Only available when default_edit_distance_trait_type::use_max_errors is true. More...

#include <seqan3/alignment/pairwise/edit_distance_unbanded.hpp>

Inheritance diagram for seqan3::detail::edit_distance_unbanded_max_errors_policy< derived_t, edit_traits >:

Protected Member Functions
Constructors, destructor and assignment
	edit_distance_unbanded_max_errors_policy () noexcept=default
	Defaulted.

	edit_distance_unbanded_max_errors_policy (edit_distance_unbanded_max_errors_policy const &) noexcept=default
	Defaulted.

	edit_distance_unbanded_max_errors_policy (edit_distance_unbanded_max_errors_policy &&) noexcept=default
	Defaulted.

edit_distance_unbanded_max_errors_policy &	operator= (edit_distance_unbanded_max_errors_policy const &) noexcept=default
	Defaulted.

edit_distance_unbanded_max_errors_policy &	operator= (edit_distance_unbanded_max_errors_policy &&) noexcept=default
	Defaulted.

	~edit_distance_unbanded_max_errors_policy () noexcept=default
	Defaulted.

Max Error Policy: Protected Member Functions
Defaulted.
void	max_errors_init (size_t block_count) noexcept
	Initialises max_errors policy.

bool	is_last_active_cell_within_last_row () const noexcept
	Returns true if the current active cell is within the last row.

bool	prev_last_active_cell () noexcept
	Decrement the last active cell position.

void	next_last_active_cell () noexcept
	Increment the last active cell position.

bool	update_last_active_cell () noexcept
	Use the ukkonen trick and update the last active cell.

Static Protected Member Functions
static size_t	max_rows (word_type const score_mask, unsigned const last_block, score_type const score, score_type const max_errors) noexcept
	Computes the number of max rows in the current column.

Protected Attributes
friend	derived_t
	Befriends the derived type.

Max Error Policy: Protected Attributes
Defaulted.
score_type	max_errors {255}
	Which score value is considered as a hit?

size_t	last_block {0u}
	The block containing the last active cell.

word_type	last_score_mask {}
	A mask with a bit set on the position of the last row.

Additional Inherited Members
Public Types inherited from seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
using	align_config_type = std::remove_reference_t< align_config_t >
	The type of the alignment config.

using	alignment_result_type = typename alignment_traits_type::alignment_result_type
	The alignment result type generated by the algorithm.

using	alignment_traits_type = alignment_configuration_traits< align_config_type >
	The alignment algorithm traits over the alignment configuration type.

using	database_iterator = std::ranges::iterator_t< database_type >
	The type of an iterator of the database sequence.

using	database_type = std::remove_reference_t< database_t >
	The type of the database sequence.

using	query_alphabet_type = std::remove_reference_t< std::ranges::range_reference_t< query_type > >
	The alphabet type of the query sequence.

using	query_type = std::remove_reference_t< query_t >
	The type of the query sequence.

using	result_value_type = typename alignment_result_value_type_accessor< alignment_result_type >::type
	The alignment result value type.

using	score_matrix_type = edit_distance_score_matrix_full< word_type, score_type, is_semi_global, use_max_errors >
	The type of the score matrix.

using	score_type = typename alignment_traits_type::original_score_type
	The type of the score.

using	trace_matrix_type = edit_distance_trace_matrix_full< word_type, is_semi_global, use_max_errors >
	The type of the trace matrix.

using	word_type = word_t
	The type of one machine word.

Static Public Attributes inherited from seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
static constexpr bool	compute_begin_positions
	Whether the alignment configuration indicates to compute and/or store the begin positions.

static constexpr bool	compute_end_positions
	Whether the alignment configuration indicates to compute and/or store the end positions.

static constexpr bool	compute_matrix = compute_score_matrix \|\| compute_trace_matrix
	Whether the alignment configuration indicates to compute and/or store the score or trace matrix.

static constexpr bool	compute_score = true
	Whether the alignment configuration indicates to compute and/or store the score.

static constexpr bool	compute_score_matrix = false
	Whether the alignment configuration indicates to compute and/or store the score matrix.

static constexpr bool	compute_sequence_alignment = alignment_traits_type::compute_sequence_alignment
	Whether the alignment configuration indicates to compute and/or store the alignment of the sequences.

static constexpr bool	compute_trace_matrix = compute_begin_positions \|\| compute_sequence_alignment
	Whether the alignment configuration indicates to compute and/or store the trace matrix.

static constexpr bool	is_global = !is_semi_global
	Whether the alignment is a global alignment or not.

static constexpr bool	is_semi_global = is_semi_global_t::value
	Whether the alignment is a semi-global alignment or not.

static constexpr bool	use_max_errors = align_config_type::template exists<align_cfg::min_score>()
	When true the computation will use the ukkonen trick with the last active cell and bounds the error to config.max_errors.

static constexpr uint8_t	word_size = bits_of<word_type>
	The size of one machine word.

Detailed Description

template<typename derived_t, typename edit_traits>
class seqan3::detail::edit_distance_unbanded_max_errors_policy< derived_t, edit_traits >

Only available when default_edit_distance_trait_type::use_max_errors is true.

Member Function Documentation

◆ max_rows()

template<typename derived_t , typename edit_traits >

static size_t seqan3::detail::edit_distance_unbanded_max_errors_policy< derived_t, edit_traits >::max_rows	(	word_type const	score_mask,
		unsigned const	last_block,
		score_type const	score,
		score_type const	max_errors
	)

inlinestaticprotectednoexcept

Computes the number of max rows in the current column.

Template Parameters

score_type The type of the score.

Parameters

score_mask	The mask with a bit set at the position where the score change.
last_block	The block containing the last active cell.
score	The score of the current column.
max_errors	Which score value is considered as a hit?

Returns: Number of max rows in the current column.

◆ update_last_active_cell()

template<typename derived_t , typename edit_traits >

bool seqan3::detail::edit_distance_unbanded_max_errors_policy< derived_t, edit_traits >::update_last_active_cell ( )

inlineprotectednoexcept

Use the ukkonen trick and update the last active cell.

Returns: true if computation should be aborted, false if computation should continue.

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

edit_distance_unbanded.hpp

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ max_rows()

◆ update_last_active_cell()