input_format_concept.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2019, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2019, 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/gap/gapped.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/quality/aliases.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/core/type_list.hpp>
#include <seqan3/io/alignment_file/header.hpp>
#include <seqan3/io/alignment_file/input_options.hpp>
#include <seqan3/io/alignment_file/sam_tag_dictionary.hpp>

namespace seqan3::detail
{

template <typename t>
class alignment_file_input_format
{};

} // namespace seqan3::detail

namespace seqan3
{

template <typename t>
SEQAN3_CONCEPT AlignmentFileInputFormat =
    requires (detail::alignment_file_input_format<t>                              & v,
              std::ifstream                                                       & stream,
              alignment_file_input_options<dna5>                                  & options,
              std::vector<dna5_vector>                                            & ref_sequences,
              alignment_file_header<>                                             & header,
              dna5_vector                                                         & seq,
              std::vector<phred42>                                                & qual,
              std::string                                                         & id,
              int32_t                                                             & offset,
              dna5_vector                                                         & ref_seq,
              std::optional<int32_t>                                              & ref_id,
              std::optional<int32_t>                                              & ref_offset,
              std::pair<std::vector<gapped<dna4>>, std::vector<gapped<dna4>>>     & align,
              uint16_t                                                            & flag,
              uint8_t                                                             & mapq,
              std::tuple<std::optional<int32_t>, std::optional<int32_t>, int32_t> & mate,
              sam_tag_dictionary                                                  & tag_dict,
              double                                                              & e_value,
              double                                                              & bit_score)
{
    t::file_extensions;
    // std::Same<decltype(t::file_extensions), std::vector<std::string>>;

    { v.read(stream,
             options,
             ref_sequences,
             header,
             seq,
             qual,
             id,
             offset,
             ref_seq,
             ref_id,
             ref_offset,
             align,
             flag,
             mapq,
             mate,
             tag_dict,
             e_value,
             bit_score)};

    { v.read(stream,
             options,
             std::ignore,
             header,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore,
             std::ignore)};
};


} // namespace seqan3

namespace seqan3::detail
{

template <typename t>
constexpr bool is_type_list_of_alignment_file_input_formats_v = false;

template <typename ... ts>
constexpr bool is_type_list_of_alignment_file_input_formats_v<type_list<ts...>> =
    (AlignmentFileInputFormat<ts> && ...);

template <typename t>
SEQAN3_CONCEPT TypeListOfAlignmentFileInputFormats = is_type_list_of_alignment_file_input_formats_v<t>;

} // namespace seqan3::detail