SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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_rateoperator= (max_error_rate const &) noexcept=default
 Copy assignment.
 
constexpr max_error_rateoperator= (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.

A mismatch corresponds to diverging bases between text and query for a certain position. 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_tA template parameter pack with the error types.
Parameters
[in]errorsA 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


The documentation for this class was generated from the following file:
seqan3::search_cfg::deletion
A strong type of underlying type uint8_t or double that represents the number or rate of deletions.
Definition: max_error_common.hpp:130
seqan3::search_cfg::max_error_rate
A configuration element for the maximum number of errors in percent of the query length across all er...
Definition: max_error_rate.hpp:46
seqan3::configuration
Collection of elements to configure an algorithm.
Definition: configuration.hpp:81
max_error_rate.hpp
Provides the configuration for maximum number of errors in percent of the query length across all err...
seqan3::search_cfg::substitution
A strong type of underlying type uint8_t or double that represents the number or rate of substitution...
Definition: max_error_common.hpp:64
seqan3::search_cfg::total
A strong type of underlying type uint8_t or double that represents the number or rate of total errors...
Definition: max_error_common.hpp:30
seqan3::search_cfg::insertion
A strong type of underlying type uint8_t or double that represents the number or rate of insertions.
Definition: max_error_common.hpp:97