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 
14 #pragma once
15 
16 #include <fstream>
17 #include <string>
18 #include <vector>
19 
25 
26 namespace seqan3::detail
27 {
28 
39 template <typename format_type>
40 struct sequence_file_input_format_exposer : public format_type
41 {
42 public:
43 
44  // Can't use `using format_type::read_sequence_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_sequence_record interface.
47  template <typename ...ts>
48  void read_sequence_record(ts && ...args)
49  {
50  format_type::read_sequence_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 sequence_file_input_format = requires (detail::sequence_file_input_format_exposer<t> & v,
74  std::ifstream & f,
75  sequence_file_input_options<dna5> & options,
76  std::vector<dna5> & seq,
77  std::string & id,
78  std::vector<phred42> & qual,
79  std::vector<qualified<dna5, phred42>> & seq_qual)
80 {
81  t::file_extensions;
82 
83  SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_sequence_record(f, options, seq, id, qual), std::same_as, void);
84  SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_sequence_record(f, options, seq_qual, id, seq_qual), std::same_as, void);
85  SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_sequence_record(f, options, std::ignore, std::ignore, std::ignore),
86  std::same_as, void);
87 };
89 
124 
125 } // namespace seqan3
126 
127 namespace seqan3::detail
128 {
129 
135 template <typename t>
136 constexpr bool is_type_list_of_sequence_file_input_formats_v = false;
137 
143 template <typename ...ts>
144 constexpr bool is_type_list_of_sequence_file_input_formats_v<type_list<ts...>> =
146 
152 template <typename t>
153 SEQAN3_CONCEPT type_list_of_sequence_file_input_formats = is_type_list_of_sequence_file_input_formats_v<t>;
154 } // namespace seqan3::detail
Provides seqan3::dna5, container aliases and string literals.
The generic concept for sequence file in formats.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides seqan3::phred42 quality scores.
#define SEQAN3_RETURN_TYPE_CONSTRAINT(expression, concept_name,...)
Same as writing {expression} -> concept_name<type1[, ...]> in a concept definition.
Definition: platform.hpp:57
Provides quality alphabet composites.
Provides seqan3::sequence_file_input_options.
Provides seqan3::type_list.