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

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

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

Protected Types
using	base_t = edit_distance_unbanded_global_policy< derived_t, edit_traits >
	The base policy of this policy.

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

	edit_distance_unbanded_semi_global_policy (edit_distance_unbanded_semi_global_policy const &) noexcept=default
	Defaulted.

	edit_distance_unbanded_semi_global_policy (edit_distance_unbanded_semi_global_policy &&) noexcept=default
	Defaulted.

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

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

	~edit_distance_unbanded_semi_global_policy () noexcept=default
	Defaulted.

Semi-Global Policy: Protected Member Functions
Defaulted.
void	score_init () noexcept
	Initialises semi-global policy.

void	update_best_score () noexcept
	Update the current best known score if the current score is better.

size_t	end_positions_first () const noexcept
	Returns the first component of the end_positions.

Protected Member Functions inherited from seqan3::detail::edit_distance_unbanded_global_policy< derived_t, edit_traits >
	edit_distance_unbanded_global_policy () noexcept=default
	Defaulted.

	edit_distance_unbanded_global_policy (edit_distance_unbanded_global_policy const &) noexcept=default
	Defaulted.

	edit_distance_unbanded_global_policy (edit_distance_unbanded_global_policy &&) noexcept=default
	Defaulted.

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

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

	~edit_distance_unbanded_global_policy () noexcept=default
	Defaulted.

void	score_init () noexcept
	Initialises global policy.

bool	is_valid () const noexcept
	Returns true if the computation produced a valid alignment.

seqan3::detail::advanceable_alignment_coordinate	invalid_coordinate () const noexcept
	Returns an invalid_coordinate for this alignment.

void	update_best_score () noexcept
	Update the current best known score if the current score is better.

size_t	end_positions_first () const noexcept
	Returns the first component of the end_positions.

Protected Attributes
friend	derived_t
	Befriends the derived type.

Semi-Global Policy: Protected Attributes
Defaulted.
database_iterator	_best_score_col {}
	In which column the best score of the alignment is located. Will only be tracked if is_semi_global is true.

Protected Attributes inherited from seqan3::detail::edit_distance_unbanded_global_policy< derived_t, edit_traits >
friend	derived_t
	Befriends the derived type.

score_type	_best_score {}
	The best score of the alignment in the last row (if is_semi_global = true) or the last entry in the score matrix (if is_global = true).

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.

Public Member Functions inherited from seqan3::detail::edit_distance_unbanded_global_policy< derived_t, edit_traits >
std::optional< score_type >	score () const noexcept
	Return the score of the alignment. Only available if default_edit_distance_trait_type::compute_score is true.

seqan3::detail::advanceable_alignment_coordinate	end_positions () const noexcept
	Return the end position of the alignment Only available if default_edit_distance_trait_type::compute_end_positions is true.

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_semi_global_policy< derived_t, edit_traits >

Only available when default_edit_distance_trait_type::is_semi_global is true.

Member Function Documentation

◆ end_positions_first()

template<typename derived_t , typename edit_traits >

size_t seqan3::detail::edit_distance_unbanded_semi_global_policy< derived_t, edit_traits >::end_positions_first ( ) const

inlineprotectednoexcept

Returns the first component of the end_positions.

◆ update_best_score()

template<typename derived_t , typename edit_traits >

void seqan3::detail::edit_distance_unbanded_semi_global_policy< derived_t, edit_traits >::update_best_score ( )

inlineprotectednoexcept

Update the current best known score if the current score is better.

Member Data Documentation

◆ _best_score_col

template<typename derived_t , typename edit_traits >

database_iterator seqan3::detail::edit_distance_unbanded_semi_global_policy< derived_t, edit_traits >::_best_score_col {}

protected

In which column the best score of the alignment is located. Will only be tracked if is_semi_global is true.

If is_global is true this is always at the last entry in the score matrix, i.e. at position (|query|, |database|).

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

edit_distance_unbanded.hpp

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ end_positions_first()

◆ update_best_score()

Member Data Documentation

◆ _best_score_col