seqan3::search_cfg::max_error_rate< errors_t > Class Template Reference

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...

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

Inheritance diagram for seqan3::search_cfg::max_error_rate< errors_t >:

Public Member Functions
Constructor, destructor and assignment
Defaulted all standard constructor.
constexpr	max_error_rate () noexcept=default
	Default constructor.
constexpr	max_error_rate (max_error_rate const &) noexcept=default
	Copy constructor.
constexpr	max_error_rate (max_error_rate &&) noexcept=default
	Move constructor.
constexpr max_error_rate &	operator= (max_error_rate const &) noexcept=default
	Copy assignment.
constexpr max_error_rate &	operator= (max_error_rate &&) noexcept=default
	Move assignment.
	~max_error_rate () noexcept=default
	Destructor.
constexpr	max_error_rate (errors_t &&...errors)
	Constructs the object from a set of error specifiers. More...

Public Attributes
std::array< double, 4 >	value
	The stored config value.

Related Functions
(Note that these are not member functions.)
Type deduction guides
	max_error_rate () -> max_error_rate<>
	Deduces empty list of error specifiers.
template<typename ... errors_t>
	max_error_rate (errors_t &&...) -> max_error_rate< remove_cvref_t< errors_t >... >
	Deduces template arguments from the passed error specifiers.

Detailed Description

template<typename ... errors_t>
class seqan3::search_cfg::max_error_rate< errors_t >

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.

Constructor & Destructor Documentation

max_error_rate()

template<typename ... errors_t>

constexpr seqan3::search_cfg::max_error_rate< errors_t >::max_error_rate ( errors_t &&...  errors )

inlineconstexpr

Constructs the object from a set of error specifiers.

Template Parameters

errors_t

A template parameter pack with the error types.

Parameters

[in]

errors

A pack of error specifiers.

This configuration can be used to specify the total rates of error types. It restricts the rates of substitutions, insertions, deletions and total errors within the search to the given values and will behave as follows:

Behaviour	Set all error types to total	Set total to substitution	Set total to insertion	Set total to deletion	Set total to substitution + insertion	Set total to substitution + deletion	Set total to insertion + deletion
seqan3::search_cfg::total	✅
seqan3::search_cfg::substitution		✅			✅	✅
seqan3::search_cfg::insertion			✅		✅		✅
seqan3::search_cfg::deletion				✅		✅	✅

If seqan3::search_cfg::total and any other error type are specified, all types are set to the respective values.

Example

#include <seqan3/search/configuration/max_error_rate.hpp>
 
int main()
{
    // Allow 10% errors of any type.
    seqan3::configuration const cfg1 = seqan3::search_cfg::max_error_rate{seqan3::search_cfg::total{0.1}};
 
    // Do not allow substitutions. Allow at most 10% errors.
    seqan3::configuration const cfg2 = seqan3::search_cfg::max_error_rate{seqan3::search_cfg::total{0.1},
                                                                          seqan3::search_cfg::substitution{0},
                                                                          seqan3::search_cfg::insertion{0.1},
                                                                          seqan3::search_cfg::deletion{0.1}};
 
    // Sets total errors to 20%.
    seqan3::configuration const cfg3 = seqan3::search_cfg::max_error_rate{seqan3::search_cfg::substitution{0},
                                                                          seqan3::search_cfg::insertion{0.1},
                                                                          seqan3::search_cfg::deletion{0.1}};
 
    return 0;
}

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

• seqan3/search/configuration/max_error_rate.hpp