SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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auxiliary.hpp
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1// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
2// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
3// SPDX-License-Identifier: BSD-3-Clause
4
10#pragma once
11
12#include <concepts>
13#include <sstream>
14#include <type_traits>
15#include <unordered_map>
16#include <vector>
17
21
22namespace seqan3::custom
23{
24
47template <typename t>
49{}; // forward
50
52template <typename t>
53struct argument_parsing<t const> : argument_parsing<t>
54{};
55
56template <typename t>
57struct argument_parsing<t &> : argument_parsing<t>
58{};
59
60template <typename t>
61struct argument_parsing<t const &> : argument_parsing<t>
62{};
64
65} // namespace seqan3::custom
66
67namespace seqan3::detail::adl_only
68{
69
71template <typename t>
73
77template <typename option_t>
78struct enumeration_names_cpo : public detail::customisation_point_object<enumeration_names_cpo<option_t>, 1>
79{
83 using base_t::base_t;
84
88 template <typename option_type>
93
97 template <typename option_type = option_t>
98 static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<1>)(
100 );
101
111 template <typename option_type = option_t>
112 static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<0>)(
114 );
115};
116
117} // namespace seqan3::detail::adl_only
118
119namespace seqan3
120{
121
160template <typename option_type>
161 requires requires {
164 };
166inline auto const enumeration_names = detail::adl_only::enumeration_names_cpo<option_type>{}();
168
182template <typename option_type>
183concept named_enumeration = requires {
184 {
185 seqan3::enumeration_names<option_type>
186 };
187 };
189
203template <typename option_type>
207
222template <typename char_t, typename option_type>
224inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, option_type && op)
225{
226 for (auto & [key, value] : enumeration_names<option_type>)
227 {
228 if (op == value)
229 return s << key;
230 }
231
232 return s << "<UNKNOWN_VALUE>";
233}
235
248enum option_spec
249{
250 standard = 0,
256 advanced = 2,
264};
265
267enum class update_notifications
268{
269 on,
270 off
271};
272
286struct argument_parser_meta_data // holds all meta information
287{
321 unsigned man_page_section{1};
337};
338
339} // namespace seqan3
std::unordered_map< std::string_view, t > enumeration_names(t)=delete
Poison-pill overload to prevent non-ADL forms of unqualified lookup.
Helper utilities for defining customisation point objects (CPOs).
Provides seqan3::debug_stream and related types.
debug_stream_type< char_t > & operator<<(debug_stream_type< char_t > &stream, alignment_t &&alignment)
Stream operator for alignments, which are represented as tuples of aligned sequences.
Definition debug_stream_alignment.hpp:107
auto const enumeration_names
Return a conversion map from std::string_view to option_type.
Definition auxiliary.hpp:162
option_spec
Used to further specify argument_parser options/flags.
Definition auxiliary.hpp:245
@ standard
The default were no checking or special displaying is happening.
Definition auxiliary.hpp:246
@ advanced
Definition auxiliary.hpp:252
@ hidden
Definition auxiliary.hpp:256
@ required
Definition auxiliary.hpp:247
#define SEQAN3_CPO_OVERLOAD(...)
A macro that helps to define a seqan3::detail::customisation_point_object.
Definition customisation_point.hpp:104
Checks whether the the type can be used in an add_(positional_)option call on the argument parser.
Concept for input streams.
Checks whether the free function seqan3::enumeration_names can be called on the type.
Stream concepts.
A namespace for third party and standard library specialisations of SeqAn customisation points.
Definition char.hpp:39
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
update_notifications
Indicates whether application allows automatic update notifications by the seqan3::argument_parser.
Definition auxiliary.hpp:264
@ off
Automatic update notifications should be disabled.
@ on
Automatic update notifications should be enabled.
std::string long_copyright
Detailed copyright information that will be displayed when the user specifies "--copyright" on the co...
Definition auxiliary.hpp:309
std::string man_page_title
The title of your man page when exported by specifying "--export-help man" on the common line.
Definition auxiliary.hpp:315
std::string email
The author's e-mail address for correspondence.
Definition auxiliary.hpp:297
std::string short_copyright
Brief copyright (and/or license) information.
Definition auxiliary.hpp:305
std::string date
The date that the application was last updated. Keep this updated, ! since it will tell your users th...
Definition auxiliary.hpp:301
std::string author
Your name ;-)
Definition auxiliary.hpp:295
std::string version
The version information MAJOR.MINOR.PATH (e.g. 3.1.3)
Definition auxiliary.hpp:291
std::string app_name
The application name that will be displayed on the help page.
Definition auxiliary.hpp:289
std::vector< std::string > synopsis
Add lines of usage to the synopsis section of the help page (e.g. "./my_read_mapper [OPTIONS] FILE1 F...
Definition auxiliary.hpp:327
std::string short_description
A short description of the application (e.g. "A tool for mapping reads to the genome").
Definition auxiliary.hpp:293
std::string url
A link to your github/gitlab project with the newest release.
Definition auxiliary.hpp:303
std::string citation
How users shall cite your application.
Definition auxiliary.hpp:311
std::vector< std::string > description
A more detailed description that is displayed on the help page in the section "DESCRIPTION"....
Definition auxiliary.hpp:323
std::vector< std::string > examples
Provide some examples on how to use your tool and what standard parameters might be appropriate in di...
Definition auxiliary.hpp:332
unsigned man_page_section
The man page section info (type man man on the command line for more information).
Definition auxiliary.hpp:317
A type that can be specialised to provide customisation point implementations for the seqan3::argumen...
Definition auxiliary.hpp:49
seqan3::detail::customisation_point_object (CPO) definition for seqan3::enumeration_names.
Definition auxiliary.hpp:79
A CRTP base-class that defines a customisation_point_object (CPO).
Definition customisation_point.hpp:138
A tag that allows controlled overload resolution via implicit base conversion rules.
Definition customisation_point.hpp:29
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