input_format_concept.hpp

Go to the documentation of this file.

// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <fstream>
#include <string>
#include <vector>
 
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/quality/qualified.hpp>
#include <seqan3/core/type_list/type_list.hpp>
#include <seqan3/io/sequence_file/input_options.hpp>
 
namespace seqan3::detail
{
 
template <typename format_type>
struct sequence_file_input_format_exposer : public format_type
{
public:
 
    // Can't use `using format_type::read_sequence_record` as it produces a hard failure in the format concept check
    // for types that do not model the format concept, i.e. don't offer the proper read_sequence_record interface.
    template <typename ...ts>
    void read_sequence_record(ts && ...args)
    {
        format_type::read_sequence_record(std::forward<ts>(args)...);
    }
};
 
} // namespace seqan3::detail
 
namespace seqan3
{
 
template <typename t>
SEQAN3_CONCEPT sequence_file_input_format = requires (detail::sequence_file_input_format_exposer<t> & v,
                                                      std::ifstream                                 & f,
                                                      sequence_file_input_options<dna5, false>      & options,
                                                      std::vector<dna5>                             & seq,
                                                      std::string                                   & id,
                                                      std::vector<phred42>                          & qual,
                                                      std::vector<qualified<dna5, phred42>>         & seq_qual)
{
    t::file_extensions;
 
    SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_sequence_record(f, options, seq, id, qual), std::same_as, void);
    SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_sequence_record(f, options, seq_qual, id, seq_qual), std::same_as, void);
    SEQAN3_RETURN_TYPE_CONSTRAINT(v.read_sequence_record(f, options, std::ignore, std::ignore, std::ignore),
                                  std::same_as, void);
};
 
 
} // namespace seqan3
 
namespace seqan3::detail
{
 
template <typename t>
constexpr bool is_type_list_of_sequence_file_input_formats_v = false;
 
template <typename ...ts>
constexpr bool is_type_list_of_sequence_file_input_formats_v<type_list<ts...>> =
    (sequence_file_input_format<ts> && ...);
 
template <typename t>
SEQAN3_CONCEPT type_list_of_sequence_file_input_formats = is_type_list_of_sequence_file_input_formats_v<t>;
} // namespace seqan3::detail