SeqAn3  3.1.0
The Modern C++ library for sequence analysis.
auxiliary.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2021, 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/std/concepts>
16 #include <sstream>
17 #include <seqan3/std/type_traits>
18 #include <unordered_map>
19 #include <vector>
20 
25 
26 namespace seqan3::custom
27 {
28 
51 template <typename t>
53 {}; // forward
54 
56 template <typename t>
57 struct argument_parsing<t const> : argument_parsing<t>
58 {};
59 
60 template <typename t>
61 struct argument_parsing<t &> : argument_parsing<t>
62 {};
63 
64 template <typename t>
65 struct argument_parsing<t const &> : argument_parsing<t>
66 {};
68 
69 } // seqan3::custom
70 
71 namespace seqan3::detail::adl_only
72 {
73 
75 template <typename t>
77 
81 template <typename option_t>
82 struct enumeration_names_cpo : public detail::customisation_point_object<enumeration_names_cpo<option_t>, 1>
83 {
85  using base_t = detail::customisation_point_object<enumeration_names_cpo<option_t>, 1>;
87  using base_t::base_t;
88 
92  template <typename option_type>
93  using option_or_type_identity
95  seqan3::is_constexpr_default_constructible_v<std::remove_cvref_t<option_type>>,
98 
102  template <typename option_type = option_t>
103  static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<1>)
104  (
106  );
107 
117  template <typename option_type = option_t>
118  static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<0>)
119  (
120  /*return*/ enumeration_names(option_or_type_identity<option_type>{}) /*;*/
121  );
122 };
123 
124 } // namespace seqan3::detail::adl_only
125 
126 namespace seqan3
127 {
128 
167 template <typename option_type>
169  requires requires { { detail::adl_only::enumeration_names_cpo<option_type>{}() }; }
171 inline auto const enumeration_names = detail::adl_only::enumeration_names_cpo<option_type>{}();
173 
187 template <typename option_type>
188 SEQAN3_CONCEPT named_enumeration = requires
189 {
190  { seqan3::enumeration_names<option_type> };
191 };
193 
207 template <typename option_type>
211 
226 template <typename char_t, typename option_type>
230 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, option_type && op)
231 {
232  for (auto & [key, value] : enumeration_names<option_type>)
233  {
234  if (op == value)
235  return s << key;
236  }
237 
238  return s << "<UNKNOWN_VALUE>";
239 }
241 
254 enum option_spec
255 {
256  standard = 0,
257  required = 1,
262  advanced = 2,
266  hidden = 4
270 };
271 
273 enum class update_notifications
274 {
275  on,
276  off
277 };
278 
292 struct argument_parser_meta_data // holds all meta information
293 {
327  unsigned man_page_section{1};
343 };
344 
345 } // namespace seqan3
Provides various type traits on generic types.
The <concepts> header from C++20's standard library.
Helper utilities for defining customisation point objects (CPOs).
#define SEQAN3_CPO_OVERLOAD(...)
A macro that helps to define a seqan3::detail::customisation_point_object.
Definition: customisation_point.hpp:102
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:101
auto const enumeration_names
Return a conversion map from std::string_view to option_type.
Definition: auxiliary.hpp:165
option_spec
Used to further specify argument_parser options/flags.
Definition: auxiliary.hpp:249
@ standard
The default were no checking or special displaying is happening.
Definition: auxiliary.hpp:250
@ advanced
Definition: auxiliary.hpp:256
@ hidden
Definition: auxiliary.hpp:260
@ required
Definition: auxiliary.hpp:251
typename remove_cvref< t >::type remove_cvref_t
Return the input type with const, volatile and references removed (transformation_trait shortcut).
Definition: type_traits:73
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:44
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
update_notifications
Indicates whether application allows automatic update notifications by the seqan3::argument_parser.
Definition: auxiliary.hpp:268
@ 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:313
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:319
std::string email
The author's e-mail address for correspondence.
Definition: auxiliary.hpp:301
std::string short_copyright
Brief copyright (and/or license) information.
Definition: auxiliary.hpp:309
std::string date
The date that the application was last updated. Keep this updated, ! since it will tell your users th...
Definition: auxiliary.hpp:305
std::string author
Your name ;-)
Definition: auxiliary.hpp:299
std::string version
The version information MAJOR.MINOR.PATH (e.g. 3.1.3)
Definition: auxiliary.hpp:295
std::string app_name
The application name that will be displayed on the help page.
Definition: auxiliary.hpp:293
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:331
std::string short_description
A short description of the application (e.g. "A tool for mapping reads to the genome").
Definition: auxiliary.hpp:297
std::string url
A link to your github/gitlab project with the newest release.
Definition: auxiliary.hpp:307
std::string citation
How users shall cite your application.
Definition: auxiliary.hpp:315
std::vector< std::string > description
A more detailed description that is displayed on the help page in the section "DESCRIPTION"....
Definition: auxiliary.hpp:327
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:336
unsigned man_page_section
The man page section info (type man man on the command line for more information).
Definition: auxiliary.hpp:321
A type that can be specialised to provide customisation point implementations for the seqan3::argumen...
Definition: auxiliary.hpp:53
The identity transformation (a transformation_trait that returns the input).
Definition: type_traits:87
The <type_traits> header from C++20's standard library.