SeqAn3
The Modern C++ library for sequence analysis.
seqan3::structure_file_input_format Interface 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:

Related Functions

(Note that these are not member functions.)

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. More...
 
static inline std::vector< std::stringfile_extensions
 The format type is required to provide a vector of all supported file extensions.
 

Detailed Description

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".

Friends And Related Function Documentation

◆ read_structure_record()

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_typeInput stream, must satisfy seqan3::Istream with char.
seq_typeType of the seqan3::field::seq input; must satisfy std::ranges::output_range over a seqan3::alphabet.
id_typeType of the seqan3::field::id input; must satisfy std::ranges::output_range over a seqan3::alphabet.
bpp_typeType 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_typeType of the seqan3::field::structure input; must satisfy std::ranges::output_range over a seqan3::rna_structure_alphabet.
energy_typeType of the seqan3::field::energy input; must satisfy std::is_floating_point.
react_typeType of the seqan3::field::react and seqan3::field::react_err input; must satisfy std::is_floating_point.
comment_typeType of the seqan3::field::comment input; must satisfy std::ranges::output_range over a seqan3::alphabet.
offset_typeType of the seqan3::field::offset input; must satisfy std::numeric_limits::is_integer.
Parameters
[in,out]streamThe input stream to read from.
[in]optionsFile specific options passed to the format.
[out]seqThe buffer for seqan3::field::seq input, i.e. the "sequence".
[out]idThe buffer for seqan3::field::id input, e.g. the header line.
[out]bppThe buffer for seqan3::field::bpp input.
[out]structureThe buffer for seqan3::field::structure input.
[out]energyThe buffer for seqan3::field::energy input.
[out]reactThe buffer for seqan3::field::react input.
[out]react_errThe buffer for seqan3::field::react_err input.
[out]commentThe buffer for seqan3::field::comment input.
[out]offsetThe buffer for seqan3::field::offset input.

Additional requirements

Implemented in seqan3::format_vienna.


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