seqan3::detail::edit_distance_unbanded_trace_matrix_policy< derived_t, edit_traits > Class Template Reference

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

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

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

Public Member Functions
Trace matrix Policy: Public Member Functions
Defaulted.
trace_matrix_type const &	trace_matrix () const noexcept
	Return the trace matrix of the alignment.
seqan3::detail::advanceable_alignment_coordinate	begin_positions () const noexcept
	Return the begin position of the alignment. Only available if default_edit_distance_trait_type::compute_begin_positions is true.
auto	alignment () const noexcept
	Return the alignment, i.e. the actual base pair matching. Only available if default_edit_distance_trait_type::compute_sequence_alignment is true.

Protected Member Functions
Constructors, destructor and assignment
	edit_distance_unbanded_trace_matrix_policy () noexcept=default
	Defaulted.
	edit_distance_unbanded_trace_matrix_policy (edit_distance_unbanded_trace_matrix_policy const &) noexcept=default
	Defaulted.
	edit_distance_unbanded_trace_matrix_policy (edit_distance_unbanded_trace_matrix_policy &&) noexcept=default
	Defaulted.
edit_distance_unbanded_trace_matrix_policy &	operator= (edit_distance_unbanded_trace_matrix_policy const &) noexcept=default
	Defaulted.
edit_distance_unbanded_trace_matrix_policy &	operator= (edit_distance_unbanded_trace_matrix_policy &&) noexcept=default
	Defaulted.
	~edit_distance_unbanded_trace_matrix_policy () noexcept=default
	Defaulted.
Trace matrix Policy: Protected Member Functions
Defaulted.
void	trace_matrix_init (size_t block_count)
	Initialises trace-matrix policy.

Protected Attributes
friend	derived_t
	Befriends the derived type.
Trace matrix Policy: Protected Attributes
Defaulted.
std::vector< word_type >	hp {}
	The machine word which stores the positive horizontal differences.
std::vector< word_type >	db {}
	The machine word which stores if trace_directions::diagonal is true.
trace_matrix_type	_trace_matrix {}
	The trace matrix of the edit distance alignment.

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 Descriptionno-api

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

Only available when default_edit_distance_trait_type::compute_trace_matrix is true.

Member Function Documentation

trace_matrix_init() [no-api]

template<typename derived_t , typename edit_traits >

void seqan3::detail::edit_distance_unbanded_trace_matrix_policy< derived_t, edit_traits >::trace_matrix_init ( size_t  block_count )

no-apiinlineprotected

Initialises trace-matrix policy.

Exception

Strong exception guarantee.

Member Data Documentation

db [no-api]

template<typename derived_t , typename edit_traits >

std::vector<word_type> seqan3::detail::edit_distance_unbanded_trace_matrix_policy< derived_t, edit_traits >::db {}

no-apiprotected

The machine word which stores if trace_directions::diagonal is true.

hp [no-api]

template<typename derived_t , typename edit_traits >

std::vector<word_type> seqan3::detail::edit_distance_unbanded_trace_matrix_policy< derived_t, edit_traits >::hp {}

no-apiprotected

The machine word which stores the positive horizontal differences.

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

• edit_distance_unbanded.hpp