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SeqAn3
3.0.1
The Modern C++ library for sequence analysis.
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Go to the documentation of this file.
19 #include <type_traits>
24 #pragma GCC diagnostic push
25 #pragma GCC diagnostic ignored "-Wdeprecated-declarations"
36 #include <seqan3/io/detail/record.hpp>
164 template <detail::fields_specialisation selected_field_
ids_ = fields<field::seq, field::
id, field::structure>,
165 detail::type_list_of_structure_file_output_formats val
id_formats_ = type_list<format_vienna>>
193 static_assert([] () constexpr
195 for (
field f : selected_field_ids::as_array)
196 if (!field_ids::contains(f))
200 "You selected a field that is not valid for structure files, please refer to the documentation "
201 "of structure_file_output::field_ids for the accepted values.");
203 static_assert([] () constexpr
208 }(),
"You may not select field::structured_seq and either of field::seq and field::structure "
209 "at the same time.");
227 using iterator = detail::out_file_iterator<structure_file_output>;
267 primary_stream{
new std::ofstream{filename, std::ios_base::out | std::ios::binary}, stream_deleter_default}
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>
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>
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 { requires detail::is_type_specialisation_of_v<remove_cvref_t<record_t>,
record>; }
395 write_record(detail::get_or_ignore<field::seq>(r),
396 detail::get_or_ignore<field::id>(r),
397 detail::get_or_ignore<field::bpp>(r),
398 detail::get_or_ignore<field::structure>(r),
399 detail::get_or_ignore<field::structured_seq>(r),
400 detail::get_or_ignore<field::energy>(r),
401 detail::get_or_ignore<field::react>(r),
402 detail::get_or_ignore<field::react_err>(r),
403 detail::get_or_ignore<field::comment>(r),
404 detail::get_or_ignore<field::offset>(r));
428 template <
typename tuple_t>
433 write_record(detail::get_or_ignore<selected_field_ids::index_of(
field::seq)>(t),
434 detail::get_or_ignore<selected_field_ids::index_of(
field::id)>(t),
435 detail::get_or_ignore<selected_field_ids::index_of(
field::bpp)>(t),
438 detail::get_or_ignore<selected_field_ids::index_of(
field::energy)>(t),
439 detail::get_or_ignore<selected_field_ids::index_of(
field::react)>(t),
441 detail::get_or_ignore<selected_field_ids::index_of(
field::comment)>(t),
442 detail::get_or_ignore<selected_field_ids::index_of(
field::offset)>(t));
468 template <
typename arg_t,
typename ...arg_types>
495 template <std::ranges::input_range rng_t>
499 for (
auto &&
record : range)
531 template <std::ranges::input_range rng_t>
540 template <std::ranges::input_range rng_t>
557 return *secondary_stream;
575 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
577 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
580 using format_type =
typename detail::variant_from_tags<
valid_formats,
581 detail::structure_file_output_format_exposer>::type;
587 template <
typename seq_type,
590 typename structure_type,
591 typename structured_seq_type,
592 typename energy_type,
594 typename comment_type,
595 typename offset_type>
596 void write_record(seq_type &&
seq,
603 react_type && react_error,
607 static_assert(detail::decays_to_ignore_v<structured_seq_type> ||
608 (detail::decays_to_ignore_v<seq_type> && detail::decays_to_ignore_v<structure_type>),
609 "You may not select field::structured_seq and either of field::seq and field::structure "
610 "at the same time.");
612 assert(!format.valueless_by_exception());
615 if constexpr (!detail::decays_to_ignore_v<structured_seq_type>)
617 f.write_structure_record(*secondary_stream,
631 f.write_structure_record(*secondary_stream,
655 template <output_stream stream_t,
658 detail::fields_specialisation selected_field_ids>
659 structure_file_output(stream_t &&, file_format
const &, selected_field_ids
const &)
660 -> structure_file_output<selected_field_ids,
661 type_list<file_format>>;
664 template <output_stream stream_t,
666 detail::fields_specialisation selected_field_ids>
667 structure_file_output(stream_t &, file_format
const &, selected_field_ids
const &)
668 -> structure_file_output<selected_field_ids,
669 type_list<file_format>>;
673 #pragma GCC diagnostic pop
void emplace_back(arg_t &&arg, arg_types &&... args)
Write a record to the file by passing individual fields.
Definition: output.hpp:469
Provides seqan3::views::zip.
The "sequence", usually a range of nucleotides or amino acids.
void push_back(record_t &&r) requires tuple_like< record_t > &&requires
Write a seqan3::record to the file.
Definition: output.hpp:391
friend structure_file_output operator|(rng_t &&range, structure_file_output &&f) requires tuple_like< reference_t< rng_t >>
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: output.hpp:541
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
Provides various utility functions required only for output.
valid_formats_ valid_formats
A seqan3::type_list with the possible formats.
Definition: output.hpp:176
Provides seqan3::tuple_like.
Sequence (SEQ) relative start position (0-based), unsigned value.
void const_iterator
The const iterator type is void, because files are not const-iterable.
Definition: output.hpp:229
char stream_char_type
Character type of the stream(s).
Definition: output.hpp:178
Base pair probability matrix of interactions, usually a matrix of float numbers.
void reference
The reference type (void).
Definition: output.hpp:219
void push_back(tuple_t &&t) requires tuple_like< tuple_t >
Write a record in form of a std::tuple to the file.
Definition: output.hpp:429
selected_field_ids_ selected_field_ids
A seqan3::fields list with the fields selected for the record.
Definition: output.hpp:174
Provides seqan3::views::convert.
The identifier, usually a string.
A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ...
Definition: output.hpp:166
const auto move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:68
Provides the seqan3::record template and the seqan3::field enum.
Fixed interactions, usually a string of structure alphabet characters.
This header includes C++17 filesystem support and imports it into namespace seqan3::filesystem (indep...
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.
constexpr bool contains
Whether a type occurs in a pack or not.
Definition: traits.hpp:193
A class template that holds a choice of seqan3::field.
Definition: record.hpp:165
Energy of a folded sequence, represented by one float number.
The concept std::same_as<T, U> is satisfied if and only if T and U denote the same type.
iterator begin() noexcept
Returns an iterator to current position in the file.
Definition: output.hpp:348
std::ranges::default_sentinel_t sentinel
The type returned by end().
Definition: output.hpp:231
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
Meta-header for the structure module. It includes all headers from alphabet/structure/.
Provides seqan3::structure_file_output_options.
void value_type
The value type (void).
Definition: output.hpp:217
structure_file_output()=delete
Default constructor is explicitly deleted, you need to give a stream or file name.
Comment field of arbitrary content, usually a string.
Provides exceptions used in the I/O module.
~structure_file_output()=default
Destructor is defaulted.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:36
Sequence and fixed interactions combined in one range.
Whether a type behaves like a tuple.
sentinel end() noexcept
Returns a sentinel for comparison with iterator.
Definition: output.hpp:367
void const_reference
The const reference type (void).
Definition: output.hpp:221
Adaptations of concepts from the Ranges TS.
friend structure_file_output & operator|(rng_t &&range, structure_file_output &f) requires tuple_like< reference_t< rng_t >>
Write a range of records (or tuples) to the file.
Definition: output.hpp:532
Reactivity values of the sequence characters given in a vector of float numbers.
field
An enumerator for the fields used in file formats.
Definition: record.hpp:64
The class template that file records are based on; behaves like an std::tuple.
Definition: record.hpp:225
The options type defines various option members that influence the behaviour of all or some formats.
Definition: output_options.hpp:23
Reactivity error values given in a vector corresponding to REACT.
structure_file_output & operator=(rng_t &&range) requires tuple_like< reference_t< rng_t >>
Write a range of records (or tuples) to the file.
Definition: output.hpp:496
Provides the seqan3::detail::out_file_iterator class template.
Provides traits for seqan3::type_list.
void size_type
The size type (void).
Definition: output.hpp:223
structure_file_output(std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition: output.hpp:265
detail::out_file_iterator< structure_file_output > iterator
The iterator type of this view (an output iterator).
Definition: output.hpp:227
Provides seqan3::views::get.
structure_file_output_options options
The options are public and its members can be set directly.
Definition: output.hpp:550