sequence_file/input_format_concept.hpp

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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
 
#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)...);
    }
    void read_sequence_record(ts &&... args) {…}
};
struct sequence_file_input_format_exposer : public format_type {…};
 
} // 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
{};
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