SeqAn3  3.2.0-rc.1
The Modern C++ library for sequence analysis.
structure_file/input_format_concept.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2022, 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 <fstream>
16 #include <set>
17 #include <string>
18 #include <utility>
19 #include <vector>
20 
26 
27 namespace seqan3::detail
28 {
29 
40 template <typename format_type>
41 struct structure_file_input_format_exposer : public format_type
42 {
43 public:
44  // Can't use `using format_type::read_structure_record` as it produces a hard failure in the format concept check
45  // for types that do not model the format concept, i.e. don't offer the proper read_structure_record interface.
47  template <typename... ts>
48  void read_structure_record(ts &&... args)
49  {
50  format_type::read_structure_record(std::forward<ts>(args)...);
51  }
52 };
53 
54 } // namespace seqan3::detail
55 
56 namespace seqan3
57 {
58 
72 template <typename t>
74  requires (detail::structure_file_input_format_exposer<t> & v,
75  std::ifstream & f,
76  structure_file_input_options<rna5, false> & options,
77  rna5_vector & seq,
78  std::string & id,
80  std::vector<wuss51> & structure,
81  std::vector<structured_rna<rna5, wuss51>> & structured_seq,
82  double energy,
83  double react,
84  double react_err,
85  std::string & comment,
86  size_t offset) {
87  t::file_extensions;
88 
89  {
90  v.read_structure_record(f, options, seq, id, bpp, structure, energy, react, react_err, comment, offset)
91  } -> std::same_as<void>;
92 
93  {
94  v.read_structure_record(f,
95  options,
96  seq,
97  id,
98  bpp,
99  std::ignore,
100  std::ignore,
101  std::ignore,
102  std::ignore,
103  std::ignore,
104  std::ignore)
105  } -> std::same_as<void>;
106 
107  {
108  v.read_structure_record(f,
109  options,
110  structured_seq,
111  id,
112  std::ignore,
113  structured_seq,
114  energy,
115  std::ignore,
116  std::ignore,
117  std::ignore,
118  std::ignore)
119  } -> std::same_as<void>;
120 
121  {
122  v.read_structure_record(f,
123  options,
124  std::ignore,
125  std::ignore,
126  std::ignore,
127  std::ignore,
128  std::ignore,
129  std::ignore,
130  std::ignore,
131  std::ignore,
132  std::ignore)
133  } -> std::same_as<void>;
134  // the last is required to be compile time valid, but should always throw at run-time.
135  };
137 
198 
199 } // namespace seqan3
200 
201 namespace seqan3::detail
202 {
203 
209 template <typename t>
210 constexpr bool is_type_list_of_structure_file_input_formats_v = false;
211 
217 template <typename... ts>
218 constexpr bool is_type_list_of_structure_file_input_formats_v<type_list<ts...>> =
220 
226 template <typename t>
227 concept type_list_of_structure_file_input_formats = is_type_list_of_structure_file_input_formats_v<t>;
228 } // namespace seqan3::detail
requires requires
The rank_type of the semi-alphabet; defined as the return type of seqan3::to_rank....
Definition: alphabet/concept.hpp:164
The generic concept for structure file in formats.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides seqan3::rna5, container aliases and string literals.
Provides seqan3::structure_file_input_options.
Provides the composite of nucleotide with structure alphabets.
Provides seqan3::type_list.
Provides the WUSS format for RNA structure.