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max_error.hpp
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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
#pragma once
#include <variant>
#include <seqan3/core/configuration/pipeable_config_element.hpp>
#include <seqan3/search/configuration/detail.hpp>
#include <seqan3/search/configuration/max_error_common.hpp>
#include <seqan3/search/detail/search_common.hpp>
namespace seqan3::search_cfg
{
class max_error_total : private pipeable_config_element
{
public:
std::variant<error_count, error_rate> error{error_count{0}};
max_error_total() = default;
max_error_total(max_error_total const &) = default;
max_error_total(max_error_total &&) = default;
max_error_total & operator=(max_error_total const &) = default;
max_error_total & operator=(max_error_total &&) = default;
~max_error_total() = default;
constexpr explicit max_error_total(error_count error) : error{std::move(error)}
{}
constexpr explicit max_error_total(error_rate error) : error{std::move(error)}
{}
static constexpr detail::search_config_id id{detail::search_config_id::max_error_total};
};
class max_error_substitution : private pipeable_config_element
{
public:
std::variant<error_count, error_rate> error{error_count{0}};
max_error_substitution() = default;
max_error_substitution(max_error_substitution const &) = default;
max_error_substitution(max_error_substitution &&) = default;
max_error_substitution & operator=(max_error_substitution const &) = default;
max_error_substitution & operator=(max_error_substitution &&) = default;
~max_error_substitution() = default;
constexpr explicit max_error_substitution(error_count error) : error{std::move(error)}
{}
constexpr explicit max_error_substitution(error_rate error) : error{std::move(error)}
{}
static constexpr detail::search_config_id id{detail::search_config_id::max_error_substitution};
};
class max_error_insertion : private pipeable_config_element
{
public:
std::variant<error_count, error_rate> error{error_count{0}};
max_error_insertion() = default;
max_error_insertion(max_error_insertion const &) = default;
max_error_insertion(max_error_insertion &&) = default;
max_error_insertion & operator=(max_error_insertion const &) = default;
max_error_insertion & operator=(max_error_insertion &&) = default;
~max_error_insertion() = default;
constexpr explicit max_error_insertion(error_count error) : error{std::move(error)}
{}
constexpr explicit max_error_insertion(error_rate error) : error{std::move(error)}
{}
static constexpr detail::search_config_id id{detail::search_config_id::max_error_insertion};
};
class max_error_deletion : private pipeable_config_element
{
public:
std::variant<error_count, error_rate> error{error_count{0}};
max_error_deletion() = default;
max_error_deletion(max_error_deletion const &) = default;
max_error_deletion(max_error_deletion &&) = default;
max_error_deletion & operator=(max_error_deletion const &) = default;
max_error_deletion & operator=(max_error_deletion &&) = default;
~max_error_deletion() = default;
constexpr explicit max_error_deletion(error_count error) : error{std::move(error)}
{}
constexpr explicit max_error_deletion(error_rate error) : error{std::move(error)}
{}
static constexpr detail::search_config_id id{detail::search_config_id::max_error_deletion};
};
} // namespace seqan3::search_cfg
seqan3::search_cfg::max_error_deletion::operator=
max_error_deletion & operator=(max_error_deletion &&)=default
Defaulted.
seqan3::search_cfg::max_error_deletion::~max_error_deletion
~max_error_deletion()=default
Defaulted.
seqan3::search_cfg::max_error_deletion::max_error_deletion
max_error_deletion()=default
Defaulted.
seqan3::search_cfg::max_error_deletion::max_error_deletion
constexpr max_error_deletion(error_count error)
Initialises the deletion error with the given seqan3::search_cfg::error_count.
Definition max_error.hpp:188
seqan3::search_cfg::max_error_deletion::max_error_deletion
max_error_deletion(max_error_deletion &&)=default
Defaulted.
seqan3::search_cfg::max_error_deletion::max_error_deletion
max_error_deletion(max_error_deletion const &)=default
Defaulted.
seqan3::search_cfg::max_error_deletion::max_error_deletion
constexpr max_error_deletion(error_rate error)
Initialises the deletion error with the given seqan3::search_cfg::error_rate.
Definition max_error.hpp:194
seqan3::search_cfg::max_error_deletion::operator=
max_error_deletion & operator=(max_error_deletion const &)=default
Defaulted.
seqan3::search_cfg::max_error_deletion::error
std::variant< error_count, error_rate > error
The error count or error rate.
Definition max_error.hpp:173
seqan3::search_cfg::max_error_insertion::~max_error_insertion
~max_error_insertion()=default
Defaulted.
seqan3::search_cfg::max_error_insertion::max_error_insertion
max_error_insertion(max_error_insertion &&)=default
Defaulted.
seqan3::search_cfg::max_error_insertion::max_error_insertion
max_error_insertion(max_error_insertion const &)=default
Defaulted.
seqan3::search_cfg::max_error_insertion::error
std::variant< error_count, error_rate > error
The error count or error rate.
Definition max_error.hpp:127
seqan3::search_cfg::max_error_insertion::max_error_insertion
constexpr max_error_insertion(error_rate error)
Initialises the insertion error with the given seqan3::search_cfg::error_rate.
Definition max_error.hpp:148
seqan3::search_cfg::max_error_insertion::operator=
max_error_insertion & operator=(max_error_insertion const &)=default
Defaulted.
seqan3::search_cfg::max_error_insertion::max_error_insertion
max_error_insertion()=default
Defaulted.
seqan3::search_cfg::max_error_insertion::operator=
max_error_insertion & operator=(max_error_insertion &&)=default
Defaulted.
seqan3::search_cfg::max_error_insertion::max_error_insertion
constexpr max_error_insertion(error_count error)
Initialises the insertion error with the given seqan3::search_cfg::error_count.
Definition max_error.hpp:142
seqan3::search_cfg::max_error_substitution::operator=
max_error_substitution & operator=(max_error_substitution &&)=default
Defaulted.
seqan3::search_cfg::max_error_substitution::max_error_substitution
max_error_substitution()=default
Defaulted.
seqan3::search_cfg::max_error_substitution::max_error_substitution
constexpr max_error_substitution(error_count error)
Initialises the substitution error with the given seqan3::search_cfg::error_count.
Definition max_error.hpp:97
seqan3::search_cfg::max_error_substitution::max_error_substitution
max_error_substitution(max_error_substitution const &)=default
Defaulted.
seqan3::search_cfg::max_error_substitution::max_error_substitution
constexpr max_error_substitution(error_rate error)
Initialises the substitution error with the given seqan3::search_cfg::error_rate.
Definition max_error.hpp:103
seqan3::search_cfg::max_error_substitution::max_error_substitution
max_error_substitution(max_error_substitution &&)=default
Defaulted.
seqan3::search_cfg::max_error_substitution::~max_error_substitution
~max_error_substitution()=default
Defaulted.
seqan3::search_cfg::max_error_substitution::error
std::variant< error_count, error_rate > error
The error count or error rate.
Definition max_error.hpp:82
seqan3::search_cfg::max_error_substitution::operator=
max_error_substitution & operator=(max_error_substitution const &)=default
Defaulted.
seqan3::search_cfg::max_error_total::operator=
max_error_total & operator=(max_error_total const &)=default
Defaulted.
seqan3::search_cfg::max_error_total::max_error_total
constexpr max_error_total(error_count error)
Initialises the total error with the given seqan3::search_cfg::error_count.
Definition max_error.hpp:52
seqan3::search_cfg::max_error_total::max_error_total
max_error_total(max_error_total &&)=default
Defaulted.
seqan3::search_cfg::max_error_total::~max_error_total
~max_error_total()=default
Defaulted.
seqan3::search_cfg::max_error_total::error
std::variant< error_count, error_rate > error
The error count or error rate.
Definition max_error.hpp:37
seqan3::search_cfg::max_error_total::operator=
max_error_total & operator=(max_error_total &&)=default
Defaulted.
seqan3::search_cfg::max_error_total::max_error_total
constexpr max_error_total(error_rate error)
Initialises the total error with the given seqan3::search_cfg::error_rate.
Definition max_error.hpp:58
seqan3::search_cfg::max_error_total::max_error_total
max_error_total(max_error_total const &)=default
Defaulted.
seqan3::search_cfg::max_error_total::max_error_total
max_error_total()=default
Defaulted.
max_error_common.hpp
Provides the error types for maximum number of errors.
seqan3::search_cfg
A special sub namespace for the search configurations.
std
SeqAn specific customisations in the standard namespace.
pipeable_config_element.hpp
Provides seqan3::pipeable_config_element.
detail.hpp
Provides compatibility matrix for search configurations.
search_common.hpp
Provides data structures used by different search algorithms.
seqan3::pipeable_config_element
Adds pipe interface to configuration elements.
Definition pipeable_config_element.hpp:29
seqan3::search_cfg::error_count
A strong type of underlying type uint8_t that represents the number of errors.
Definition max_error_common.hpp:29
seqan3::search_cfg::error_rate
A strong type of underlying type double that represents the rate of errors.
Definition max_error_common.hpp:43
variant
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