sequence_file/input_format_concept.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2023, 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/io/sequence_file/input_options.hpp>
#include <seqan3/utility/type_list/type_list.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>
concept sequence_file_input_format =
    requires (detail::sequence_file_input_format_exposer<t> & v,
              std::ifstream & f,
              sequence_file_input_options<dna5> & options,
              std::streampos & position_buffer,
              std::vector<dna5> & seq,
              std::string & id,
              std::vector<phred42> & qual,
              std::vector<qualified<dna5, phred42>> & seq_qual) {
        t::file_extensions;
 
        {
            v.read_sequence_record(f, options, position_buffer, seq, id, qual)
            } -> std::same_as<void>;
        {
            v.read_sequence_record(f, options, position_buffer, seq_qual, id, seq_qual)
            } -> std::same_as<void>;
        {
            v.read_sequence_record(f, options, position_buffer, std::ignore, std::ignore, std::ignore)
            } -> std::same_as<void>;
    };
 
// Workaround for https://github.com/doxygen/doxygen/issues/9379
#if SEQAN3_DOXYGEN_ONLY(1) 0
template <typename t>
class sequence_file_input_format
{};
#endif
 
 
} // 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>
concept type_list_of_sequence_file_input_formats = is_type_list_of_sequence_file_input_formats_v<t>;
} // namespace seqan3::detail