s/seqan3/seqan3-doc_3.4.0+ds-3_all.deb

// 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 <seqan3/core/configuration/configuration.hpp>

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

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

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

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


namespace seqan3::search_cfg

{


constexpr configuration default_configuration = max_error_total{error_count{0}} | max_error_substitution{error_count{0}}

                                              | max_error_insertion{error_count{0}} | max_error_deletion{error_count{0}}

                                              | output_query_id{} | output_reference_id{}

                                              | output_reference_begin_position{} | hit_all{};


} // namespace seqan3::search_cfg

seqan3::configuration
Collection of elements to configure an algorithm.
Definition configuration.hpp:42

seqan3::search_cfg::hit_all
Configuration element to receive all hits within the error bounds.
Definition hit.hpp:31

seqan3::search_cfg::max_error_deletion
Configuration element that represents the number or rate of deletion errors.
Definition max_error.hpp:170

seqan3::search_cfg::max_error_insertion
Configuration element that represents the number or rate of insertion errors.
Definition max_error.hpp:124

seqan3::search_cfg::max_error_total
Configuration element that represents the number or rate of total errors.
Definition max_error.hpp:34

seqan3::search_cfg::output_query_id
Include the query_id in the seqan3::search_result returned by a call to seqan3::search.
Definition search/configuration/output.hpp:28

seqan3::search_cfg::output_reference_begin_position
Include the reference_begin_position in the seqan3::search_result returned by a call to seqan3::searc...
Definition search/configuration/output.hpp:78

seqan3::search_cfg::output_reference_id
Include the reference_id in the seqan3::search_result returned by a call to seqan3::search.
Definition search/configuration/output.hpp:53

configuration.hpp
Provides seqan3::configuration and utility functions.

seqan3::search_cfg::default_configuration
constexpr configuration default_configuration
The default configuration: Compute all exact matches.
Definition default_configuration.hpp:26

hit.hpp
Provides the configuration to define the hit strategies "hit_strata", "hit_all", "hit_all_best",...

max_error.hpp
Provides the configuration for maximum number of errors for all error types.

seqan3::search_cfg
A special sub namespace for the search configurations.

detail.hpp
Provides compatibility matrix for search configurations.

output.hpp
Provides the configuration for the content of the search result.

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