LocARNA::ExtRnaData Class Reference

represent sparsified data of RNA ensemble extended by in loop probabilities More...

#include <ext_rna_data.hh>

Inheritance diagram for LocARNA::ExtRnaData:

List of all members.

Public Member Functions
	ExtRnaData (const RnaEnsemble &rna_ensemble, double p_bpcut, double p_bpilcut, double p_uilcut, double max_bps_length_ratio, double max_uil_length_ratio, double max_bpil_length_ratio, const PFoldParams &pfoldparams)
	Construct from RnaEnsemble with cutoff probability.
	ExtRnaData (const std::string &filename, double p_bpcut, double p_bpilcut, double p_uilcut, double max_bps_length_ratio, double max_uil_length_ratio, double max_bpil_length_ratio, const PFoldParams &pfoldparams)
	Construct from input file.
	~ExtRnaData ()
	destructor
double	arc_in_loop_cutoff_prob () const
	Get base pair in loop cutoff probability.
double	arc_in_loop_prob (pos_type i, pos_type j, pos_type p, pos_type q) const
	Get base pair in loop probability.
double	arc_external_prob (pos_type i, pos_type j) const
	Get base pair in loop probability.
double	unpaired_in_loop_cutoff_prob () const
	Get unpaired base in loop cutoff probability.
double	unpaired_in_loop_prob (pos_type k, pos_type p, pos_type q) const
	Get base pair in loop probability.
double	unpaired_external_prob (pos_type k) const
	Get base pair in loop probability.
std::ostream &	write_size_info (std::ostream &out) const
	Write object size information.
std::ostream &	write_pp (std::ostream &out, double p_outbpcut=0, double p_outbpilcut=0, double p_outuilcut=0) const
Protected Member Functions
virtual std::istream &	read_pp (std::istream &in)
virtual void	init_from_fixed_structure (const RnaStructure &structure, const PFoldParams &pfoldparams)
	initialize from fixed structure
virtual void	init_from_rna_ensemble (const RnaEnsemble &rna_ensemble, const PFoldParams &pfoldparams)
	initialize from rna ensemble
virtual bool	inloopprobs_ok () const
	check in loop probabilities
Friends
class	ExtRnaDataImpl

---

Detailed Description

represent sparsified data of RNA ensemble extended by in loop probabilities

knows sequence, cutoff probability and base pair probabilities greater than the cutoff probability

Note:

This class knows the cutoff probabilities of its data. These cutoffs can be different from the cutoffs in classes like BasePairs which define the structure elements that are considered by algorithms.

put the extension of extended pp format as additional record after the regular pp-data, such that extended pp files can be read as non-extended ones

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Constructor & Destructor Documentation

LocARNA::ExtRnaData::ExtRnaData	(	const RnaEnsemble &	rna_ensemble,
		double	p_bpcut,
		double	p_bpilcut,
		double	p_uilcut,
		double	max_bps_length_ratio,
		double	max_uil_length_ratio,
		double	max_bpil_length_ratio,
		const PFoldParams &	pfoldparams
	)

Construct from RnaEnsemble with cutoff probability.

Parameters:

rna_ensemble	RNA ensemble data
p_bpcut	cutoff probability for base pairs
p_bpilcut	cutoff probability for base pairs in loops
p_uilcut	cutoff probability for unpaired bases in loops
pfoldparams	parameters for partition folding

Note:

requires that rnaensemble has in loop probabilities

LocARNA::ExtRnaData::ExtRnaData	(	const std::string &	filename,
		double	p_bpcut,
		double	p_bpilcut,
		double	p_uilcut,
		double	max_bps_length_ratio,
		double	max_uil_length_ratio,
		double	max_bpil_length_ratio,
		const PFoldParams &	pfoldparams
	)

Construct from input file.

Parameters:

filename	input file name
p_bpcut	cutoff probability for base pairs
p_bpilcut	cutoff probability for base pairs in loops
p_uilcut	cutoff probability for unpaired bases in loops
pfoldparams	parameters for partition folding

Note:

autodetect format of input; for fa or aln input formats, predict base pair probabilities

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Member Function Documentation

double LocARNA::ExtRnaData::arc_external_prob	(	pos_type	i,
		pos_type	j
	)		const

Get base pair in loop probability.

Parameters:

i	left sequence position
j	right sequence position

Returns:

probability of basepair (i,j) in external loop if above threshold; otherwise, 0

double LocARNA::ExtRnaData::arc_in_loop_cutoff_prob

(

)

const

Get base pair in loop cutoff probability.

Returns:

cutoff probability p_bpcut

double LocARNA::ExtRnaData::arc_in_loop_prob	(	pos_type	i,
		pos_type	j,
		pos_type	p,
		pos_type	q
	)		const

Get base pair in loop probability.

Parameters:

i	left sequence position of inner base pair
j	right sequence position of inner base pair
p	left sequence position of closing base pair
q	right sequence position of closing base pair

Returns:

joint probability of basepair (i,j) in loop of (p,q) if above threshold; otherwise, 0

void LocARNA::ExtRnaData::init_from_fixed_structure	(	const RnaStructure &	structure,
		const PFoldParams &	pfoldparams
	)		[protected, virtual]

initialize from fixed structure

Parameters:

structure	fixed structure
pfoldparams	folding parameters

Note:

overloaded to initialize with additional information (in loop probabilities)

Reimplemented from LocARNA::RnaData.

void LocARNA::ExtRnaData::init_from_rna_ensemble	(	const RnaEnsemble &	rna_ensemble,
		const PFoldParams &	pfoldparams
	)		[protected, virtual]

initialize from rna ensemble

Parameters:

rna_ensemble	rna ensemble
pfoldparams	folding parameters

Note:

overloaded to initialize with additional information (in loop probabilities)

Precondition:

bp cutoff prob is initialized

Reimplemented from LocARNA::RnaData.

bool LocARNA::ExtRnaData::inloopprobs_ok

(

)

const [protected, virtual]

check in loop probabilities

Returns:

true iff loop probabilities are available or not required

Note:

use to indicate the need for recomputation in read_autodetect(); always true in RnaData

Reimplemented from LocARNA::RnaData.

std::istream & LocARNA::ExtRnaData::read_pp

(

std::istream &

in

)

[protected, virtual]

Read data in pp format 2.0 with in-loop probabilities

Parameters:

in	input stream

See also:

RnaData::read_pp()

Reimplemented from LocARNA::RnaData.

double LocARNA::ExtRnaData::unpaired_external_prob

(

pos_type

k

)

const

Get base pair in loop probability.

Parameters:

k	sequence position (unpaired base)

Returns:

probability of base k unpaired in external loop if above threshold; otherwise, 0

double LocARNA::ExtRnaData::unpaired_in_loop_cutoff_prob

(

)

const

Get unpaired base in loop cutoff probability.

Returns:

cutoff probability p_bpcut

double LocARNA::ExtRnaData::unpaired_in_loop_prob	(	pos_type	k,
		pos_type	p,
		pos_type	q
	)		const

Get base pair in loop probability.

Parameters:

k	sequence position (unpaired base)
p	left sequence position of closing base pair
q	right sequence position of closing base pair

Returns:

joint probability of unpaired base k in loop of (p,q) if above threshold; otherwise, 0

std::ostream & LocARNA::ExtRnaData::write_pp	(	std::ostream &	out,
		double	p_outbpcut = 0,
		double	p_outbpilcut = 0,
		double	p_outuilcut = 0
	)		const

Write data in extended pp format

Parameters:

out	output stream
p_outbpcut	cutoff probability
p_outbpilcut	cutoff probability base pairs in loop
p_outuilcut	cutoff probability unpaired in loop

Returns:

stream

Writes only base pairs with probabilities greater than p_outbpcut; base pairs in loops, p_outbpilcut; unpaired bases in loops, p_outuilcut

std::ostream & LocARNA::ExtRnaData::write_size_info

(

std::ostream &

out

)

const

Write object size information.

Parameters:

out	output stream

Writes numbers of stored probabilities to stream

Reimplemented from LocARNA::RnaData.

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

• src/LocARNA/ext_rna_data.hh
• src/LocARNA/rna_data.cc