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 <set>
#include <string>
#include <utility>
#include <vector>
 
#include <seqan3/alphabet/nucleotide/rna5.hpp>
#include <seqan3/alphabet/structure/structured_rna.hpp>
#include <seqan3/alphabet/structure/wuss.hpp>
#include <seqan3/core/type_list/type_list.hpp>
#include <seqan3/io/structure_file/input_options.hpp>
 
namespace seqan3::detail
{
 
template <typename format_type>
struct structure_file_input_format_exposer : public format_type
{
public:
    // Can't use `using format_type::read_structure_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_structure_record interface.
    template <typename ...ts>
    void read_structure_record(ts && ...args)
    {
        format_type::read_structure_record(std::forward<ts>(args)...);
    }
};
 
} // namespace seqan3::detail
 
namespace seqan3
{
 
template <typename t>
SEQAN3_CONCEPT structure_file_input_format = requires(detail::structure_file_input_format_exposer<t> & v,
                                                      std::ifstream & f,
                                                      structure_file_input_options<rna5, false> & options,
                                                      rna5_vector & seq,
                                                      std::string & id,
                                                      std::vector<std::set<std::pair<double, size_t>>> & bpp,
                                                      std::vector<wuss51> & structure,
                                                      std::vector<structured_rna<rna5, wuss51>> & structured_seq,
                                                      double energy,
                                                      double react,
                                                      double react_err,
                                                      std::string & comment,
                                                      size_t offset)
{
    t::file_extensions;
 
    { v.read_structure_record(f, options, seq,            id,          bpp,         structure,
                              energy,         react,       react_err,   comment,        offset)      } -> void;
 
    { v.read_structure_record(f, options, seq,            id,          bpp,         std::ignore,
                              std::ignore,    std::ignore, std::ignore, std::ignore,    std::ignore) } -> void;
 
    { v.read_structure_record(f, options, structured_seq, id,          std::ignore, structured_seq,
                              energy,         std::ignore, std::ignore, std::ignore,    std::ignore) } -> void;
 
    { v.read_structure_record(f, options, std::ignore,    std::ignore, std::ignore, std::ignore,
                              std::ignore,    std::ignore, std::ignore, std::ignore,    std::ignore) } -> void;
    // the last is required to be compile time valid, but should always throw at run-time.
};
 
 
} // namespace seqan3
 
namespace seqan3::detail
{
 
template <typename t>
constexpr bool is_type_list_of_structure_file_input_formats_v = false;
 
template <typename ...ts>
constexpr bool is_type_list_of_structure_file_input_formats_v<type_list<ts...>>
                = (structure_file_input_format<ts> && ...);
 
template <typename t>
SEQAN3_CONCEPT type_list_of_structure_file_input_formats = is_type_list_of_structure_file_input_formats_v<t>;
} // namespace seqan3::detail