seqan3::structure_file_input_format< t > Interface Template Reference

The generic concept for structure file in formats. More...

#include <seqan3/io/structure_file/input_format_concept.hpp>

Inheritance diagram for seqan3::structure_file_input_format< t >:

Related Symbols
(Note that these are not member symbols.)
Requirements for seqan3::structure_file_input_format
You can expect these members on all types that implement seqan3::structure_file_input_format.
void	read_structure_record (stream_type &stream, structure_file_input_options< seq_legal_alph_type, structured_seq_combined > const &options, seq_type &seq, id_type &id, bpp_type &bpp, structure_type &structure, energy_type &energy, react_type &react, react_type &react_err, comment_type &comment, offset_type &offset)
	Read from the specified stream and back-insert into the given field buffers.
static inline std::vector< std::string >	file_extensions
	The format type is required to provide a vector of all supported file extensions.

Detailed Description

template<typename t>
interface seqan3::structure_file_input_format< t >

The generic concept for structure file in formats.

The details of this concept are only relevant to developers who wish to implement their own format. The requirements for this concept are given as related functions and type traits. Types that satisfy this concept are shown as "implementing this interface".

Remarks

For a complete overview, take a look at Structure File

Friends And Related Symbol Documentation

read_structure_record()

template<typename t >

void read_structure_record ( stream_type &  stream, structure_file_input_options< seq_legal_alph_type, structured_seq_combined > const &  options, seq_type &  seq, id_type &  id, bpp_type &  bpp, structure_type &  structure, energy_type &  energy, react_type &  react, react_type &  react_err, comment_type &  comment, offset_type &  offset  )

related

Read from the specified stream and back-insert into the given field buffers.

Template Parameters

stream_type	Input stream, must satisfy seqan3::input_stream_over with char.
seq_type	Type of the seqan3::field::seq input; must satisfy std::ranges::output_range over a seqan3::alphabet.
id_type	Type of the seqan3::field::id input; must satisfy std::ranges::output_range over a seqan3::alphabet.
bpp_type	Type of the seqan3::field::bpp input; must satisfy std::ranges::output_range over a set of pair of types satisfying std::is_floating_point and std::numeric_limits::is_integer, respectively.
structure_type	Type of the seqan3::field::structure input; must satisfy std::ranges::output_range over a seqan3::rna_structure_alphabet.
energy_type	Type of the seqan3::field::energy input; must satisfy std::is_floating_point.
react_type	Type of the seqan3::field::react and seqan3::field::react_err input; must satisfy std::is_floating_point.
comment_type	Type of the seqan3::field::comment input; must satisfy std::ranges::output_range over a seqan3::alphabet.
offset_type	Type of the seqan3::field::offset input; must satisfy std::numeric_limits::is_integer.

Parameters

[in,out]	stream	The input stream to read from.
[in]	options	File specific options passed to the format.
[out]	seq	The buffer for seqan3::field::seq input, i.e. the "sequence".
[out]	id	The buffer for seqan3::field::id input, e.g. the header line.
[out]	bpp	The buffer for seqan3::field::bpp input.
[out]	structure	The buffer for seqan3::field::structure input.
[out]	energy	The buffer for seqan3::field::energy input.
[out]	react	The buffer for seqan3::field::react input.
[out]	react_err	The buffer for seqan3::field::react_err input.
[out]	comment	The buffer for seqan3::field::comment input.
[out]	offset	The buffer for seqan3::field::offset input.

Additional requirements

• The function must also accept std::ignore as parameter for any of the fields. [This is enforced by the concept checker!]
• In this case the data read for that field shall be discarded by the format.
• Instead of passing the fields seqan3::field::seq and seqan3::field::structure, you may also pass seqan3::field::structured_seq to both parameters. If you do, the std::ranges::range_value_t of the argument must be a specialisation of seqan3::structured_rna and the second template parameter to seqan3::structure_file_input_options must be set to true.

Implemented in seqan3::format_vienna.

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The documentation for this interface was generated from the following file:

• structure_file/input_format_concept.hpp