SeqAn3  3.0.1
The Modern C++ library for sequence analysis.
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 
13 #pragma once
14 
15 #include <seqan3/core/algorithm/configuration.hpp>
16 #include <seqan3/search/configuration/detail.hpp>
17 #include <seqan3/search/configuration/max_error.hpp>
18 #include <seqan3/search/configuration/max_error_rate.hpp>
19 #include <seqan3/search/configuration/mode.hpp>
20 #include <seqan3/search/configuration/output.hpp>
21 
22 namespace seqan3::search_cfg
23 {
24 
28 inline constexpr configuration default_configuration = max_error{total{0}, substitution{0}, insertion{0}, deletion{0}} |
29  output{text_position} |
30  mode{all};
31 
32 } // namespace seqan3::search_cfg
mode.hpp
Provides the mode configuration to define the search modes "all", "all_best", "best" and "strata".
configuration.hpp
Provides seqan3::detail::configuration and utility functions.
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
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: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::default_configuration
constexpr configuration default_configuration
The default configuration.
Definition: default_configuration.hpp:28
seqan3::search_cfg::all
constexpr detail::search_mode_all all
Configuration element to receive all hits within the error bounds.
Definition: mode.hpp:43
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::max_error
A configuration element for the maximum number of errors across all error types (mismatches,...
Definition: max_error.hpp:43
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
seqan3::search_cfg::text_position
constexpr detail::search_output_text_position text_position
Configuration element to receive all hits within the lowest number of errors.
Definition: output.hpp:42
output.hpp
Provides the configuration for returning positions in the text.