SeqAn3
Configuration

Data structures and utility functions for configuring search algorithm. More...

Collaboration diagram for Configuration:

Classes

struct  seqan3::search_cfg::deletion< value_t >
 A strong type of underlying type uint8_t or double that represents the number or rate of deletions. More...
 
struct  seqan3::search_cfg::insertion< value_t >
 A strong type of underlying type uint8_t or double that represents the number or rate of insertions. More...
 
struct  seqan3::search_cfg::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  seqan3::search_cfg::substitution< value_t >
 A strong type of underlying type uint8_t or double that represents the number or rate of substitutions. More...
 
struct  seqan3::search_cfg::total< value_t >
 A strong type of underlying type uint8_t or double that represents the number or rate of total errors. More...
 

Variables

constexpr detail::search_config_max_error_adaptor seqan3::search_cfg::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...
 
constexpr detail::search_config_max_error_rate_adaptor seqan3::search_cfg::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...
 
detail::search_config_mode_adaptor< seqan3::detail::search_config_mode > constexpr seqan3::search_cfg::mode
 Configuration element to determine the search mode.
 
detail::search_config_output_adaptor< seqan3::detail::search_config_output > constexpr seqan3::search_cfg::output
 Configuration element to determine the output type of hits.
 

Detailed Description

Data structures and utility functions for configuring search algorithm.

Todo:
Write detailed landing page.

Variable Documentation

◆ max_error

constexpr detail::search_config_max_error_adaptor seqan3::search_cfg::max_error
inline

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.

An insertion corresponds to a base inserted into the query that does not occur in the text at the position, a deletion corresponds to a base deleted from the query sequence that does occur in the indexed text. Deletions at the beginning and at the end of the sequence are not considered during a search.

◆ max_error_rate

constexpr detail::search_config_max_error_rate_adaptor seqan3::search_cfg::max_error_rate
inline

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.

An insertion corresponds to a base inserted into the query that does not occur in the text at the position, a deletion corresponds to a base deleted from the query sequence that does occur in the indexed text. Deletions at the beginning and at the end of the sequence are not considered during a search.