21 #include <type_traits>
30 #include <seqan3/io/detail/record.hpp>
160 template <detail::fields_specialisation selected_field_
ids_ = fields<field::seq, field::
id, field::structure>,
161 detail::type_list_of_structure_file_output_formats val
id_formats_ = type_list<format_vienna>>
189 static_assert([] () constexpr
191 for (
field f : selected_field_ids::as_array)
192 if (!field_ids::contains(f))
196 "You selected a field that is not valid for structure files, please refer to the documentation "
197 "of structure_file_output::field_ids for the accepted values.");
199 static_assert([] () constexpr
204 }(),
"You may not select field::structured_seq and either of field::seq and field::structure "
205 "at the same time.");
223 using iterator = detail::out_file_iterator<structure_file_output>;
265 primary_stream->rdbuf()->pubsetbuf(stream_buffer.
data(), stream_buffer.
size());
267 std::ios_base::out | std::ios::binary);
269 if (!primary_stream->good())
270 throw file_open_error{
"Could not open file " + filename.
string() +
" for writing."};
273 secondary_stream = detail::make_secondary_ostream(*primary_stream, filename);
276 detail::set_format(format, filename);
295 template <output_stream stream_t, structure_file_output_format file_format>
297 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
char>
300 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
302 primary_stream{&stream, stream_deleter_noop},
303 secondary_stream{&stream, stream_deleter_noop},
304 format{detail::structure_file_output_format_exposer<file_format>{}}
306 static_assert(list_traits::contains<file_format, valid_formats>,
307 "You selected a format that is not in the valid_formats of this file.");
311 template <output_stream stream_t, structure_file_output_format file_format>
313 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
char>
316 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
318 primary_stream{
new stream_t{
std::move(stream)}, stream_deleter_default},
319 secondary_stream{&*primary_stream, stream_deleter_noop},
320 format{detail::structure_file_output_format_exposer<file_format>{}}
322 static_assert(list_traits::contains<file_format, valid_formats>,
323 "You selected a format that is not in the valid_formats of this file.");
390 template <
typename record_t>
393 requires detail::record_like<record_t>
396 write_record(detail::get_or_ignore<field::seq>(r),
397 detail::get_or_ignore<field::id>(r),
398 detail::get_or_ignore<field::bpp>(r),
399 detail::get_or_ignore<field::structure>(r),
400 detail::get_or_ignore<field::structured_seq>(r),
401 detail::get_or_ignore<field::energy>(r),
402 detail::get_or_ignore<field::react>(r),
403 detail::get_or_ignore<field::react_err>(r),
404 detail::get_or_ignore<field::comment>(r),
405 detail::get_or_ignore<field::offset>(r));
429 template <
typename tuple_t>
436 write_record(detail::get_or_ignore<selected_field_ids::index_of(
field::seq)>(t),
437 detail::get_or_ignore<selected_field_ids::index_of(
field::id)>(t),
438 detail::get_or_ignore<selected_field_ids::index_of(
field::bpp)>(t),
441 detail::get_or_ignore<selected_field_ids::index_of(
field::energy)>(t),
442 detail::get_or_ignore<selected_field_ids::index_of(
field::react)>(t),
444 detail::get_or_ignore<selected_field_ids::index_of(
field::comment)>(t),
445 detail::get_or_ignore<selected_field_ids::index_of(
field::offset)>(t));
471 template <
typename arg_t,
typename ...arg_types>
498 template <std::ranges::input_range rng_t>
504 for (
auto &&
record : range)
536 template <std::ranges::input_range rng_t>
547 template <std::ranges::input_range rng_t>
566 return *secondary_stream;
586 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
588 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
591 using format_type =
typename detail::variant_from_tags<
valid_formats,
592 detail::structure_file_output_format_exposer>::type;
598 template <
typename seq_type,
601 typename structure_type,
602 typename structured_seq_type,
603 typename energy_type,
605 typename comment_type,
606 typename offset_type>
607 void write_record(seq_type && seq,
610 structure_type && structure,
611 structured_seq_type && structured_seq,
612 energy_type && energy,
614 react_type && react_error,
615 comment_type && comment,
616 offset_type && offset)
618 static_assert(detail::decays_to_ignore_v<structured_seq_type> ||
619 (detail::decays_to_ignore_v<seq_type> && detail::decays_to_ignore_v<structure_type>),
620 "You may not select field::structured_seq and either of field::seq and field::structure "
621 "at the same time.");
623 assert(!
format.valueless_by_exception());
626 if constexpr (!detail::decays_to_ignore_v<structured_seq_type>)
628 f.write_structure_record(*secondary_stream,
630 structured_seq | views::elements<0>,
633 structured_seq | views::elements<1>,
642 f.write_structure_record(*secondary_stream,
667 template <output_stream stream_t,
669 detail::fields_specialisation selected_field_ids>
675 template <output_stream stream_t,
A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ...
Definition: output.hpp:163
std::default_sentinel_t sentinel
The type returned by end().
Definition: output.hpp:227
structure_file_output(stream_t &&, file_format const &, selected_field_ids const &) -> structure_file_output< selected_field_ids, type_list< file_format >>
Deduction of the selected fields, the file format and the stream type.
structure_file_output(stream_t &, file_format const &, selected_field_ids const &) -> structure_file_output< selected_field_ids, type_list< file_format >>
This is an overloaded member function, provided for convenience. It differs from the above function o...
void push_back(tuple_t &&t)
Write a record in form of a std::tuple to the file.
Definition: output.hpp:430
structure_file_output(stream_t &stream, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from an existing stream and with specified format.
Definition: output.hpp:299
void const_reference
The const reference type (void).
Definition: output.hpp:217
detail::out_file_iterator< structure_file_output > iterator
The iterator type of this view (an output iterator).
Definition: output.hpp:223
char stream_char_type
Character type of the stream(s).
Definition: output.hpp:174
void push_back(record_t &&r)
Write a seqan3::record to the file.
Definition: output.hpp:391
structure_file_output(stream_t &&stream, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: output.hpp:315
structure_file_output_options options
The options are public and its members can be set directly.
Definition: output.hpp:559
structure_file_output & operator=(structure_file_output const &)=delete
Copy assignment is explicitly deleted, because you can't have multiple access to the same file.
structure_file_output & operator=(rng_t &&range)
Write a range of records (or tuples) to the file.
Definition: output.hpp:499
selected_field_ids_ selected_field_ids
A seqan3::fields list with the fields selected for the record.
Definition: output.hpp:170
structure_file_output()=delete
Default constructor is explicitly deleted, you need to give a stream or file name.
structure_file_output(std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition: output.hpp:261
friend structure_file_output operator|(rng_t &&range, structure_file_output &&f)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: output.hpp:548
void emplace_back(arg_t &&arg, arg_types &&... args)
Write a record to the file by passing individual fields.
Definition: output.hpp:472
void size_type
The size type (void).
Definition: output.hpp:219
friend structure_file_output & operator|(rng_t &&range, structure_file_output &f)
Write a range of records (or tuples) to the file.
Definition: output.hpp:537
void reference
The reference type (void).
Definition: output.hpp:215
iterator begin() noexcept
Returns an iterator to current position in the file.
Definition: output.hpp:348
sentinel end() noexcept
Returns a sentinel for comparison with iterator.
Definition: output.hpp:367
structure_file_output & operator=(structure_file_output &&)=default
Move assignment is defaulted.
structure_file_output(structure_file_output &&)=default
Move construction is defaulted.
void value_type
The value type (void).
Definition: output.hpp:213
valid_formats_ valid_formats
A seqan3::type_list with the possible formats.
Definition: output.hpp:172
void const_iterator
The const iterator type is void, because files are not const-iterable.
Definition: output.hpp:225
~structure_file_output()=default
Destructor is defaulted.
structure_file_output(structure_file_output const &)=delete
Copy construction is explicitly deleted, because you can't have multiple access to the same file.
Provides seqan3::views::elements.
This header includes C++17 filesystem support and imports it into namespace std::filesystem (independ...
field
An enumerator for the fields used in file formats.
Definition: record.hpp:63
@ 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: traits.hpp:231
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:74
Whether a type behaves like a tuple.
Provides exceptions used in the I/O module.
Provides various utility functions required only for output.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides the seqan3::detail::out_file_iterator class template.
Adaptations of concepts from the Ranges TS.
Provides the seqan3::record template and the seqan3::field enum.
Provides seqan3::detail::record_like.
A class template that holds a choice of seqan3::field.
Definition: record.hpp:172
The class template that file records are based on; behaves like an std::tuple.
Definition: record.hpp:235
The options type defines various option members that influence the behaviour of all or some formats.
Definition: output_options.hpp:24
Type that contains multiple types.
Definition: type_list.hpp:29
Provides seqan3::structure_file_output_options.
Provides seqan3::tuple_like.
Provides traits for seqan3::type_list.
Provides seqan3::views::convert.
Provides seqan3::views::zip.