment_algorithm_state< score_t > &	state
	)		const

inlineconstexprprotectednoexcept

Checks if the last cell of the alignment matrix is a new optimum in the alignment.

Template Parameters

cell_t	The type of the last cell.
score_t	The type of the score.

Parameters

[in]	last_cell	The last cell of the alignment matrix.
[in,out]	state	The state with the current optimum to update.

This function resolves to a "NO-OP" function if the last cell has been checked already as part of the last row, last column, or in case every cell was checked.

◆ check_score_of_last_row_cell()

template<typename alignment_algorithm_t >

template<typename cell_t , typename score_t >

constexpr void seqan3::detail::find_optimum_policy< alignment_algorithm_t >::check_score_of_last_row_cell	(	cell_t const &	last_row_cell,
		alignment_algorithm_state< score_t > &	state
	)		const

inlineconstexprprotectednoexcept

Checks if a cell in the last row of the alignment matrix is a new optimum in the alignment.

Template Parameters

cell_t	The type of the alignment matrix cell.
score_t	The type of the score.

Parameters

[in]	last_row_cell	The cell of the current column in the last row of the alignment matrix.
[in,out]	state	The state with the current optimum to update.

This function resolves to a "NO-OP" function if the trait for searching the last row is set to std::false_type or if the trait for searching every cell is set to std::true_type.

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

find_optimum_policy.hpp

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Function Documentation

◆ check_and_update()

◆ check_score_of_cell()

◆ check_score_of_cells_in_last_column()

◆ check_score_of_last_cell()

◆ check_score_of_last_row_cell()