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  deletion
 A strong type of underlying type uint8_t or double that represents the number or rate of deletions. More...
 
struct  insertion
 A strong type of underlying type uint8_t or double that represents the number or rate of insertions. More...
 
class  max_error
 A configuration element for the maximum number of errors across all error types (mismatches, insertions, deletions). This is an upper bound of errors independent from error numbers of specific error types. More...
 
class  max_error_rate
 A configuration element for the maximum number of errors in percent of the query length across all error types (mismatches, insertions, deletions). This is an upper bound of errors independent from error rates of specific error types. More...
 
struct  mode
 Configuration element to determine the search mode. More...
 
struct  output
 Configuration element to determine the output type of hits. More...
 
struct  strata
 Configuration element to receive all hits with the best number of errors plus the strata value. A strong type of underlying type uint8_t that represents the number or errors for strata. All hits are found with the fewest numbererrors plus 'value'. More...
 
struct  substitution
 A strong type of underlying type uint8_t or double that represents the number or rate of substitutions. More...
 
struct  total
 A strong type of underlying type uint8_t or double that represents the number or rate of total errors. 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...
 

Variables

detail::search_mode_all constexpr all
 Configuration element to receive all hits within the error bounds.
 
detail::search_mode_all_best constexpr all_best
 Configuration element to receive all hits within the lowest number of errors.
 
detail::search_mode_best constexpr best
 Configuration element to receive one best hit (with the lowest number of errors).
 
constexpr configuration default_configuration
 The default configuration. More...
 
detail::search_output_index_cursor constexpr index_cursor
 Configuration element to receive all hits within the error bounds.
 
detail::search_output_text_position constexpr text_position
 Configuration element to receive all hits within the lowest number of errors.
 

Detailed Description

A special sub namespace for the search configurations.