SeqAn3 3.1.0
The Modern C++ library for sequence analysis.
output_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 <vector>
19
20#include <seqan3/alphabet/nucleotide/rna5.hpp>
21#include <seqan3/alphabet/structure/wuss.hpp>
22#include <seqan3/alphabet/structure/structured_rna.hpp>
23#include <seqan3/io/structure_file/output_options.hpp>
24#include <seqan3/utility/type_list/type_list.hpp>
25
26namespace seqan3::detail
27{
28
39template <typename format_type>
40struct structure_file_output_format_exposer : public format_type
41{
42public:
43 // Can't use `using format_type::write_structure_record` as it produces a hard failure in the format concept check
44 // for types that do not model the format concept, i.e. don't offer the proper write_structure_record interface.
46 template <typename ...ts>
47 void write_structure_record(ts && ...args)
48 {
49 format_type::write_structure_record(std::forward<ts>(args)...);
50 }
51};
52
53} // namespace seqan3::detail
54
55namespace seqan3
56{
57
71template <typename t>
72SEQAN3_CONCEPT structure_file_output_format = requires(detail::structure_file_output_format_exposer<t> & v,
73 std::ofstream & f,
74 structure_file_output_options & options,
75 rna5_vector & seq,
76 std::string & id,
77 std::vector<std::set<std::pair<double, size_t>>> & bpp,
78 std::vector<wuss51> & structure,
79 std::vector<structured_rna<rna5, wuss51>> & structured_seq,
80 double energy,
81 double react,
82 double react_err,
83 std::string & comment,
84 size_t offset)
85{
86 t::file_extensions;
87
88 SEQAN3_RETURN_TYPE_CONSTRAINT(v.write_structure_record(f,
89 options,
90 seq,
91 id,
92 bpp,
93 structure,
94 energy,
95 react,
96 react_err,
97 comment,
98 offset),
99 std::same_as, void);
100 SEQAN3_RETURN_TYPE_CONSTRAINT(v.write_structure_record(f,
101 options,
102 seq,
103 id,
104 bpp,
105 std::ignore,
106 std::ignore,
107 std::ignore,
108 std::ignore,
109 std::ignore,
110 std::ignore),
111 std::same_as, void);
112 SEQAN3_RETURN_TYPE_CONSTRAINT(v.write_structure_record(f,
113 options,
114 structured_seq,
115 id,
116 std::ignore,
117 structured_seq,
118 energy,
119 std::ignore,
120 std::ignore,
121 std::ignore,
122 std::ignore),
123 std::same_as, void);
124 SEQAN3_RETURN_TYPE_CONSTRAINT(v.write_structure_record(f,
125 options,
126 std::ignore,
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::same_as, void);
136 // the last is required to be compile time valid, but should always throw at run-time.
137};
139
199
200} // namespace seqan3
201
202namespace seqan3::detail
203{
204
210template <typename t>
211constexpr bool is_type_list_of_structure_file_output_formats_v = false;
212
218template <typename ...ts>
219constexpr bool is_type_list_of_structure_file_output_formats_v<type_list<ts...>>
220 = (structure_file_output_format<ts> && ...);
221
227template <typename t>
228SEQAN3_CONCEPT type_list_of_structure_file_output_formats = is_type_list_of_structure_file_output_formats_v<t>;
229} // namespace seqan3::detail
seqan3::field::energy
@ energy
Energy of a folded sequence, represented by one float number.
seqan3::field::comment
@ comment
Comment field of arbitrary content, usually a string.
seqan3::field::structure
@ structure
Fixed interactions, usually a string of structure alphabet characters.
seqan3::field::bpp
@ bpp
Base pair probability matrix of interactions, usually a matrix of float numbers.
seqan3::field::react
@ react
Reactivity values of the sequence characters given in a vector of float numbers.
seqan3::field::react_err
@ react_err
Reactivity error values given in a vector corresponding to seqan3::field::react.
seqan3::field::offset
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
seqan3::field::structured_seq
@ structured_seq
Sequence and fixed interactions combined in one range.
seqan3::field::id
@ id
The identifier, usually a string.
seqan3::field::seq
@ seq
The "sequence", usually a range of nucleotides or amino acids.
structure_file_output_format
The generic concept for structure file out formats.
seqan3
The main SeqAn3 namespace.
Definition: cigar_operation_table.hpp:2
SEQAN3_RETURN_TYPE_CONSTRAINT
#define SEQAN3_RETURN_TYPE_CONSTRAINT(expression, concept_name,...)
Same as writing {expression} -> concept_name<type1[, ...]> in a concept definition.
Definition: platform.hpp:57
rna5.hpp
Provides seqan3::rna5, container aliases and string literals.
output_options.hpp
Provides seqan3::structure_file_output_options.
structured_rna.hpp
Provides the composite of nucleotide with structure alphabets.
type_list.hpp
Provides seqan3::type_list.
wuss.hpp
Provides the WUSS format for RNA structure.