seqan3::search_cfg::max_error_substitution Class Reference

Configuration element that represents the number or rate of substitution errors. More...

#include <seqan3/search/configuration/max_error.hpp>

Inheritance diagram for seqan3::search_cfg::max_error_substitution:

Public Member Functions
Constructors, destructor and assignment
	max_error_substitution ()=default
	Defaulted.
	max_error_substitution (max_error_substitution const &)=default
	Defaulted.
	max_error_substitution (max_error_substitution &&)=default
	Defaulted.
max_error_substitution &	operator= (max_error_substitution const &)=default
	Defaulted.
max_error_substitution &	operator= (max_error_substitution &&)=default
	Defaulted.
	~max_error_substitution ()=default
	Defaulted.
	max_error_substitution (error_count error)
	Initialises the substitution error with the given seqan3::search_cfg::error_count. More...
	max_error_substitution (error_rate error)
	Initialises the substitution error with the given seqan3::search_cfg::error_rate. More...

Public Attributes
std::variant< error_count, error_rate >	error {error_count{0}}
	The error count or error rate.

Detailed Descriptionno-api

Configuration element that represents the number or rate of substitution errors.

This configuration element can be used to determine the number or rate of substitution errors that are supported. A substitution corresponds to diverging bases between text and query for a certain position.

Example

#include <seqan3/core/configuration/configuration.hpp>
#include <seqan3/search/configuration/max_error.hpp>
 
int main()
{
    // Allow 1 error of any type.
    seqan3::configuration const cfg1 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}};
 
    // Do not allow substitutions. Allow at most 1 error.
    seqan3::configuration const cfg2 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
                                       seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_count{0}} |
                                       seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_count{1}} |
                                       seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{1}};
 
    // Sets total errors to 2.
    seqan3::configuration const cfg3 = seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_count{0}} |
                                       seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_count{1}} |
                                       seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{1}};
 
    // Allow 10% errors of any type.
    seqan3::configuration const cfg4 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_rate{0.1}};
 
    // Do not allow substitutions. Allow at most 10% errors.
    seqan3::configuration const cfg5 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_rate{.1}} |
                                       seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_rate{.0}} |
                                       seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_rate{.1}} |
                                       seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_rate{.1}};
 
    // Sets total errors to 20%.
    seqan3::configuration const cfg6 = seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_rate{.0}} |
                                       seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_rate{.1}} |
                                       seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_rate{.1}};
 
    // Mixed error rate & count: Allow 2 insertions and or 2 deletions and 20% errors in total.
 
    seqan3::configuration const cfg7 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_rate{.2}} |
                                       seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_count{0}} |
                                       seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_count{2}} |
                                       seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{2}};
 
 
    return 0;
}

Constructor & Destructor Documentation

max_error_substitution() [1/2]

seqan3::search_cfg::max_error_substitution::max_error_substitution ( error_count  error )

no-apiinlineexplicit

Initialises the substitution error with the given seqan3::search_cfg::error_count.

Parameters

[in]

error

The maximal number of substitution errors allowed in the search.

max_error_substitution() [2/2]

seqan3::search_cfg::max_error_substitution::max_error_substitution ( error_rate  error )

no-apiinlineexplicit

Initialises the substitution error with the given seqan3::search_cfg::error_rate.

Parameters

[in]

error

The maximal error rate for substitutions allowed in the search.

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

• seqan3/search/configuration/max_error.hpp