LocARNA::RnaEnsembleImpl Class Reference

Implementation of RnaEnsemble. More...

#include <rna_ensemble_impl.hh>

List of all members.

Public Member Functions
	RnaEnsembleImpl (const MultipleAlignment &sequence, const PFoldParams &pfparams, bool inLoopProbs, bool use_alifold)
	Construct from sequence or multiple alignment.
	~RnaEnsembleImpl ()
	Destructor.
int	ptype_of_admissible_basepair (size_type i, size_type j) const
	Pair type of an admissible basepair.
void	compute_ensemble_probs (const PFoldParams &params, bool inLoopProbs, bool use_alifold)
	(re)compute the pair probabilities
double	arc_2_prob_noali (size_type i, size_type j) const
	Get joint probability of stacked arcs.
double	arc_2_prob_ali (size_type i, size_type j) const
	Get joint probability of stacked arcs (alifold version)
double	unpaired_in_loop_prob_ali (size_type k, size_type i, size_type j) const
	Unpaired probabilty of base in a specified loop (alifold)
double	unpaired_in_loop_prob_noali (size_type k, size_type i, size_type j) const
	Unpaired probabilty of base in a specified loop (no alifold)
double	arc_in_loop_prob_ali (size_type ip, size_type jp, size_type i, size_type j) const
	Probabilty of base pair in a specified loop (alifold)
double	arc_in_loop_prob_noali (size_type ip, size_type jp, size_type i, size_type j) const
	Probabilty of base pair in a specified loop.
void	compute_Qm2 ()
	Computes the Qm2 matrix.
void	compute_Qm2_ali ()
	Computes the Qm2 matrix (alifold)
void	compute_McCaskill_matrices (const PFoldParams &params, bool inLoopProbs)
	Computes the McCaskill matrices and keeps them accessible.
void	compute_McCaskill_alifold_matrices (const PFoldParams &params, bool inLoopProbs)
	Computes the McCaskill matrices and keeps them accessible (alifold)
Public Attributes
MultipleAlignment	sequence_
	the sequence
bool	pair_probs_available_
	whether pair probabilities are availabe
bool	stacking_probs_available_
	whether stacking probabilities are available
bool	in_loop_probs_available_
	whether "in loop" probabilities are availabe
std::vector< FLT_OR_DBL >	qm2_
	matrix qm2_ (stored VRNA-style in a vector)
std::vector< FLT_OR_DBL >	expMLbase_
	table for precomputed multi loop terms
McC_matrices_base *	McCmat_
bool	used_alifold_
	whether alifold was used to compute the McCaskill matrices
double	min_free_energy_
	minimum free energy (if computed anyway)
std::string	min_free_energy_structure_

---

Detailed Description

Implementation of RnaEnsemble.

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Constructor & Destructor Documentation

LocARNA::RnaEnsembleImpl::RnaEnsembleImpl	(	const MultipleAlignment &	sequence,
		const PFoldParams &	pfparams,
		bool	inLoopProbs,
		bool	use_alifold = true
	)

Construct from sequence or multiple alignment.

Parameters:

sequence	sequence or multiple alignment
pfparams	partition folding parameters
inLoopProbs	whether to compute in loop probabilities
use_alifold	whether to use alifold (required unless sequence is a single sequence)

LocARNA::RnaEnsembleImpl::~RnaEnsembleImpl

(

)

Destructor.

Free McCaskill DP matrices

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Member Function Documentation

double LocARNA::RnaEnsembleImpl::arc_2_prob_ali	(	size_type	i,
		size_type	j
	)		const

Get joint probability of stacked arcs (alifold version)

Parameters:

i	left sequence position
j	right sequence position

Returns:

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

double LocARNA::RnaEnsembleImpl::arc_2_prob_noali	(	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::RnaEnsembleImpl::arc_in_loop_prob_ali	(	size_type	ip,
		size_type	jp,
		size_type	i,
		size_type	j
	)		const

Probabilty of base pair in a specified loop (alifold)

`alifold-specific code

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

See also:

prob_basepair_in_loop()

Note:

pre: loop probs available, alifold used

double LocARNA::RnaEnsembleImpl::arc_in_loop_prob_noali	(	size_type	ip,
		size_type	jp,
		size_type	i,
		size_type	j
	)		const

Probabilty of base pair in a specified loop.

`single sequence folding-specific code

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

See also:

prob_basepair_in_loop()

Note:

pre: loop probs available, alifold not used

void LocARNA::RnaEnsembleImpl::compute_ensemble_probs	(	const PFoldParams &	params,
		bool	inLoopProbs,
		bool	use_alifold
	)

(re)compute the pair probabilities

Parameters:

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

void LocARNA::RnaEnsembleImpl::compute_McCaskill_alifold_matrices	(	const PFoldParams &	params,
		bool	inLoopProbs
	)

Computes the McCaskill matrices and keeps them accessible (alifold)

Allocates and fills the McCaskill alifold matrices.

Parameters:

params	parameters for partition folding
inLoopProbs	whether to compute and keep information for in loop probablities

void LocARNA::RnaEnsembleImpl::compute_McCaskill_matrices	(	const PFoldParams &	params,
		bool	inLoopProbs
	)

Computes the McCaskill matrices and keeps them accessible.

Allocates and fills the McCaskill matrices.

Precondition:

sequence_ has exactly one row

Parameters:

params	parameters for partition folding
inLoopProbs	whether to compute information for in loop probablities

void LocARNA::RnaEnsembleImpl::compute_Qm2

(

)

Computes the Qm2 matrix.

The method creates and fills the Qm2 matrix needed for prob_unpaired_in_loop().

Precondition:

McCaskill matrices are computed and accessible.

void LocARNA::RnaEnsembleImpl::compute_Qm2_ali

(

)

Computes the Qm2 matrix (alifold)

The method creates and fills the Qm2 matrix needed for prob_unpaired_in_loop() if alifold is used.

Precondition:

McCaskill alifold matrices are computed and accessible.

int LocARNA::RnaEnsembleImpl::ptype_of_admissible_basepair	(	size_type	i,
		size_type	j
	)		const

Pair type of an admissible basepair.

Parameters:

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

Returns:

pair type unless the base pair is not admissible, i.e. it is not complementary or has probability 0.0. Then return 0.

double LocARNA::RnaEnsembleImpl::unpaired_in_loop_prob_ali	(	size_type	k,
		size_type	i,
		size_type	j
	)		const

Unpaired probabilty of base in a specified loop (alifold)

alifold-specific version of prob_unpaired_in_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

See also:

prob_unpaired_in_loop()

Note:

pre: loop probs available, alifold used

double LocARNA::RnaEnsembleImpl::unpaired_in_loop_prob_noali	(	size_type	k,
		size_type	i,
		size_type	j
	)		const

Unpaired probabilty of base in a specified loop (no alifold)

single sequence folding-specific version of prob_unpaired_in_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

See also:

prob_unpaired_in_loop()

Note:

pre: in loop probs are available, alifold not used

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Member Data Documentation

McC_matrices_base* LocARNA::RnaEnsembleImpl::McCmat_

DP matrix data structures of VRNA's McCaskill algorithm

std::string LocARNA::RnaEnsembleImpl::min_free_energy_structure_

minimum free energy structure (if computed)

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

• src/LocARNA/rna_ensemble_impl.hh
• src/LocARNA/rna_ensemble.cc