156 requires std::is_floating_point_v<typename t::bpp_prob>;
173 requires std::is_same_v<typename t::structure_alphabet, dssp9>
180 typename t::template structured_seq_alphabet<typename t::seq_alphabet, typename t::structure_alphabet>,
181 typename t::seq_alphabet,
182 typename t::structure_alphabet>,
183 typename t::template structured_seq_alphabet<typename t::seq_alphabet, typename t::structure_alphabet>>;
190 requires std::is_floating_point_v<typename t::energy_type::value_type>;
193 requires std::is_floating_point_v<typename t::react_type>;
238 template <
typename _seq_alphabet>
247 template <
typename _
id_alphabet>
259 template <
typename _bpp_prob,
typename _bpp_partner>
263 template <
typename _bpp_item>
267 template <
typename _bpp_queue>
276 template <
typename _structure_alphabet>
282 template <
typename _seq_alphabet,
typename _structure_alphabet>
286 template <
typename _structured_seq_alphabet>
300 template <
typename _react_type>
309 template <
typename _comment_alphabet>
335 template <
typename _seq_alphabet,
typename _structure_alphabet>
394 for (
field f : selected_field_ids::as_array)
399 "You selected a field that is not valid for structure files, please refer to the documentation "
400 "of structure_file_input::field_ids for the accepted values.");
407 "You may not select field::structured_seq and either of field::seq and field::structure "
408 "at the same time.");
416 using seq_type =
typename traits_type::template seq_container<typename traits_type::seq_alphabet>;
418 using id_type =
typename traits_type::template id_container<typename traits_type::id_alphabet>;
420 using bpp_type =
typename traits_type::template bpp_container<
typename traits_type::template bpp_queue<
421 typename traits_type::template bpp_item<typename traits_type::bpp_prob, typename traits_type::bpp_partner>>>;
423 using structure_type =
typename traits_type::template structure_container<typename traits_type::structure_alphabet>;
426 typename traits_type::template structured_seq_alphabet<
typename traits_type::seq_alphabet,
427 typename traits_type::structure_alphabet>>;
431 using react_type =
typename traits_type::template react_container<typename traits_type::react_type>;
433 using comment_type =
typename traits_type::template comment_container<typename traits_type::comment_alphabet>;
514 ->open(filename, std::ios_base::in | std::ios::binary);
517 throw file_open_error{
"Could not open file " + filename.
string() +
" for reading."};
541 template <input_stream stream_t, structure_file_input_format file_format>
542 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
char>
544 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
547 format{detail::structure_file_input_format_exposer<file_format>{}}
549 static_assert(list_traits::contains<file_format, valid_formats>,
550 "You selected a format that is not in the valid_formats of this file.");
557 template <input_stream stream_t, structure_file_input_format file_format>
558 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
char>
560 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
563 format{detail::structure_file_input_format_exposer<file_format>{}}
565 static_assert(list_traits::contains<file_format, valid_formats>,
566 "You selected a format that is not in the valid_formats of this file.");
717 assert(!
format.valueless_by_exception());
725 "You may not select field::structured_seq and field::structure at the same time.");
727 "You may not select field::structured_seq and field::seq at the same time.");
768template <input_stream stream_type,
777template <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:46
Input iterator necessary for providing a range-like interface in input file.
Definition: in_file_iterator.hpp:41
The protein structure alphabet of the characters "HGIEBTSCX"..
Definition: dssp9.hpp:63
The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap..
Definition: rna15.hpp:51
The five letter RNA alphabet of A,C,G,U and the unknown character N..
Definition: rna5.hpp:49
A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet....
Definition: structured_aa.hpp:55
A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet....
Definition: structured_rna.hpp:56
Auxiliary concept that checks whether a type is a specialisation of seqan3::fields.
Definition: detail/record.hpp:35
Provides auxiliary data structures and functions for seqan3::record and seqan3::fields.
Provides the dssp format for protein structure.
field
An enumerator for the fields used in file formats.
Definition: record.hpp:63
void set_format(format_variant_type &format, std::filesystem::path const &file_name)
Sets the file format according to the file name extension.
Definition: io/detail/misc.hpp:68
auto make_secondary_istream(std::basic_istream< char_t > &primary_stream, std::filesystem::path &filename) -> std::unique_ptr< std::basic_istream< char_t >, std::function< void(std::basic_istream< char_t > *)> >
Depending on the magic bytes of the given stream, return a decompression stream or forward the primar...
Definition: misc_input.hpp:80
@ 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.
constexpr bool contains
Whether a type occurs in a type list or not.
Definition: type_list/traits.hpp:252
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:29
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:128
static constexpr bool contains(field f)
Whether a field is contained in the parameter pack.
Definition: record.hpp:149
void clear() noexcept(noexcept(std::apply(expander, std::declval< record & >())))
Clears containers that provide .clear() and (re-)initialises all other elements with = {}.
Definition: record.hpp:237
Type that contains multiple types.
Definition: type_list.hpp:29
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.