seqan3::detail::edit_distance_algorithm< config_t, traits_t > Class Template Reference

This algorithm unifies different edit distance implementations and uses the appropriate one depending on the given configuration. More...

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

Inheritance diagram for seqan3::detail::edit_distance_algorithm< config_t, traits_t >:

Private Types
using	alignment_result_type = typename configuration_traits_type::alignment_result_type
	The configured alignment result type.
using	configuration_traits_type = alignment_configuration_traits< config_t >
	The configuration traits for the selected alignment algorithm.

Constructors, destructor and assignment
std::shared_ptr< std::remove_cvref_t< config_t > >	cfg_ptr {}
	The alignment configuration stored on the heap.
constexpr	edit_distance_algorithm ()=default
	Defaulted.
constexpr	edit_distance_algorithm (edit_distance_algorithm const &)=default
	Defaulted.
constexpr	edit_distance_algorithm (edit_distance_algorithm &&)=default
	Defaulted.
constexpr edit_distance_algorithm &	operator= (edit_distance_algorithm const &)=default
	Defaulted.
constexpr edit_distance_algorithm &	operator= (edit_distance_algorithm &&)=default
	Defaulted.
	~edit_distance_algorithm ()=default
	Defaulted.
constexpr	edit_distance_algorithm (config_t const &cfg)
	Constructs the wrapper with the passed configuration.
template<indexed_sequence_pair_range indexed_sequence_pairs_t, typename callback_t > requires std::invocable<callback_t, alignment_result_type>
constexpr void	operator() (indexed_sequence_pairs_t &&indexed_sequence_pairs, callback_t &&callback)
	}
template<std::ranges::forward_range first_range_t, std::ranges::forward_range second_range_t, typename callback_t >
constexpr void	compute_single_pair (size_t const idx, first_range_t &&first_range, second_range_t &&second_range, callback_t &&callback)
	Invokes the actual alignment computation for a single pair of sequences.

Detailed Descriptionno-api

template<typename config_t, typename traits_t>
class seqan3::detail::edit_distance_algorithm< config_t, traits_t >

This algorithm unifies different edit distance implementations and uses the appropriate one depending on the given configuration.

Template Parameters

config_t	The configuration type.
traits_t	The traits type.

This wrapper class is used to decouple the sequence types from the algorithm class type. Within the alignment configuration a std::function object storing this wrapper is returned if an edit distance should be computed. On invocation it delegates the call to the actual implementation of the edit distance algorithm, while the interface is unified with the execution model of the pairwise alignment algorithms.

Constructor & Destructor Documentation

edit_distance_algorithm() [no-api]

template<typename config_t , typename traits_t >

constexpr seqan3::detail::edit_distance_algorithm< config_t, traits_t >::edit_distance_algorithm ( config_t const &  cfg )

no-apiinlineconstexpr

Constructs the wrapper with the passed configuration.

Parameters

cfg	The configuration to be passed to the algorithm.

The configuration is copied once to the heap during construction and maintained by a std::shared_ptr. The configuration is not passed to the function-call-operator of this function object in order to avoid incompatible configurations between the passed configuration and the one used during configuration of this class. Further, the function object will be stored in a std::function which requires copyable objects and in parallel executions the function object must be copied as well.

Member Function Documentation

compute_single_pair() [no-api]

template<typename config_t , typename traits_t >

template<std::ranges::forward_range first_range_t, std::ranges::forward_range second_range_t, typename callback_t >

constexpr void seqan3::detail::edit_distance_algorithm< config_t, traits_t >::compute_single_pair ( size_t const  idx, first_range_t &&  first_range, second_range_t &&  second_range, callback_t &&  callback  )

no-apiinlineconstexprprivate

Invokes the actual alignment computation for a single pair of sequences.

Template Parameters

first_range_t	The type of the first sequence (or packed sequences); must model std::ranges::forward_range.
second_range_t	The type of the second sequence (or packed sequences); must model std::ranges::forward_range.
callback_t	The callback to call on the computed alignment result.

Parameters

[in]	idx	The index of the current sequence pair.
[in]	first_range	The first sequence (or packed sequences).
[in]	second_range	The second sequence (or packed sequences).
[in]	callback	The callback to invoke on an alignment result.

operator()() [no-api]

template<typename config_t , typename traits_t >

template<indexed_sequence_pair_range indexed_sequence_pairs_t, typename callback_t >
requires std::invocable<callback_t, alignment_result_type>

constexpr void seqan3::detail::edit_distance_algorithm< config_t, traits_t >::operator() ( indexed_sequence_pairs_t &&  indexed_sequence_pairs, callback_t &&  callback  )

no-apiinlineconstexpr

}

Invokes the alignment computation for every indexed sequence pair contained in the given range.

Template Parameters

indexed_sequence_pairs_t	The type of the range of the indexed sequence pairs; must model seqan3::detail::indexed_sequence_pairs.
callback_t	The type of the callback function that is called with the alignment result; must model std::invocable accepting one argument of type seqan3::alignment_result.

Parameters

[in]	indexed_sequence_pairs	The indexed sequence pairs to align.
[in]	callback	The callback function to be invoked with the alignment result; must model std::invocable with the respective seqan3::alignment_result type.

Computes for each contained sequence pair the respective alignment and invokes the given callback for each alignment result.

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

• edit_distance_algorithm.hpp