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 <string>
17#include <vector>
18
24
25namespace seqan3::detail
26{
27
40template <typename format_type>
41struct sequence_file_output_format_exposer : public format_type
42{
43public:
44
45 // Can't use `using format_type::write_sequence_record` as it produces a hard failure in the format concept check
46 // for types that do not model the format concept, i.e. don't offer the proper write_sequence_record interface.
48 template <typename ...ts>
49 void write_sequence_record(ts && ...args)
50 {
51 format_type::write_sequence_record(std::forward<ts>(args)...);
52 }
53};
54
55} // namespace seqan3::detail
56
57namespace seqan3
58{
59
71template <typename t>
72SEQAN3_CONCEPT sequence_file_output_format = requires (detail::sequence_file_output_format_exposer<t> & v,
73 std::ofstream & f,
74 sequence_file_output_options & options,
75 dna5_vector & seq,
78 std::vector<dna5q> & seq_qual)
79{
80 t::file_extensions;
81
82 SEQAN3_RETURN_TYPE_CONSTRAINT(v.write_sequence_record(f, options, seq, id, qual), std::same_as, void);
83 SEQAN3_RETURN_TYPE_CONSTRAINT(v.write_sequence_record(f, options, std::ignore, id, std::ignore),
84 std::same_as, void);
85 SEQAN3_RETURN_TYPE_CONSTRAINT(v.write_sequence_record(f, options, std::ignore, std::ignore, std::ignore),
86 std::same_as, void);
87 // the last is required to be compile time valid, but should always throw at run-time.
88};
90
125
126} // namespace seqan3
127
128namespace seqan3::detail
129{
130
136template <typename t>
137constexpr bool is_type_list_of_sequence_file_output_formats_v = false;
138
144template <typename ...ts>
145constexpr bool is_type_list_of_sequence_file_output_formats_v<type_list<ts...>> =
147
153template <typename t>
154SEQAN3_CONCEPT type_list_of_sequence_file_output_formats = is_type_list_of_sequence_file_output_formats_v<t>;
155} // namespace seqan3::detail
Provides aliases for qualified.
Provides seqan3::dna5, container aliases and string literals.
@ id
The identifier, usually a string.
@ seq
The "sequence", usually a range of nucleotides or amino acids.
@ qual
The qualities, usually in Phred score notation.
The generic concept for sequence file out formats.
The main SeqAn3 namespace.
Definition: cigar_operation_table.hpp:2
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 seqan3::sequence_file_output_options.
Provides seqan3::type_list.