SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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default_configuration.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
4 // This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5 // shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
6 // -----------------------------------------------------------------------------------------------------
7 
14 #pragma once
15 
16 #include <seqan3/core/algorithm/configuration.hpp>
17 #include <seqan3/search/configuration/detail.hpp>
18 #include <seqan3/search/configuration/max_error.hpp>
19 #include <seqan3/search/configuration/hit.hpp>
20 #include <seqan3/search/configuration/output.hpp>
21 
22 namespace seqan3::search_cfg
23 {
24 
32 inline const configuration default_configuration = max_error_total{error_count{0}} |
33  max_error_substitution{error_count{0}} |
34  max_error_insertion{error_count{0}} |
35  max_error_deletion{error_count{0}} |
36  output_query_id{} |
37  output_reference_id{} |
38  output_reference_begin_position{} |
39  hit_all{};
40 } // namespace seqan3::search_cfg
configuration.hpp
Provides seqan3::detail::configuration and utility functions.
seqan3::search_cfg::max_error_total
Configuration element that represents the number or rate of total errors.
Definition: max_error.hpp:36
detail.hpp
Provides compatibility matrix for search configurations.
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.
seqan3::configuration
Collection of elements to configure an algorithm.
Definition: configuration.hpp:82
seqan3::search_cfg::error_count
A strong type of underlying type uint8_t that represents the number of errors.
Definition: max_error_common.hpp:30
hit.hpp
Provides the configuration to define the hit strategies "hit_strata", "hit_all", "hit_all_best",...
output.hpp
Provides the configuration for the content of the search result.
seqan3::search_cfg::default_configuration
const configuration default_configuration
The default configuration: Compute all exact matches.
Definition: default_configuration.hpp:32