seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t > Struct Template Reference

The default traits type for the edit distance algorithm. More...

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

Inheritance diagram for seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >:

Public Types
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
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<std::ranges::viewable_range database_t, std::ranges::viewable_range query_t, typename align_config_t, typename is_semi_global_t, typename word_t = uint_fast64_t>
struct seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >

The default traits type for the edit distance algorithm.

Member Data Documentation

compute_begin_positions

template<std::ranges::viewable_range database_t, std::ranges::viewable_range query_t, typename align_config_t , typename is_semi_global_t , typename word_t = uint_fast64_t>

constexpr bool seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >::compute_begin_positions

staticconstexpr

Initial value:

=
        alignment_traits_type::compute_begin_positions || compute_sequence_alignment

Whether the alignment configuration indicates to compute and/or store the begin positions.

compute_end_positions

template<std::ranges::viewable_range database_t, std::ranges::viewable_range query_t, typename align_config_t , typename is_semi_global_t , typename word_t = uint_fast64_t>

constexpr bool seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >::compute_end_positions

staticconstexpr

Initial value:

=
        alignment_traits_type::compute_end_positions || compute_begin_positions

Whether the alignment configuration indicates to compute and/or store the end positions.

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

• edit_distance_fwd.hpp