seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t > Class Template Reference

The algorithm that performs a unidirectional search on an FM index using trivial backtracking. More...

#include <seqan3/search/detail/unidirectional_search_algorithm.hpp>

Inheritance diagram for seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >:

Public Member Functions
template<typename indexed_query_t , typename callback_t > requires (std::tuple_size_v<indexed_query_t> == 2) && std::ranges::forward_range<std::tuple_element_t<1, indexed_query_t>> && std::invocable<callback_t, search_result_type>
void	operator() (indexed_query_t &&indexed_query, callback_t &&callback)
	Searches a query sequence in an FM index using trivial backtracking.
Constructors, destructor and assignment
	unidirectional_search_algorithm ()=default
	Defaulted.
	unidirectional_search_algorithm (unidirectional_search_algorithm const &)=default
	Defaulted.
	unidirectional_search_algorithm (unidirectional_search_algorithm &&)=default
	Defaulted.
unidirectional_search_algorithm &	operator= (unidirectional_search_algorithm const &)=default
	Defaulted.
unidirectional_search_algorithm &	operator= (unidirectional_search_algorithm &&)=default
	Defaulted.
	~unidirectional_search_algorithm ()=default
	Defaulted.
	unidirectional_search_algorithm (configuration_t const &cfg, index_t const &index)
	Constructs from a configuration object and an index.

Private Types
using	search_result_type = typename traits_t::search_result_type
	The search result type.
using	traits_t = search_traits< configuration_t >
	The search configuration traits.

Private Member Functions
template<typename query_t >
void	perform_search_by_hit_strategy (std::vector< typename index_t::cursor_type > &internal_hits, query_t &query, search_param error_state)
	Calls search_trivial depending on the search strategy (hit configuration) given in the configuration.
template<bool abort_on_hit, typename query_t >
bool	search_trivial (typename index_t::cursor_type cur, query_t &query, typename index_t::cursor_type::size_type const query_pos, search_param const error_left, error_type const prev_error)
	Searches a query sequence in an index using trivial backtracking.

Private Attributes
std::function< void(typename index_t::cursor_type const &)>	delegate
	A function object that stores the on-hit-delegate to be executed whenever a hit in the index is found.
index_t const *	index_ptr {nullptr}
	A pointer to the fm index which is used to perform the unidirectional search.
uint8_t	stratum {}
	The stratum value if set.

Detailed Description

template<typename configuration_t, typename index_t, typename... policies_t>
class seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >

The algorithm that performs a unidirectional search on an FM index using trivial backtracking.

Template Parameters

configuration_t	The search configuration type.
index_t	The type of index.

Constructor & Destructor Documentation

unidirectional_search_algorithm()

template<typename configuration_t , typename index_t , typename... policies_t>

seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >::unidirectional_search_algorithm ( configuration_t const &  cfg, index_t const &  index  )

inline

Constructs from a configuration object and an index.

Template Parameters

configuration_t	The search configuration type.
index_t	The type of index.

Parameters

[in]	cfg	The configuration object that guides the search algorithm.
[in]	index	The index used in the algorithm.

Initialises the stratum value from the configuration if it was set by the user.

Member Function Documentation

operator()()

template<typename configuration_t , typename index_t , typename... policies_t>

template<typename indexed_query_t , typename callback_t >
requires (std::tuple_size_v<indexed_query_t> == 2) && std::ranges::forward_range<std::tuple_element_t<1, indexed_query_t>> && std::invocable<callback_t, search_result_type>

void seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >::operator() ( indexed_query_t &&  indexed_query, callback_t &&  callback  )

inline

Searches a query sequence in an FM index using trivial backtracking.

Template Parameters

indexed_query_t	The type of the indexed query sequence; must model seqan3::tuple_like with exactly two elements and the second tuple element must model std::ranges::forward_range over the index's alphabet.
callback_t	The callback type to be invoked on a search result; must model std::invocable with the search result.

Parameters

[in]	indexed_query	The indexed query sequence to be searched in the index.
[in]	callback	The callback to call on a search result.

The indexed_query parameter is a pair of an index and a query which shall be searched in the index. The search result can then be identified by the index that was associated with the given query.

Complexity

\(O(|query|^e)\) where \(e\) is the maximum number of errors.

perform_search_by_hit_strategy()

template<typename configuration_t , typename index_t , typename... policies_t>

template<typename query_t >

void seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >::perform_search_by_hit_strategy ( std::vector< typename index_t::cursor_type > &  internal_hits, query_t &  query, search_param  error_state  )

inlineprivate

Calls search_trivial depending on the search strategy (hit configuration) given in the configuration.

Template Parameters

query_t

Must model std::ranges::input_range over the index's alphabet.

Parameters

[in,out]	internal_hits	The result vector to be filled.
[in]	query	Query sequence to be searched with the cursor.
[in]	error_state	Number of errors for matching the query sequence.

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

• unidirectional_search_algorithm.hpp