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
26namespace seqan3::detail
27{
28
39template <typename format_type>
40struct sequence_file_input_format_exposer : public format_type
41{
42public:
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
56namespace seqan3
57{
58
72template <typename t>
73SEQAN3_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,
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
127namespace seqan3::detail
128{
129
135template <typename t>
136constexpr bool is_type_list_of_sequence_file_input_formats_v = false;
137
143template <typename ...ts>
144constexpr bool is_type_list_of_sequence_file_input_formats_v<type_list<ts...>> =
146
152template <typename t>
153SEQAN3_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.
@ 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 in 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 quality alphabet composites.
Provides seqan3::sequence_file_input_options.
Provides seqan3::type_list.