seqan3::search_cfg::max_error_deletion Class Reference

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

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

Inheritance diagram for seqan3::search_cfg::max_error_deletion:

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

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 deletion errors.

See also

Configuration

This configuration element can be used to determine the number or rate of deletion errors that are supported. A deletion corresponds to a base deleted from the query sequence that does occur in the text. Deletions at the beginning and at the end of the sequence are not considered during a search.

Example

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#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_deletion() [1/2] [no-api]

constexpr seqan3::search_cfg::max_error_deletion::max_error_deletion ( error_count  error )

no-apiinlineexplicitconstexpr

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

Parameters

[in]

error

The maximal number of deletion errors allowed in the search.

max_error_deletion() [2/2] [no-api]

constexpr seqan3::search_cfg::max_error_deletion::max_error_deletion ( error_rate  error )

no-apiinlineexplicitconstexpr

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

Parameters

[in]

error

The maximal error rate for deletions allowed in the search.

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

• max_error.hpp