#include <rna_data_impl.hh>

Collaboration diagram for LocARNA::RnaDataImpl:

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Classes
class	keyvec

Public Types
typedef RnaData::arc_prob_matrix_t	arc_prob_matrix_t
	type for matrix of arc probabilities

Public Member Functions
	RnaDataImpl (RnaData *self, const RnaData &rna_dataA, const RnaData &rna_dataB, const Alignment::edges_t &alignment, double p_expA, double p_expB)
	Construct as consensus of two aligned RNAs. More...

	RnaDataImpl (RnaData *self, double p_bpcut)
	Almost empty constructor. More...

void	init_from_fixed_structure (const SequenceAnnotation &structure, bool stacking)
	initialize from fixed structure More...

void	init_from_rna_ensemble (const RnaEnsemble &rna_ensemble, const PFoldParams &pfoldparams)
	initialize from rna ensemble More...

std::istream &	read_pp_sequence (std::istream &in)
	read sequence section of pp-format More...

std::istream &	read_pp_arc_probabilities (std::istream &in)
	read section of base pair probabilities of pp-format More...

std::ostream &	write_pp_sequence (std::ostream &out) const
	write section of base pair probabilities of pp-format More...

std::ostream &	write_pp_arc_probabilities (std::ostream &out, double p_outbpcut, bool stacking) const
	write section of base pair probabilities of pp-format More...

void	init_as_consensus_dot_plot (const Alignment::edges_t &edges, const RnaData &rna_dataA, const RnaData &rna_dataB, double p_expA, double p_expB, bool stacking)
	Initialize as consensus of two aligned RNAs. More...

double	consensus_probability (double pA, double pB, size_t sizeA, size_t sizeB, double p_expA, double p_expB) const
	Consensus probability. More...

void	drop_worst_bps (size_t keep)
	Drop base pairs with lowest probability. More...

Public Attributes
RnaData *	self_

MultipleAlignment	sequence_
	the sequence

double	p_bpcut_
	cutoff probabilitiy for base pair

arc_prob_matrix_t	arc_probs_

arc_prob_matrix_t	arc_2_probs_

bool	has_stacking_
	whether stacking probabilities are available

Detailed Description

Implementation of RnaData.

Constructor & Destructor Documentation

LocARNA::RnaDataImpl::RnaDataImpl	(	RnaData *	self,
		const RnaData &	rna_dataA,
		const RnaData &	rna_dataB,
		const Alignment::edges_t &	alignment,
		double	p_expA,
		double	p_expB
	)

Construct as consensus of two aligned RNAs.

Parameters

self	pointer to corresponding RnaData object
rna_dataA	data of RNA A
rna_dataB	data of RNA B
alignment	pairwise alignment of A and B
p_expA	background probability A
p_expB	background probability B

LocARNA::RnaDataImpl::RnaDataImpl	(	RnaData *	self,
		double	p_bpcut
	)

Almost empty constructor.

Parameters

self	pointer to corresponding RnaData object
p_bpcut	cutoff probability

Member Function Documentation

double LocARNA::RnaDataImpl::consensus_probability	(	double	pA,
		double	pB,
		size_t	sizeA,
		size_t	sizeB,
		double	p_expA,
		double	p_expB
	)		const

Consensus probability.

Parameters

pA	probability A
pB	probability B
sizeA	number of rows in sequence A
sizeB	number of rows in sequence B
p_expA	background probability A
p_expB	background probability B

Precondition: p_bpcut_ is initialized

Essentially computes a weighted geometric mean; some care is taken, to avoid total extinction and to restrict the accumulation of (small) probabilities.

Returns: consensus probability

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

Drop base pairs with lowest probability.

Parameters

keep	the maximum number of base pairs to keep

void LocARNA::RnaDataImpl::init_as_consensus_dot_plot	(	const Alignment::edges_t &	edges,
		const RnaData &	rna_dataA,
		const RnaData &	rna_dataB,
		double	p_expA,
		double	p_expB,
		bool	stacking
	)

Initialize as consensus of two aligned RNAs.

Parameters

edges	alignment edges
rna_dataA	rna data A
rna_dataB	rna data B
p_expA	background probability A
p_expB	background probability B
stacking	if true, stacking consensus is computed

void LocARNA::RnaDataImpl::init_from_fixed_structure	(	const SequenceAnnotation &	structure,
		bool	stacking
	)

initialize from fixed structure

Parameters

structure	fixed structure
stacking	whether to initialize stacking terms

void LocARNA::RnaDataImpl::init_from_rna_ensemble	(	const RnaEnsemble &	rna_ensemble,
		const PFoldParams &	pfoldparams
	)

initialize from rna ensemble

Parameters

rna_ensemble	rna ensemble
pfoldparams	folding parameters. if stacking, initialize stacking terms; if noLP, drop lonely pairs

std::istream & LocARNA::RnaDataImpl::read_pp_arc_probabilities ( std::istream & in )

read section of base pair probabilities of pp-format

Parameters

in	input stream

Reads only base pairs with probabilities greater than p_bpcut_; reads stacking only if has_stacking_

std::istream & LocARNA::RnaDataImpl::read_pp_sequence ( std::istream & in )

read sequence section of pp-format

Parameters

in	input stream

Returns: stream

this section comprises sequence/multiple alignment (possibly including sequence anchor annotation)

std::ostream & LocARNA::RnaDataImpl::write_pp_arc_probabilities	(	std::ostream &	out,
		double	p_outbpcut,
		bool	stacking
	)		const

write section of base pair probabilities of pp-format

Write arc probabilities.

Parameters

out	ouput stream
p_outbpcut	cutoff probabilitiy
stacking	whether to write stacking probabilities; if stacking but !has_stacking_, no stacking terms are written but flag #STACKS is written to output

Returns: stream

Write only base pairs with probabilities greater than p_outbpcut

Writes arc and stacking probabilities to stream; filters by probability threshold p_outbpcut

std::ostream & LocARNA::RnaDataImpl::write_pp_sequence ( std::ostream & out ) const

write section of base pair probabilities of pp-format

Parameters

out	ouput stream

Returns: stream

Member Data Documentation

arc_prob_matrix_t LocARNA::RnaDataImpl::arc_2_probs_

sparse array for all probabilities that a pair (i,j) and its immediately inner pair (i+1,j-1) are formed simultaneously above threshold; analogous to arc_probs_

Note: arc_2_probs_ has entry (i,j) implies arc_probs_ has entry (i,j)

arc_prob_matrix_t LocARNA::RnaDataImpl::arc_probs_

sparse array for all arc probabilities above threshold; the array is used when reading in the probabilities and for merging probs during pp-output

RnaData* LocARNA::RnaDataImpl::self_

pointer to corresponding non-impl object

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

src/LocARNA/rna_data_impl.hh
src/LocARNA/rna_data.cc

Classes

Public Types

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation