input.hpp

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// -----------------------------------------------------------------------------------------------------
// 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 <cassert>
#include <fstream>
#include <limits>
#include <optional>
#include <string>
#include <type_traits>
#include <utility>
#include <variant>
#include <vector>
 
// remove the following after range-v3 is updated to 1.0
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
 
#include <seqan3/alphabet/adaptation/char.hpp>
#include <seqan3/alphabet/aminoacid/all.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
#include <seqan3/alphabet/nucleotide/rna5.hpp>
#include <seqan3/alphabet/structure/all.hpp>
#include <seqan3/core/type_list/traits.hpp>
#include <seqan3/io/stream/concept.hpp>
#include <seqan3/io/exception.hpp>
#include <seqan3/std/filesystem>
#include <seqan3/io/record.hpp>
#include <seqan3/io/detail/in_file_iterator.hpp>
#include <seqan3/io/detail/misc_input.hpp>
#include <seqan3/io/detail/record.hpp>
#include <seqan3/io/structure_file/input_format_concept.hpp>
#include <seqan3/io/structure_file/input_options.hpp>
#include <seqan3/io/structure_file/format_vienna.hpp>
#include <seqan3/range/container/concatenated_sequences.hpp>
 
namespace seqan3
{
// ----------------------------------------------------------------------------
// structure_file_input_traits
// ----------------------------------------------------------------------------
 
template <typename t>
SEQAN3_CONCEPT structure_file_input_traits = requires(t v)
{
    // TODO(joergi-w) The expensive concept checks are currently omitted. Check again when compiler has improved.
    // sequence
    requires writable_alphabet<typename t::seq_alphabet>;
    requires writable_alphabet<typename t::seq_legal_alphabet>;
    requires explicitly_convertible_to<typename t::seq_legal_alphabet, typename t::seq_alphabet>;
    requires sequence_container<typename t::template seq_container<typename t::seq_alphabet>>;
 
    // id
    requires writable_alphabet<typename t::id_alphabet>;
    requires sequence_container<typename t::template id_container<typename t::id_alphabet>>;
 
    // bpp
    requires std::is_floating_point_v<typename t::bpp_prob>;
    requires std::numeric_limits<typename t::bpp_partner>::is_integer;
 
//    requires container // TODO check Associative container Concept when implemented
//        <typename t::template bpp_queue
//            <typename t::template bpp_item
//                <typename t::bpp_prob, typename t::bpp_partner>>>
//        && requires(typename t::template bpp_queue // TODO maybe implement also a version that allows emplace_back
//            <typename t::template bpp_item
//                <typename t::bpp_prob, typename t::bpp_partner>> value) { value.emplace(1.0, 1); };
//    requires sequence_container
//        <typename t::template bpp_container
//            <typename t::template bpp_queue
//                 <typename t::template bpp_item
//                      <typename t::bpp_prob, typename t::bpp_partner>>>>;
 
    // structure
    requires std::is_same_v<typename t::structure_alphabet, dssp9> // TODO(joergi-w) add aa_structure_concept
          || rna_structure_alphabet<typename t::structure_alphabet>;
    requires sequence_container<typename t::template structure_container<typename t::structure_alphabet>>;
 
    // structured sequence: tuple composites of seq and structure
    requires std::is_base_of_v<alphabet_tuple_base
        <typename t::template structured_seq_alphabet
            <typename t::seq_alphabet, typename t::structure_alphabet>,
             typename t::seq_alphabet, typename t::structure_alphabet>,
        typename t::template structured_seq_alphabet<typename t::seq_alphabet, typename t::structure_alphabet>>;
//    requires sequence_container
//        <typename t::template structured_seq_container
//            <typename t::template structured_seq_alphabet
//                <typename t::seq_alphabet, typename t::structure_alphabet>>>;
 
    // energy: std::optional of floating point number
    requires std::is_floating_point_v<typename t::energy_type::value_type>;
 
    // reactivity [error]
    requires std::is_floating_point_v<typename t::react_type>;
    requires sequence_container<typename t::template react_container<typename t::react_type>>;
 
    // comment
    requires writable_alphabet<typename t::comment_alphabet>;
    requires sequence_container<typename t::template comment_container<typename t::comment_alphabet>>;
 
    // offset
    requires std::numeric_limits<typename t::offset_type>::is_integer;
};
 
// ----------------------------------------------------------------------------
// structure_file_input_default_traits
// ----------------------------------------------------------------------------
 
struct structure_file_input_default_traits_rna
{
    // sequence
 
    using seq_alphabet                       = rna5;
 
    using seq_legal_alphabet                 = rna15;
 
    template <typename _seq_alphabet>
    using seq_container                      = std::vector<_seq_alphabet>;
 
    // id
 
    using id_alphabet                        = char;
 
    template <typename _id_alphabet>
    using id_container                       = std::basic_string<_id_alphabet>;
 
    // base pair probability structure
 
    using bpp_prob                           = double;
 
    using bpp_partner                        = size_t;
 
    template <typename _bpp_prob, typename _bpp_partner>
    using bpp_item                           = std::pair<_bpp_prob, _bpp_partner>;
 
    template <typename _bpp_item>
    using bpp_queue                          = std::set<_bpp_item>;
 
    template <typename _bpp_queue>
    using bpp_container                      = std::vector<_bpp_queue>;
 
    // fixed structure
 
    using structure_alphabet                 = wuss51;
 
    template <typename _structure_alphabet>
    using structure_container                = std::vector<_structure_alphabet>;
 
    // combined sequence and structure
 
    template <typename _seq_alphabet, typename _structure_alphabet>
    using structured_seq_alphabet            = structured_rna<_seq_alphabet, _structure_alphabet>;
 
    template <typename _structured_seq_alphabet>
    using structured_seq_container           = std::vector<_structured_seq_alphabet>;
 
    // energy
 
    using energy_type                        = std::optional<double>;
 
    // reactivity [error]
 
    using react_type                         = double;
 
    template <typename _react_type>
    using react_container                    = std::vector<_react_type>;
 
    // comment
 
    using comment_alphabet                   = char;
 
    template <typename _comment_alphabet>
    using comment_container                  = std::basic_string<_comment_alphabet>;
 
    // offset
 
    using offset_type                        = size_t;
};
 
struct structure_file_input_default_traits_aa : structure_file_input_default_traits_rna
{
    using seq_alphabet             = aa27;
    using seq_legal_alphabet       = aa27;
    using structure_alphabet       = dssp9;
    template <typename _seq_alphabet, typename _structure_alphabet>
    using structured_seq_alphabet  = structured_aa<_seq_alphabet, _structure_alphabet>;
};
 
// ----------------------------------------------------------------------------
// structure_file_input
// ----------------------------------------------------------------------------
 
template <structure_file_input_traits traits_type_ = structure_file_input_default_traits_rna,
          detail::fields_specialisation selected_field_ids_ = fields<field::seq, field::id, field::structure>,
          detail::type_list_of_structure_file_input_formats valid_formats_ = type_list<format_vienna>>
class structure_file_input
{
public:
    using traits_type        = traits_type_;
    using selected_field_ids = selected_field_ids_;
    using valid_formats      = valid_formats_;
    using stream_char_type   = char;
 
    using field_ids = fields<field::seq,
                             field::id,
                             field::bpp,
                             field::structure,
                             field::structured_seq,
                             field::energy,
                             field::react,
                             field::react_err,
                             field::comment,
                             field::offset>;
 
    static_assert([]() constexpr
                  {
                      for (field f : selected_field_ids::as_array)
                          if (!field_ids::contains(f))
                              return false;
                      return true;
                  }(),
                  "You selected a field that is not valid for structure files, please refer to the documentation "
                  "of structure_file_input::field_ids for the accepted values.");
 
    static_assert([]() constexpr
                  {
                      return !(selected_field_ids::contains(field::structured_seq) &&
                               (selected_field_ids::contains(field::seq) ||
                               (selected_field_ids::contains(field::structure))));
                  }(), "You may not select field::structured_seq and either of field::seq and field::structure "
                       "at the same time.");
 
    using seq_type            = typename traits_type::template seq_container<typename traits_type::seq_alphabet>;
    using id_type             = typename traits_type::template id_container<typename traits_type::id_alphabet>;
    using bpp_type            = typename traits_type::template bpp_container
        <typename traits_type::template bpp_queue
            <typename traits_type::template bpp_item
                <typename traits_type::bpp_prob, typename traits_type::bpp_partner>>>;
    using structure_type      = typename traits_type::template structure_container
        <typename traits_type::structure_alphabet>;
    using structured_seq_type = typename traits_type::template structured_seq_container
        <typename traits_type::template structured_seq_alphabet
            <typename traits_type::seq_alphabet, typename traits_type::structure_alphabet>>;
    using energy_type         = typename traits_type::energy_type;
    using react_type          = typename traits_type::template react_container<typename traits_type::react_type>;
    using comment_type        = typename traits_type::template comment_container
        <typename traits_type::comment_alphabet>;
    using offset_type         = typename traits_type::offset_type;
 
    using field_types    = type_list<seq_type, id_type, bpp_type, structure_type, structured_seq_type, energy_type,
                                     react_type, react_type, comment_type, offset_type>;
 
    using record_type    = record<detail::select_types_with_ids_t<field_types, field_ids, selected_field_ids>,
                                  selected_field_ids>;
 
    using value_type      = record_type;
    using reference       = record_type &;
    using const_reference = void;
    using size_type       = size_t;
    using difference_type = std::make_signed_t<size_t>;
    using iterator        = detail::in_file_iterator<structure_file_input>;
    using const_iterator  = void;
    using sentinel        = std::ranges::default_sentinel_t;
 
    structure_file_input()                                         = delete;
    structure_file_input(structure_file_input const &)             = delete;
    structure_file_input & operator=(structure_file_input const &) = delete;
    structure_file_input(structure_file_input &&)                  = default;
    structure_file_input & operator=(structure_file_input &&)      = default;
    ~structure_file_input()                                        = default;
 
    structure_file_input(std::filesystem::path filename,
                         selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :
        primary_stream{new std::ifstream{filename, std::ios_base::in | std::ios::binary}, stream_deleter_default}
    {
        if (!primary_stream->good())
            throw file_open_error{"Could not open file " + filename.string() + " for reading."};
 
        // possibly add intermediate decompression stream
        secondary_stream = detail::make_secondary_istream(*primary_stream, filename);
 
        // initialise format handler
        detail::set_format(format, filename);
    }
 
    template <input_stream stream_t, structure_file_input_format file_format>
        requires std::same_as<typename std::remove_reference_t<stream_t>::char_type, char>
    structure_file_input(stream_t & stream,
                         file_format const & SEQAN3_DOXYGEN_ONLY(format_tag),
                         selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :
        primary_stream{&stream, stream_deleter_noop},
        format{detail::structure_file_input_format_exposer<file_format>{}}
    {
        static_assert(list_traits::contains<file_format, valid_formats>,
                      "You selected a format that is not in the valid_formats of this file.");
 
        // possibly add intermediate decompression stream
        secondary_stream = detail::make_secondary_istream(*primary_stream);
    }
 
    template <input_stream stream_t, structure_file_input_format file_format>
        requires std::same_as<typename std::remove_reference_t<stream_t>::char_type, char>
    structure_file_input(stream_t && stream,
                         file_format const & SEQAN3_DOXYGEN_ONLY(format_tag),
                         selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :
        primary_stream{new stream_t{std::move(stream)}, stream_deleter_default},
        format{detail::structure_file_input_format_exposer<file_format>{}}
    {
        static_assert(list_traits::contains<file_format, valid_formats>,
                      "You selected a format that is not in the valid_formats of this file.");
 
        // possibly add intermediate compression stream
        secondary_stream = detail::make_secondary_istream(*primary_stream);
    }
 
    iterator begin()
    {
        // buffer first record
        if (!first_record_was_read)
        {
            read_next_record();
            first_record_was_read = true;
        }
 
        return {*this};
    }
 
    sentinel end() noexcept
    {
        return {};
    }
 
    reference front() noexcept
    {
        return *begin();
    }
 
    structure_file_input_options<typename traits_type::seq_legal_alphabet,
                                 selected_field_ids::contains(field::structured_seq)> options;
 
protected:
 
    record_type record_buffer;
 
    using stream_ptr_t = std::unique_ptr<std::basic_istream<stream_char_type>,
                                         std::function<void(std::basic_istream<stream_char_type>*)>>;
    static void stream_deleter_noop(std::basic_istream<stream_char_type> *) {}
    static void stream_deleter_default(std::basic_istream<stream_char_type> * ptr) { delete ptr; }
 
    stream_ptr_t primary_stream{nullptr, stream_deleter_noop};
    stream_ptr_t secondary_stream{nullptr, stream_deleter_noop};
 
    bool first_record_was_read{false};
    bool at_end{false};
 
    using format_type = typename detail::variant_from_tags<valid_formats,
                                                           detail::structure_file_input_format_exposer>::type;
    format_type format;
 
    void read_next_record()
    {
        // clear the record
        record_buffer.clear();
 
        // at end if we could not read further
        if ((std::istreambuf_iterator<stream_char_type>{*secondary_stream} ==
             std::istreambuf_iterator<stream_char_type>{}))
        {
            at_end = true;
            return;
        }
 
        assert(!format.valueless_by_exception());
        std::visit([&] (auto & f)
        {
            // read new record
            if constexpr (selected_field_ids::contains(field::structured_seq))
            {
                static_assert(!selected_field_ids::contains(field::structure),
                              "You may not select field::structured_seq and field::structure at the same time.");
                static_assert(!selected_field_ids::contains(field::seq),
                              "You may not select field::structured_seq and field::seq at the same time.");
                f.read_structure_record(*secondary_stream,
                                        options,
                                        detail::get_or_ignore<field::structured_seq>(record_buffer), // seq
                                        detail::get_or_ignore<field::id>(record_buffer),
                                        detail::get_or_ignore<field::bpp>(record_buffer),
                                        detail::get_or_ignore<field::structured_seq>(record_buffer), // structure
                                        detail::get_or_ignore<field::energy>(record_buffer),
                                        detail::get_or_ignore<field::react>(record_buffer),
                                        detail::get_or_ignore<field::react_err>(record_buffer),
                                        detail::get_or_ignore<field::comment>(record_buffer),
                                        detail::get_or_ignore<field::offset>(record_buffer));
            }
            else
            {
                f.read_structure_record(*secondary_stream,
                                        options,
                                        detail::get_or_ignore<field::seq>(record_buffer),
                                        detail::get_or_ignore<field::id>(record_buffer),
                                        detail::get_or_ignore<field::bpp>(record_buffer),
                                        detail::get_or_ignore<field::structure>(record_buffer),
                                        detail::get_or_ignore<field::energy>(record_buffer),
                                        detail::get_or_ignore<field::react>(record_buffer),
                                        detail::get_or_ignore<field::react_err>(record_buffer),
                                        detail::get_or_ignore<field::comment>(record_buffer),
                                        detail::get_or_ignore<field::offset>(record_buffer));
            }
        }, format);
    }
 
    friend iterator;
};
 
template <input_stream stream_type,
          structure_file_input_format file_format,
          detail::fields_specialisation selected_field_ids>
structure_file_input(stream_type && stream, file_format const &, selected_field_ids const &)
    -> structure_file_input<typename structure_file_input<>::traits_type,       // actually use the default
                            selected_field_ids,
                            type_list<file_format>>;
 
template <input_stream stream_type,
          structure_file_input_format file_format,
          detail::fields_specialisation selected_field_ids>
structure_file_input(stream_type & stream, file_format const &, selected_field_ids const &)
    -> structure_file_input<typename structure_file_input<>::traits_type,       // actually use the default
                            selected_field_ids,
                            type_list<file_format>>;
 
} // namespace seqan3
 
#pragma GCC diagnostic pop