Structure File

Provides files and formats for handling structure data. More...

Collaboration diagram for Structure File:

Classes
class	seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >
	A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ... More...
struct	seqan3::structure_file_input_default_traits_aa
	A traits type that specifies input as amino acids. More...
struct	seqan3::structure_file_input_default_traits_rna
	The default traits for seqan3::structure_file_input. More...
interface	structure_file_input_format
	The generic concept for structure file in formats. More...
struct	seqan3::detail::structure_file_input_format_exposer< format_type >
	Internal class used to expose the actual format interface to read structure records from the file. More...
struct	seqan3::structure_file_input_options< seq_legal_alphabet, structured_seq_combined >
	The options type defines various option members that influence the behaviour of all or some formats. More...
interface	structure_file_input_traits
	The requirements a traits_type for seqan3::structure_file_input must meet. More...
class	seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
	A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ... More...
interface	structure_file_output_format
	The generic concept for structure file out formats. More...
struct	seqan3::detail::structure_file_output_format_exposer< format_type >
	Internal class used to expose the actual format interface to write structure records into the file. More...
struct	seqan3::structure_file_output_options
	The options type defines various option members that influence the behaviour of all or some formats. More...
class	seqan3::structure_record< field_types, field_ids >
	The record type of seqan3::structure_file_input. More...

Functions
template<typename structure_alph_type , typename bpp_type , std::ranges::range structure_type>
void	seqan3::detail::bpp_from_rna_structure (bpp_type &bpp, structure_type const &structure, double weight=1.)
	Transforms a structure annotation string into a base pair probability matrix. More...

Detailed Description

Provides files and formats for handling structure data.

Function Documentation

bpp_from_rna_structure()

template<typename structure_alph_type , typename bpp_type , std::ranges::range structure_type>

void seqan3::detail::bpp_from_rna_structure ( bpp_type &  bpp, structure_type const &  structure, double  weight = 1.  )

inline

Transforms a structure annotation string into a base pair probability matrix.

Exceptions

seqan3::parse_error

if unpaired brackets are found in the structure annotation.

Template Parameters

structure_alph_type	The type of the structure alphabet; must satisfy seqan3::rna_structure_alphabet.
bpp_type	The type of the target matrix.
structure_type	The range type of the structure annotation.

Parameters

[out]	bpp	The target matrix that receives the base pair probabilities.
[in]	structure	The source structure annotation.
[in]	weight	The weight to be assigned to all interactions present. As the source allows only one interaction partner, the weight defaults to 1.0.