SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::search_cfg Namespace Reference

A special sub namespace for the search configurations. More...

Classes

struct  error_count
 A strong type of underlying type uint8_t that represents the number of errors. More...
 
struct  error_rate
 A strong type of underlying type double that represents the rate of errors. More...
 
class  hit
 A dynamic configuration element to configure the hit strategy at runtime. More...
 
struct  hit_strata
 Configuration element to receive all hits with the best number of errors plus the given stratum. All hits are found with the fewest number of errors plus 'stratum'. More...
 
class  max_error_deletion
 Configuration element that represents the number or rate of deletion errors. More...
 
class  max_error_insertion
 Configuration element that represents the number or rate of insertion errors. More...
 
class  max_error_substitution
 Configuration element that represents the number or rate of substitution errors. More...
 
class  max_error_total
 Configuration element that represents the number or rate of total errors. More...
 
struct  on_result
 Configuration element to provide a user defined callback function for the search. More...
 

Typedefs

using parallel = seqan3::detail::parallel_mode< std::integral_constant< detail::search_config_id, detail::search_config_id::parallel > >
 Enables the parallel execution of the search algorithm if possible for the given configuration. More...
 

Functions

Type deduction guides
template<std::move_constructible callback_t>
 on_result (callback_t &&) -> on_result< std::decay_t< callback_t >>
 Deduces the callback type from a forwarding constructor argument.
 

Variables

const configuration default_configuration
 The default configuration: Compute all exact matches. More...
 
constexpr detail::hit_all_tag hit_all
 Configuration element to receive all hits within the error bounds. More...
 
constexpr detail::hit_all_best_tag hit_all_best
 Configuration element to receive all hits with the lowest number of errors within the error bounds. More...
 
constexpr detail::hit_single_best_tag hit_single_best
 Configuration element to receive a single best hit with the lowest number of errors within the error bounds. More...
 
constexpr detail::output_index_cursor_tag output_index_cursor
 Include the index_cursor in the seqan3::search_result returned by a call to seqan3::search. More...
 
constexpr detail::output_query_id_tag output_query_id
 Include the query_id in the seqan3::search_result returned by a call to seqan3::search. More...
 
constexpr detail::output_reference_begin_position_tag output_reference_begin_position
 Include the reference_begin_position in the seqan3::search_result returned by a call to seqan3::search. More...
 
constexpr detail::output_reference_id_tag output_reference_id
 Include the reference_id in the seqan3::search_result returned by a call to seqan3::search. More...
 

Detailed Description

A special sub namespace for the search configurations.