31#include <seqan3/io/detail/record.hpp>
153 requires std::is_floating_point_v<typename t::bpp_prob>;
170 requires std::is_same_v<typename t::structure_alphabet, dssp9>
177 typename t::template structured_seq_alphabet<typename t::seq_alphabet, typename t::structure_alphabet>,
178 typename t::seq_alphabet,
179 typename t::structure_alphabet>,
180 typename t::template structured_seq_alphabet<typename t::seq_alphabet, typename t::structure_alphabet>>;
187 requires std::is_floating_point_v<typename t::energy_type::value_type>;
190 requires std::is_floating_point_v<typename t::react_type>;
235 template <
typename _seq_alphabet>
244 template <
typename _
id_alphabet>
256 template <
typename _bpp_prob,
typename _bpp_partner>
260 template <
typename _bpp_item>
264 template <
typename _bpp_queue>
273 template <
typename _structure_alphabet>
279 template <
typename _seq_alphabet,
typename _structure_alphabet>
283 template <
typename _structured_seq_alphabet>
297 template <
typename _react_type>
306 template <
typename _comment_alphabet>
332 template <
typename _seq_alphabet,
typename _structure_alphabet>
392 for (
field f : selected_field_ids::as_array)
393 if (!field_ids::contains(f))
397 "You selected a field that is not valid for structure files, please refer to the documentation "
398 "of structure_file_input::field_ids for the accepted values.");
406 "You may not select field::structured_seq and either of field::seq and field::structure "
407 "at the same time.");
415 using seq_type =
typename traits_type::template seq_container<typename traits_type::seq_alphabet>;
417 using id_type =
typename traits_type::template id_container<typename traits_type::id_alphabet>;
419 using bpp_type =
typename traits_type::template bpp_container<
typename traits_type::template bpp_queue<
420 typename traits_type::template bpp_item<typename traits_type::bpp_prob, typename traits_type::bpp_partner>>>;
422 using structure_type =
typename traits_type::template structure_container<typename traits_type::structure_alphabet>;
425 typename traits_type::template structured_seq_alphabet<
typename traits_type::seq_alphabet,
426 typename traits_type::structure_alphabet>>;
430 using react_type =
typename traits_type::template react_container<typename traits_type::react_type>;
432 using comment_type =
typename traits_type::template comment_container<typename traits_type::comment_alphabet>;
468 using iterator = detail::in_file_iterator<structure_file_input>;
509 primary_stream{new
std::ifstream{}, stream_deleter_default}
511 primary_stream->rdbuf()->pubsetbuf(stream_buffer.
data(), stream_buffer.
size());
513 ->open(filename, std::ios_base::in | std::ios::binary);
515 if (!primary_stream->good())
519 secondary_stream = detail::make_secondary_istream(*primary_stream, filename);
522 detail::set_format(format, filename);
540 template <input_stream stream_t, structure_file_input_format file_format>
541 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
char>
543 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
545 primary_stream{&stream, stream_deleter_noop},
546 format{detail::structure_file_input_format_exposer<file_format>{}}
548 static_assert(list_traits::contains<file_format, valid_formats>,
549 "You selected a format that is not in the valid_formats of this file.");
552 secondary_stream = detail::make_secondary_istream(*primary_stream);
556 template <input_stream stream_t, structure_file_input_format file_format>
557 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
char>
559 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
561 primary_stream{new stream_t{
std::move(stream)}, stream_deleter_default},
562 format{detail::structure_file_input_format_exposer<file_format>{}}
564 static_assert(list_traits::contains<file_format, valid_formats>,
565 "You selected a format that is not in the valid_formats of this file.");
568 secondary_stream = detail::make_secondary_istream(*primary_stream);
593 if (!first_record_was_read)
596 first_record_was_read =
true;
651 selected_field_ids::contains(field::structured_seq)>
683 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
685 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
688 bool first_record_was_read{
false};
694 typename detail::variant_from_tags<valid_formats, detail::structure_file_input_format_exposer>::type;
700 void read_next_record()
703 record_buffer.
clear();
706 position_buffer = secondary_stream->tellg();
716 assert(!
format.valueless_by_exception());
721 if constexpr (selected_field_ids::contains(field::structured_seq))
723 static_assert(!selected_field_ids::contains(field::structure),
724 "You may not select field::structured_seq and field::structure at the same time.");
725 static_assert(!selected_field_ids::contains(field::seq),
726 "You may not select field::structured_seq and field::seq at the same time.");
727 f.read_structure_record(*secondary_stream,
729 detail::get_or_ignore<field::structured_seq>(record_buffer),
730 detail::get_or_ignore<field::id>(record_buffer),
731 detail::get_or_ignore<field::bpp>(record_buffer),
732 detail::get_or_ignore<field::structured_seq>(record_buffer),
733 detail::get_or_ignore<field::energy>(record_buffer),
734 detail::get_or_ignore<field::react>(record_buffer),
735 detail::get_or_ignore<field::react_err>(record_buffer),
736 detail::get_or_ignore<field::comment>(record_buffer),
737 detail::get_or_ignore<field::offset>(record_buffer));
741 f.read_structure_record(*secondary_stream,
743 detail::get_or_ignore<field::seq>(record_buffer),
744 detail::get_or_ignore<field::id>(record_buffer),
745 detail::get_or_ignore<field::bpp>(record_buffer),
746 detail::get_or_ignore<field::structure>(record_buffer),
747 detail::get_or_ignore<field::energy>(record_buffer),
748 detail::get_or_ignore<field::react>(record_buffer),
749 detail::get_or_ignore<field::react_err>(record_buffer),
750 detail::get_or_ignore<field::comment>(record_buffer),
751 detail::get_or_ignore<field::offset>(record_buffer));
767template <input_stream stream_type,
768 structure_file_input_format file_format,
769 detail::fields_specialisation selected_field_ids>
776template <input_stream stream_type,
Provides seqan3::aa27, container aliases and string literals.
Provides alphabet adaptations for standard char types.
The twenty-seven letter amino acid alphabet.
Definition aa27.hpp:43
The protein structure alphabet of the characters "HGIEBTSCX".
Definition dssp9.hpp:59
The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap.
Definition rna15.hpp:48
The five letter RNA alphabet of A,C,G,U and the unknown character N.
Definition rna5.hpp:46
A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet.
Definition structured_aa.hpp:52
A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet.
Definition structured_rna.hpp:53
Provides the dssp format for protein structure.
field
An enumerator for the fields used in file formats.
Definition record.hpp:60
@ energy
Energy of a folded sequence, represented by one float number.
@ comment
Comment field of arbitrary content, usually a string.
@ structure
Fixed interactions, usually a string of structure alphabet characters.
@ bpp
Base pair probability matrix of interactions, usually a matrix of float numbers.
@ react
Reactivity values of the sequence characters given in a vector of float numbers.
@ react_err
Reactivity error values given in a vector corresponding to seqan3::field::react.
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
@ structured_seq
Sequence and fixed interactions combined in one range.
@ id
The identifier, usually a string.
@ seq
The "sequence", usually a range of nucleotides or amino acids.
Provides the seqan3::detail::in_file_iterator class template.
Checks whether from can be explicitly converted to to.
A concept that indicates whether an alphabet represents RNA structure.
A more refined container concept than seqan3::container.
Refines seqan3::alphabet and adds assignability.
Provides exceptions used in the I/O module.
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
SeqAn specific customisations in the standard namespace.
Provides seqan3::rna15, container aliases and string literals.
Provides seqan3::rna5, container aliases and string literals.
A class template that holds a choice of seqan3::field.
Definition record.hpp:125
Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem.
Definition io/exception.hpp:36
void clear() noexcept(noexcept(std::apply(expander, std::declval< record & >().as_base())))
Clears containers that provide .clear() and (re-)initialises all other elements with = {}.
Definition record.hpp:242
Type that contains multiple types.
Definition type_list.hpp:26
Provides seqan3::structure_record.
Provides the composite of aminoacid with structure alphabets.
Provides traits for seqan3::type_list.
Adaptations of concepts from the standard library.