Represents the raw structure ensemble data for an RNA. More...

#include <rna_ensemble.hh>

Public Member Functions
	RnaEnsemble (const MultipleAlignment &ma, const PFoldParams &params, bool inLoopProbs, bool use_alifold=true)
	Construct from sequence or multiple alignment. More...

	RnaEnsemble (const RnaEnsemble &rna_ensemble)
	copy constructor More...

RnaEnsemble &	operator= (const RnaEnsemble &rna_ensemble)
	assignment operator More...

virtual	~RnaEnsemble ()
	Clean up. More...

bool	has_base_pair_probs () const
	Availability of pair probabilities. More...

bool	has_stacking_probs () const
	Availability of stacking probabilities. More...

bool	has_in_loop_probs () const
	Availability of "in loop" probabilities. More...

const MultipleAlignment &	multiple_alignment () const
	Get the sequence. More...

size_type	length () const
	get length of sequence More...

double	min_free_energy () const
	get minimum free energy More...

std::string	min_free_energy_structure () const
	get minimum free energy structure More...

double	arc_prob (size_type i, size_type j) const
	Get arc probability. More...

double	arc_2_prob (size_type i, size_type j) const
	Get joint probability of stacked arcs. More...

double	arc_stack_prob (size_type i, size_type j) const
	Get conditional propability that a base pair is stacked. More...

double	paired_upstream_prob (size_type i) const
	Probability that a position is paired upstream. More...

double	paired_downstream_prob (size_type i) const
	Probability that a position is paired downstream. More...

double	unpaired_prob (size_type i) const
	Unpaired probability. More...

double	unpaired_in_loop_prob (size_type k, size_type i, size_type j) const
	Unpaired probabilty of base in a specified loop. More...

double	unpaired_external_prob (size_type k) const
	Unpaired probabilty of base in external 'loop'. More...

double	arc_in_loop_prob (size_type ip, size_type jp, size_type i, size_type j) const
	Probabilty of base pair in a specified loop. More...

double	arc_external_prob (size_type i, size_type j) const
	Probability of base pair in the external 'loop'. More...

Detailed Description

Represents the raw structure ensemble data for an RNA.

Can partition fold RNAs, stores dynamic programming matrices of the McCaskill algorithm. Computes special "in loop" probabilities.

Interprets structure annotation of the multiple alignment as structure constraint string; if existant, the string has to be valid! Fixed structure annotation is ignored.

Todo:: support constraints for in loop probabilities

Todo:: split up RnaEnsemble into two classes; one with and one without in-loop probabilities (like RnaData and ExtRnaData)

Note: the class guarantees that sequences are normalized (uppercase, T->U) even when read in unnormalized form, e.g. from file or stream or received from other objects

Constructor & Destructor Documentation

LocARNA::RnaEnsemble::RnaEnsemble	(	const MultipleAlignment &	ma,
		const PFoldParams &	params,
		bool	inLoopProbs,
		bool	use_alifold = `true`
	)

Construct from sequence or multiple alignment.

Computes ensemble partition functions and probabilities using McCaskill's algorithm. Optionally computes additional matrices required for in-loop probabilities.

Parameters

ma	the RNA sequence or alignment as MultipleAlignment object
params	pfolding parameters
inLoopProbs	whether in loop probabilities should be made available
use_alifold	whether alifold should be used

Precondition: unless use_alifold, sequence row number has to be 1

LocARNA::RnaEnsemble::RnaEnsemble ( const RnaEnsemble & rna_ensemble )

copy constructor

Parameters

rna_ensemble object to be copied Copies implementation object (not only pointer)

LocARNA::RnaEnsemble::~RnaEnsemble ( )

virtual

Clean up.

In most cases does nothing. If McCaskill matrices are kept, they are freed.

Member Function Documentation

double LocARNA::RnaEnsemble::arc_2_prob	(	size_type	i,
		size_type	j
	)		const

Get joint probability of stacked arcs.

Parameters

i	left sequence position
j	right sequence position

Returns: probability of basepairs (i,j) and (i+1,j-1) occuring simultaneously

double LocARNA::RnaEnsemble::arc_external_prob	(	size_type	i,
		size_type	j
	)		const

Probability of base pair in the external 'loop'.

Parameters

i	left end of inner base pair
j	right end of inner base pair

Returns: probability that i and j form a basepair and the base pair is external

Note: This method is designed for use in ExpaRNA-P; For computing these unpaired probabilities we need access to the dynamic programming matrices of the McCaskill algorithm

Precondition: McCaskill matrices are computed and generated.

See also: compute_McCaskill_matrices(), RnaEnsemble(const MultipleAlignment &sequence_, bool keepMcC)

Note: if in loop probs are unavailable, return probability 1.0

double LocARNA::RnaEnsemble::arc_in_loop_prob	(	size_type	ip,
		size_type	jp,
		size_type	i,
		size_type	j
	)		const

Probabilty of base pair in a specified loop.

Parameters

ip	left end of inner base pair
jp	right end of inner base pair
i	left end of loop enclosing base pair
j	right end of loop enclosing base pair

Returns: probability that (ip,jp) is inner base pair in the loop closed by i and j

Computes the joint probability that there is a base pair (i,j) and a base pair (k,l) (i<k<l<j) that is inner base pair of the loop closed by (i,j).

Note: This method is designed for use in ExpaRNA-P; For computing these unpaired probabilities we need access to the dynamic programming matrices of the McCaskill algorithm

Precondition: McCaskill matrices are computed and generated.

See also: compute_McCaskill_matrices(), RnaEnsemble(const MultipleAlignment &sequence_, bool keepMcC)

Note: if in loop probs are unavailable, return probability 1.0

double LocARNA::RnaEnsemble::arc_prob	(	size_type	i,
		size_type	j
	)		const

Get arc probability.

Parameters

i	left sequence position
j	right sequence position

Returns: probability of basepair (i,j)

double LocARNA::RnaEnsemble::arc_stack_prob	(	size_type	i,
		size_type	j
	)		const

Get conditional propability that a base pair is stacked.

Parameters

i	left sequence position
j	right sequence position

Returns: probability of basepairs (i,j) stacked, i.e. the conditional probability Pr[(i,j)|(i+1,j-1)].

Precondition: base pair (i+1,j-1) has probability > 0

bool LocARNA::RnaEnsemble::has_base_pair_probs ( ) const

Availability of pair probabilities.

Returns: whether probabilities are available

bool LocARNA::RnaEnsemble::has_in_loop_probs ( ) const

Availability of "in loop" probabilities.

Returns: whether probabilities are available

bool LocARNA::RnaEnsemble::has_stacking_probs ( ) const

Availability of stacking probabilities.

Returns: whether probabilities are available

size_type LocARNA::RnaEnsemble::length ( ) const

get length of sequence

Returns: sequence length

double LocARNA::RnaEnsemble::min_free_energy ( ) const

get minimum free energy

Note: this returns the mfe only if the sequence was folded by the object, e.g. in compute_ensemble_probs(); otherwise returns infinity

Returns: mfe (if available)

std::string LocARNA::RnaEnsemble::min_free_energy_structure ( ) const

get minimum free energy structure

Note: this returns the mfe structure only if the sequence was folded by the object, e.g. in compute_ensemble_probs(); otherwise returns empty string

Returns: mfes structure (if available)

const MultipleAlignment & LocARNA::RnaEnsemble::multiple_alignment ( ) const

Get the sequence.

Returns: sequence of RNA

RnaEnsemble& LocARNA::RnaEnsemble::operator= ( const RnaEnsemble & rna_ensemble )

assignment operator

Parameters

rna_ensemble object to be assigned Assigns implementation object (not only pointer)

double LocARNA::RnaEnsemble::paired_downstream_prob ( size_type i ) const

Probability that a position is paired downstream.

Parameters

i	sequence position

Returns: probability that a position i is paired with a position j<i (downstream)

Note: O(sequence.length()) implementation

See also: prob_paired_upstream

double LocARNA::RnaEnsemble::paired_upstream_prob ( size_type i ) const

Probability that a position is paired upstream.

Parameters

i	sequence position

Returns: probability that a position i is paired with a position j>i (upstream)

Note: O(sequence.length()) implementation

See also: prob_paired_downstream

double LocARNA::RnaEnsemble::unpaired_external_prob ( size_type k ) const

Unpaired probabilty of base in external 'loop'.

Parameters

k	unpaired sequence position

Returns: probability that k is unpaired and external

Note: This method is designed for use in ExpaRNA-P; For computing these unpaired probabilities we need access to the dynamic programming matrices of the McCaskill algorithm

Precondition: McCaskill matrices are computed and generated.

See also: compute_McCaskill_matrices(), RnaEnsemble(const MultipleAlignment &sequence_, bool keepMcC)

Note: if in loop probs are unavailable, return probability 1.0

double LocARNA::RnaEnsemble::unpaired_in_loop_prob	(	size_type	k,
		size_type	i,
		size_type	j
	)		const

Unpaired probabilty of base in a specified loop.

Parameters

k	unpaired sequence position
i	left end of loop enclosing base pair
j	right end of loop enclosing base pair

Returns: probability that k is unpaired in the loop closed by i and j

Computes the joint probability that there is a base pair (i,j) and a base k (i<k<j) is unpaired such that there is no base pair i<i'<k<j'<j.

Note: This method is designed for use in ExpaRNA-P; For computing these unpaired probabilities we need access to the dynamic programming matrices of the McCaskill algorithm

Precondition: McCaskill matrices are computed and generated.

See also: compute_McCaskill_matrices(), RnaEnsemble(const MultipleAlignment &sequence_, bool keepMcC)

Note: if in loop probs are unavailable, return probability 1.0

double LocARNA::RnaEnsemble::unpaired_prob ( size_type i ) const

Unpaired probability.

Parameters

i	sequence position

Returns: probability that a position i is unpaired

Note: O(sequence.length()) implementation

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

src/LocARNA/rna_ensemble.hh
src/LocARNA/rna_ensemble.cc

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation