SeqAn3  3.1.0
The Modern C++ library for sequence analysis.
input_format_concept.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 <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>
73 SEQAN3_CONCEPT structure_file_input_format = requires(detail::structure_file_input_format_exposer<t> & v,
74  std::ifstream & f,
75  structure_file_input_options<rna5, false> & options,
76  rna5_vector & seq,
77  std::string & id,
79  std::vector<wuss51> & structure,
80  std::vector<structured_rna<rna5, wuss51>> & structured_seq,
81  double energy,
82  double react,
83  double react_err,
84  std::string & comment,
85  size_t offset)
86 {
87  t::file_extensions;
88 
89  SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_structure_record(f,
90  options,
91  seq,
92  id,
93  bpp,
94  structure,
95  energy,
96  react,
97  react_err,
98  comment,
99  offset),
100  std::same_as, void);
101  SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_structure_record(f,
102  options,
103  seq,
104  id,
105  bpp,
106  std::ignore,
107  std::ignore,
108  std::ignore,
109  std::ignore,
110  std::ignore,
111  std::ignore),
112  std::same_as, void);
113  SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_structure_record(f,
114  options,
115  structured_seq,
116  id,
117  std::ignore,
118  structured_seq,
119  energy,
120  std::ignore,
121  std::ignore,
122  std::ignore,
123  std::ignore),
124  std::same_as, void);
125  SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_structure_record(f,
126  options,
127  std::ignore,
128  std::ignore,
129  std::ignore,
130  std::ignore,
131  std::ignore,
132  std::ignore,
133  std::ignore,
134  std::ignore,
135  std::ignore),
136  std::same_as, void);
137  // the last is required to be compile time valid, but should always throw at run-time.
138 };
140 
201 
202 } // namespace seqan3
203 
204 namespace seqan3::detail
205 {
206 
212 template <typename t>
213 constexpr bool is_type_list_of_structure_file_input_formats_v = false;
214 
220 template <typename ...ts>
221 constexpr bool is_type_list_of_structure_file_input_formats_v<type_list<ts...>>
223 
229 template <typename t>
230 SEQAN3_CONCEPT type_list_of_structure_file_input_formats = is_type_list_of_structure_file_input_formats_v<t>;
231 } // namespace seqan3::detail
The generic concept for structure file in formats.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
#define SEQAN3_RETURN_TYPE_CONSTRAINT(expression, concept_name,...)
Same as writing {expression} -> concept_name<type1[, ...]> in a concept definition.
Definition: platform.hpp:57
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.