#include <ext_rna_data_impl.hh>

Collaboration diagram for LocARNA::ExtRnaDataImpl:

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Public Types
typedef SparseVector< double >	arc_prob_vector_t
	vector of arc probabilities

typedef RnaDataImpl::arc_prob_matrix_t	arc_prob_matrix_t
	matrix of arc probabilities

typedef SparseMatrix< arc_prob_vector_t >	arc_prob_vector_matrix_t
	matrix of arc probability vectors

typedef SparseMatrix< arc_prob_matrix_t >	arc_prob_matrix_matrix_t
	matrix of arc probability matrices

Public Member Functions
	ExtRnaDataImpl (ExtRnaData *self, double p_bpilcut, double p_uilcut)
	Construct. More...

void	init_from_fixed_structure (const SequenceAnnotation &structure)
	initialize in loop probabilities from fixed structure More...

void	init_from_ext_rna_ensemble (const RnaEnsemble &rna_ensemble)
	initialize from rna ensemble More...

std::istream &	read_pp_in_loop_probabilities (std::istream &in)
	read in loop probability section of pp-format More...

void	read_pp_in_loop_probabilities_kwline (const std::string &line)
	read keyword line in loop probability section of pp-format More...

void	read_pp_in_loop_probabilities_line (const std::string &line)
	read probability line in loop probability section of pp-format More...

std::ostream &	write_pp_in_loop_probabilities (std::ostream &out, double p_outbpcut, double p_outbpilcut, double p_outuilcut) const
	Write in loop probability section of pp 2.0. More...

std::ostream &	write_pp_in_loop_probability_line (std::ostream &out, size_t i, size_t j, double p_bpcut, double p_ucut) const
	Write a line of in loop probabilities for one base pair. More...

std::ostream &	write_pp_basepair_in_loop_probabilities (std::ostream &out, const arc_prob_matrix_t &probs, double p_cut) const
	Write in loop base pair probabilities for a specific base pair. More...

std::ostream &	write_pp_unpaired_in_loop_probabilities (std::ostream &out, const arc_prob_vector_t &probs, double p_cut) const
	Write in loop unpaired probabilities for a specific base pair. More...

void	drop_worst_bps (size_t keep)
	Drop in loop bases and base pairs without base pairs. More...

void	drop_worst_uil (size_t keep)
	Drop unpaired bases in loops with lowest probability. More...

void	drop_worst_bpil (size_t keep)
	Drop base pairs in loops with lowest probability. More...

void	drop_worst_bpil_precise (double ratio)
	Drop base pairs in loops with lowest probability based on loop length. More...

Public Attributes
ExtRnaData *	self_

double	p_bpilcut_
	cutoff probabilitiy for base pair in loop

double	p_uilcut_
	cutoff probabilitiy for unpaired base in loop

arc_prob_matrix_matrix_t	arc_in_loop_probs_
	in loop probabilities of base pairs

arc_prob_vector_matrix_t	unpaired_in_loop_probs_
	in loop probabilities of unpaired bases

bool	has_in_loop_probs_

Detailed Description

Implementation of ExtRnaData.

Constructor & Destructor Documentation

LocARNA::ExtRnaDataImpl::ExtRnaDataImpl	(	ExtRnaData *	self,
		double	p_bpilcut,
		double	p_uilcut
	)

Construct.

Parameters

self	self pointer
p_bpilcut	probability cutoff base pair in loop
p_uilcut	probability cutoff unpaired in loop

Note: autodetects file format, see corresponding RnaDataImpl constructor

Member Function Documentation

void LocARNA::ExtRnaDataImpl::drop_worst_bpil ( size_t keep )

Drop base pairs in loops with lowest probability.

Parameters

keep	the maximum total number of base pairs in loops to keep

void LocARNA::ExtRnaDataImpl::drop_worst_bpil_precise ( double ratio )

Drop base pairs in loops with lowest probability based on loop length.

Parameters

ratio limit on number of base pairs closed by a loop divided by loop length

void LocARNA::ExtRnaDataImpl::drop_worst_bps ( size_t keep )

Drop in loop bases and base pairs without base pairs.

Parameters

keep	the maximum number of base pairs to keep

void LocARNA::ExtRnaDataImpl::drop_worst_uil ( size_t keep )

Drop unpaired bases in loops with lowest probability.

Parameters

keep	the maximum total number of unpaired bases in loops to keep

void LocARNA::ExtRnaDataImpl::init_from_ext_rna_ensemble ( const RnaEnsemble & rna_ensemble )

initialize from rna ensemble

Parameters

rna_ensemble rna ensemble

Note: overloaded to initialize with additional information (in loop probabilities); rna_ensemble must have in loop probabilities

void LocARNA::ExtRnaDataImpl::init_from_fixed_structure ( const SequenceAnnotation & structure )

initialize in loop probabilities from fixed structure

Parameters

structure fixed structure

Note: this does not initialize base pair probabilities, which is done by the corresponding method of RnaDataImpl.

std::istream & LocARNA::ExtRnaDataImpl::read_pp_in_loop_probabilities ( std::istream & in )

read in loop probability section of pp-format

Parameters

in	input stream

Returns: stream

Reads only base pairs with probabilities greater than p_bpcut_; base pairs in loops, p_bpilcut_; unpaired bases in loops, p_uilcut_

void LocARNA::ExtRnaDataImpl::read_pp_in_loop_probabilities_kwline ( const std::string & line )

read keyword line in loop probability section of pp-format

Parameters

line	input line

void LocARNA::ExtRnaDataImpl::read_pp_in_loop_probabilities_line ( const std::string & line )

read probability line in loop probability section of pp-format

Parameters

line	input line

std::ostream & LocARNA::ExtRnaDataImpl::write_pp_basepair_in_loop_probabilities	(	std::ostream &	out,
		const arc_prob_matrix_t &	probs,
		double	p_cut
	)		const

Write in loop base pair probabilities for a specific base pair.

Parameters

out	output stream
probs	in loop probability matrix of a base pair
p_cut	base pair in loop probability cutoff

Returns: output stream

std::ostream & LocARNA::ExtRnaDataImpl::write_pp_in_loop_probabilities	(	std::ostream &	out,
		double	p_outbpcut,
		double	p_outbpilcut,
		double	p_outuilcut
	)		const

Write in loop probability section of pp 2.0.

Parameters

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

Returns: output stream

std::ostream & LocARNA::ExtRnaDataImpl::write_pp_in_loop_probability_line	(	std::ostream &	out,
		size_t	i,
		size_t	j,
		double	p_bpcut,
		double	p_ucut
	)		const

Write a line of in loop probabilities for one base pair.

Parameters

out	output stream
i	left end
j	right end
p_bpcut	base pair in loop probability cutoff
p_ucut	unpaired in loop probability cutoff

Returns: output stream

std::ostream & LocARNA::ExtRnaDataImpl::write_pp_unpaired_in_loop_probabilities	(	std::ostream &	out,
		const arc_prob_vector_t &	probs,
		double	p_cut
	)		const

Write in loop unpaired probabilities for a specific base pair.

Parameters

out	output stream
probs	in loop probability vector of a base pair
p_cut	unpaired in loop probability cutoff

Returns: output stream

Member Data Documentation

bool LocARNA::ExtRnaDataImpl::has_in_loop_probs_

used in initialization, to check whether in loop probs still have to be computed

ExtRnaData* LocARNA::ExtRnaDataImpl::self_

pointer to corresponding non-impl object

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

src/LocARNA/ext_rna_data_impl.hh
src/LocARNA/rna_data.cc

Public Types

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation