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core::io::rna::RDAT Class Reference

#include <RDAT.hh>

Inheritance diagram for core::io::rna::RDAT:
Inheritance graph
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Public Member Functions

 RDAT ()
 
 RDAT (std::string const &filename)
 
 RDAT (std::string const &name, std::string const &sequence, core::Size const offset, utility::vector1< Size > const &seqpos, std::string const &structure, utility::vector1< Annotation > const &annotations, utility::vector1< utility::vector1< Annotation > > const &data_annotations, utility::vector1< utility::vector1< core::Real > > const &reactivity, utility::vector1< utility::vector1< core::Real > > const &reactivity_error, utility::vector1< std::string > const &comments)
 
 ~RDAT () override
 
void output_rdat_to_file (std::string const &filename) const
 
void read_rdat_file (std::string const &filename)
 
void fill_header_information (pose::Pose &pose)
 
void fill_data_from_features (utility::vector1< char > const &seqchars, utility::vector1< core::Size > const &resnums, utility::vector1< std::string > const &feature_names, utility::vector1< utility::vector1< core::Real > > const &all_feature_vals)
 
void output_data (utility::io::ozstream &out) const
 
bool check_rdat () const
 
std::string const & version () const
 
std::string const & name () const
 
std::string const & sequence () const
 
std::string const & structure () const
 
utility::vector1< std::string >
const & 		sequences () const
 
utility::vector1< std::string >
const & 		structures () const
 
int const & offset () const
 
utility::vector1< int > const & seqpos () const
 
utility::vector1< Annotation >
const & 		annotations () const
 
utility::vector1
< utility::vector1< Annotation >
> const & 		data_annotations () const
 
utility::vector1
< utility::vector1< core::Real >
> const & 		reactivity () const
 
utility::vector1
< utility::vector1< core::Real >
> const & 		reactivity_error () const
 
utility::vector1< std::string >
const & 		comments () const
 
utility::vector1< core::Real >
const & 		xsel () const
 
utility::vector1
< utility::vector1< core::Real >
> const & 		xsel_refine () const
 
utility::vector1
< utility::vector1< core::Real >
> const & 		trace () const
 
void set_version (std::string const &setting)
 
void set_name (std::string const &setting)
 
void set_sequence (std::string const &setting)
 
void set_structure (std::string const &setting)
 
void set_sequences (utility::vector1< std::string > const &setting)
 
void set_structures (utility::vector1< std::string > const &setting)
 
void set_offset (int const &setting)
 
void set_seqpos (utility::vector1< int > const &setting)
 
void set_annotations (utility::vector1< Annotation > const &setting)
 
void set_data_annotations (utility::vector1< utility::vector1< Annotation > > const &setting)
 
void set_reactivity (utility::vector1< utility::vector1< core::Real > > const &setting)
 
void set_reactivity_error (utility::vector1< utility::vector1< core::Real > > const &setting)
 
void set_comments (utility::vector1< std::string > const &setting)
 
void set_xsel (utility::vector1< core::Real > const &setting)
 
void set_xsel_refine (utility::vector1< utility::vector1< core::Real > > const &setting)
 
void set_trace (utility::vector1< utility::vector1< core::Real > > const &setting)
 

Private Member Functions

void output_rdat_header (utility::io::ozstream &out) const
 
void fill_sequences_and_structures ()
 
void fill_sequences_if_empty ()
 
void fill_structures_if_empty ()
 
void fill_if_empty (std::string &data_string, utility::vector1< std::string > &data_strings, std::string const &tag) const
 
void save_data (std::string const &line, utility::vector1< utility::vector1< Real > > &var) const
 
void save_data (std::string const &line, utility::vector1< Real > &var) const
 
void save_data_with_idx (utility::vector1< std::string > &var, Size const &idx, std::string const &value) const
 
void save_data_with_idx (utility::vector1< utility::vector1< Annotation > > &var, Size const &idx, Annotation &value) const
 
Annotation get_annotation (std::string const &tag) const
 
utility::vector1< std::string > str2cell (std::string const &s) const
 
std::string remove_tag (std::string &line, std::string const &tag) const
 
void fill_data_annotations_if_empty ()
 
void fill_seqpos (std::string const &seqpos_info, std::string &sequence_seqpos)
 
bool check_sequence_seqpos (std::string const &sequence_seqpos) const
 
bool check_annotations (utility::vector1< Annotation > const &annotations) const
 
bool check_annotation (Annotation const &annotation) const
 

Private Attributes

std::string version_
 
std::string name_
 
std::string sequence_
 
std::string structure_
 
utility::vector1< std::string > sequences_
 
utility::vector1< std::string > structures_
 
int offset_
 
utility::vector1< int > seqpos_
 
utility::vector1< Annotation > annotations_
 
utility::vector1
< utility::vector1< Annotation > > 		data_annotations_
 
utility::vector1
< utility::vector1< core::Real > > 		reactivity_
 
utility::vector1
< utility::vector1< core::Real > > 		reactivity_error_
 
utility::vector1< std::string > comments_
 
utility::vector1< core::Real > xsel_
 
utility::vector1
< utility::vector1< core::Real > > 		xsel_refine_
 
utility::vector1
< utility::vector1< core::Real > > 		trace_
 

Constructor & Destructor Documentation

core::io::rna::RDAT::RDAT ( )
core::io::rna::RDAT::RDAT ( std::string const &  filename)

References read_rdat_file().

core::io::rna::RDAT::RDAT ( std::string const &  name,
std::string const &  sequence,
core::Size const  offset,
utility::vector1< Size > const &  seqpos,
std::string const &  structure,
utility::vector1< Annotation > const &  annotations,
utility::vector1< utility::vector1< Annotation > > const &  data_annotations,
utility::vector1< utility::vector1< core::Real > > const &  reactivity,
utility::vector1< utility::vector1< core::Real > > const &  reactivity_error,
utility::vector1< std::string > const &  comments 
)

References check_rdat(), and fill_sequences_and_structures().

core::io::rna::RDAT::~RDAT ( )
overridedefault

Member Function Documentation

utility::vector1< Annotation > const& core::io::rna::RDAT::annotations ( ) const
inline

References annotations_.

Referenced by core::io::rna::RNA_DataReader::get_reactivity_from_rdat().

bool core::io::rna::RDAT::check_annotation ( Annotation const &  annotation) const
private

References core::io::rna::ok_annotations.

Referenced by check_annotations().

bool core::io::rna::RDAT::check_annotations ( utility::vector1< Annotation > const &  annotations) const
private

References check_annotation(), and core::io::rna::TR().

Referenced by check_rdat().

bool core::io::rna::RDAT::check_rdat ( ) const

References annotations_, check_annotations(), data_annotations_, name_, offset_, reactivity_, seqpos_, sequence_, core::io::rna::TR(), xsel_, and xsel_refine_.

Referenced by RDAT(), and read_rdat_file().

bool core::io::rna::RDAT::check_sequence_seqpos ( std::string const &  sequence_seqpos) const
private

References offset_, seqpos_, sequence_, and core::io::rna::TR().

Referenced by read_rdat_file().

utility::vector1< std::string > const& core::io::rna::RDAT::comments ( ) const
inline

References comments_.

utility::vector1< utility::vector1< Annotation > > const& core::io::rna::RDAT::data_annotations ( ) const
inline

References data_annotations_.

Referenced by core::io::rna::RNA_DataReader::get_reactivity_from_rdat().

void core::io::rna::RDAT::fill_data_annotations_if_empty ( )
private

References data_annotations_, and reactivity_.

Referenced by read_rdat_file().

void core::io::rna::RDAT::fill_data_from_features ( utility::vector1< char > const &  seqchars,
utility::vector1< core::Size > const &  resnums,
utility::vector1< std::string > const &  feature_names,
utility::vector1< utility::vector1< core::Real > > const &  all_feature_vals 
)

References data_annotations_, offset_, reactivity_, seqpos_, and sequence_.

void core::io::rna::RDAT::fill_header_information ( pose::Pose &  pose)

References annotations_, comments_, core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), name_, offset_, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), sequence_, core::pose::Pose::size(), and structure_.

void core::io::rna::RDAT::fill_if_empty ( std::string &  data_string,
utility::vector1< std::string > &  data_strings,
std::string const &  tag 
) const
private

References core::io::rna::TR().

Referenced by read_rdat_file().

void core::io::rna::RDAT::fill_seqpos ( std::string const &  seqpos_info,
std::string &  sequence_seqpos 
)
private

References core::io::rna::numbers, seqpos_, and str2cell().

Referenced by read_rdat_file().

void core::io::rna::RDAT::fill_sequences_and_structures ( )
private

References fill_sequences_if_empty(), and fill_structures_if_empty().

Referenced by RDAT(), and read_rdat_file().

void core::io::rna::RDAT::fill_sequences_if_empty ( )
private

References data_annotations_, core::io::rna::numbers, offset_, core::chemical::rings::q, reactivity_, save_data_with_idx(), sequence_, sequences_, and core::io::rna::TR().

Referenced by fill_sequences_and_structures().

void core::io::rna::RDAT::fill_structures_if_empty ( )
private

References data_annotations_, reactivity_, save_data_with_idx(), structure_, and structures_.

Referenced by fill_sequences_and_structures().

Annotation core::io::rna::RDAT::get_annotation ( std::string const &  tag) const
private

Referenced by read_rdat_file().

std::string const& core::io::rna::RDAT::name ( ) const
inline

References name_.

int const& core::io::rna::RDAT::offset ( ) const
inline

References offset_.

void core::io::rna::RDAT::output_data ( utility::io::ozstream &  out) const

References data_annotations_, offset_, reactivity_, reactivity_error_, seqpos_, and sequence_.

Referenced by output_rdat_to_file().

void core::io::rna::RDAT::output_rdat_header ( utility::io::ozstream &  out) const
private

References annotations_, comments_, name_, offset_, sequence_, structure_, and version_.

Referenced by output_rdat_to_file().

void core::io::rna::RDAT::output_rdat_to_file ( std::string const &  filename) const

References core::conformation::membrane::out, output_data(), output_rdat_header(), and core::io::rna::TR().

utility::vector1< utility::vector1< core::Real > > const& core::io::rna::RDAT::reactivity ( ) const
inline

References reactivity_.

Referenced by core::io::rna::RNA_DataReader::get_reactivity_from_rdat().

utility::vector1< utility::vector1< core::Real > > const& core::io::rna::RDAT::reactivity_error ( ) const
inline

References reactivity_error_.

void core::io::rna::RDAT::read_rdat_file ( std::string const &  filename)

References annotations_, check_rdat(), check_sequence_seqpos(), comments_, data_annotations_, fill_data_annotations_if_empty(), fill_if_empty(), fill_seqpos(), fill_sequences_and_structures(), get_annotation(), name_, offset_, reactivity_, reactivity_error_, remove_tag(), save_data(), save_data_with_idx(), sequence_, sequences_, str2cell(), core::chemical::orbitals::strip_whitespace(), structure_, structures_, core::io::rna::TR(), trace_, version_, and xsel_.

Referenced by RDAT().

std::string core::io::rna::RDAT::remove_tag ( std::string &  line,
std::string const &  tag 
) const
private

Referenced by read_rdat_file().

void core::io::rna::RDAT::save_data ( std::string const &  line,
utility::vector1< utility::vector1< Real > > &  var 
) const
private

References str2cell().

Referenced by read_rdat_file().

void core::io::rna::RDAT::save_data ( std::string const &  line,
utility::vector1< Real > &  var 
) const
private

References str2cell().

void core::io::rna::RDAT::save_data_with_idx ( utility::vector1< std::string > &  var,
Size const &  idx,
std::string const &  value 
) const
private

Referenced by fill_sequences_if_empty(), fill_structures_if_empty(), and read_rdat_file().

void core::io::rna::RDAT::save_data_with_idx ( utility::vector1< utility::vector1< Annotation > > &  var,
Size const &  idx,
Annotation &  value 
) const
private
utility::vector1< int > const& core::io::rna::RDAT::seqpos ( ) const
inline

References seqpos_.

Referenced by core::io::rna::RNA_DataReader::get_reactivity_from_rdat().

std::string const& core::io::rna::RDAT::sequence ( ) const
inline

References sequence_.

utility::vector1< std::string > const& core::io::rna::RDAT::sequences ( ) const
inline

References sequences_.

void core::io::rna::RDAT::set_annotations ( utility::vector1< Annotation > const &  setting)
inline

References annotations_.

void core::io::rna::RDAT::set_comments ( utility::vector1< std::string > const &  setting)
inline

References comments_.

void core::io::rna::RDAT::set_data_annotations ( utility::vector1< utility::vector1< Annotation > > const &  setting)
inline

References data_annotations_.

void core::io::rna::RDAT::set_name ( std::string const &  setting)
inline

References name_.

void core::io::rna::RDAT::set_offset ( int const &  setting)
inline

References offset_.

void core::io::rna::RDAT::set_reactivity ( utility::vector1< utility::vector1< core::Real > > const &  setting)
inline

References reactivity_.

void core::io::rna::RDAT::set_reactivity_error ( utility::vector1< utility::vector1< core::Real > > const &  setting)
inline

References reactivity_error_.

void core::io::rna::RDAT::set_seqpos ( utility::vector1< int > const &  setting)
inline

References seqpos_.

void core::io::rna::RDAT::set_sequence ( std::string const &  setting)
inline

References sequence_.

void core::io::rna::RDAT::set_sequences ( utility::vector1< std::string > const &  setting)
inline

References sequences_.

void core::io::rna::RDAT::set_structure ( std::string const &  setting)
inline

References structure_.

void core::io::rna::RDAT::set_structures ( utility::vector1< std::string > const &  setting)
inline

References structures_.

void core::io::rna::RDAT::set_trace ( utility::vector1< utility::vector1< core::Real > > const &  setting)
inline

References trace_.

void core::io::rna::RDAT::set_version ( std::string const &  setting)
inline

References version_.

void core::io::rna::RDAT::set_xsel ( utility::vector1< core::Real > const &  setting)
inline

References xsel_.

void core::io::rna::RDAT::set_xsel_refine ( utility::vector1< utility::vector1< core::Real > > const &  setting)
inline

References xsel_refine_.

utility::vector1< std::string > core::io::rna::RDAT::str2cell ( std::string const &  s) const
private

Referenced by fill_seqpos(), read_rdat_file(), and save_data().

std::string const& core::io::rna::RDAT::structure ( ) const
inline

References structure_.

utility::vector1< std::string > const& core::io::rna::RDAT::structures ( ) const
inline

References structures_.

utility::vector1< utility::vector1< core::Real > > const& core::io::rna::RDAT::trace ( ) const
inline

References trace_.

std::string const& core::io::rna::RDAT::version ( ) const
inline

References version_.

utility::vector1< core::Real > const& core::io::rna::RDAT::xsel ( ) const
inline

References xsel_.

utility::vector1< utility::vector1< core::Real > > const& core::io::rna::RDAT::xsel_refine ( ) const
inline

References xsel_refine_.

Member Data Documentation

utility::vector1< Annotation > core::io::rna::RDAT::annotations_
private

Referenced by annotations(), check_rdat(), fill_header_information(), output_rdat_header(), read_rdat_file(), and set_annotations().

utility::vector1< std::string > core::io::rna::RDAT::comments_
private

Referenced by comments(), fill_header_information(), output_rdat_header(), read_rdat_file(), and set_comments().

utility::vector1< utility::vector1< Annotation > > core::io::rna::RDAT::data_annotations_
private

Referenced by check_rdat(), data_annotations(), fill_data_annotations_if_empty(), fill_data_from_features(), fill_sequences_if_empty(), fill_structures_if_empty(), output_data(), read_rdat_file(), and set_data_annotations().

std::string core::io::rna::RDAT::name_
private

Referenced by check_rdat(), fill_header_information(), name(), output_rdat_header(), read_rdat_file(), and set_name().

int core::io::rna::RDAT::offset_
private

Referenced by check_rdat(), check_sequence_seqpos(), fill_data_from_features(), fill_header_information(), fill_sequences_if_empty(), offset(), output_data(), output_rdat_header(), read_rdat_file(), and set_offset().

utility::vector1< utility::vector1< core::Real > > core::io::rna::RDAT::reactivity_
private

Referenced by check_rdat(), fill_data_annotations_if_empty(), fill_data_from_features(), fill_sequences_if_empty(), fill_structures_if_empty(), output_data(), reactivity(), read_rdat_file(), and set_reactivity().

utility::vector1< utility::vector1< core::Real > > core::io::rna::RDAT::reactivity_error_
private

Referenced by output_data(), reactivity_error(), read_rdat_file(), and set_reactivity_error().

utility::vector1< int > core::io::rna::RDAT::seqpos_
private

Referenced by check_rdat(), check_sequence_seqpos(), fill_data_from_features(), fill_seqpos(), output_data(), seqpos(), and set_seqpos().

std::string core::io::rna::RDAT::sequence_
private

Referenced by check_rdat(), check_sequence_seqpos(), fill_data_from_features(), fill_header_information(), fill_sequences_if_empty(), output_data(), output_rdat_header(), read_rdat_file(), sequence(), and set_sequence().

utility::vector1< std::string > core::io::rna::RDAT::sequences_
private

Referenced by fill_sequences_if_empty(), read_rdat_file(), sequences(), and set_sequences().

std::string core::io::rna::RDAT::structure_
private

Referenced by fill_header_information(), fill_structures_if_empty(), output_rdat_header(), read_rdat_file(), set_structure(), and structure().

utility::vector1< std::string > core::io::rna::RDAT::structures_
private

Referenced by fill_structures_if_empty(), read_rdat_file(), set_structures(), and structures().

utility::vector1< utility::vector1< core::Real > > core::io::rna::RDAT::trace_
private

Referenced by read_rdat_file(), set_trace(), and trace().

std::string core::io::rna::RDAT::version_
private

Referenced by output_rdat_header(), read_rdat_file(), set_version(), and version().

utility::vector1< core::Real > core::io::rna::RDAT::xsel_
private

Referenced by check_rdat(), read_rdat_file(), set_xsel(), and xsel().

utility::vector1< utility::vector1< core::Real > > core::io::rna::RDAT::xsel_refine_
private

Referenced by check_rdat(), set_xsel_refine(), and xsel_refine().

The documentation for this class was generated from the following files:
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