LocARNA::RnaEnsembleImpl Class Reference

Implementation of RnaEnsemble. More...

#include <rna_ensemble_impl.hh>

Collaboration diagram for LocARNA::RnaEnsembleImpl:

Public Member Functions
	RnaEnsembleImpl (const MultipleAlignment &sequence, const PFoldParams &pfparams, bool inLoopProbs, bool use_alifold)
	Construct from sequence or multiple alignment. More...
	~RnaEnsembleImpl ()
	Destructor. More...
int	ptype_of_admissible_basepair (size_type i, size_type j) const
	Pair type of an admissible basepair. More...
void	compute_ensemble_probs (const PFoldParams &params, bool inLoopProbs, bool use_alifold)
	(re)compute the pair probabilities More...
double	arc_2_prob_noali (size_type i, size_type j) const
	Get joint probability of stacked arcs. More...
double	arc_2_prob_ali (size_type i, size_type j) const
	Get joint probability of stacked arcs (alifold version) More...
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) More...
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) More...
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) More...
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. More...
void	compute_Qm2 ()
	Computes the Qm2 matrix. More...
void	compute_Qm2_ali ()
	Computes the Qm2 matrix (alifold) More...
void	compute_McCaskill_matrices (const PFoldParams &params, bool inLoopProbs)
	Computes the McCaskill matrices and keeps them accessible. More...
void	compute_McCaskill_alifold_matrices (const PFoldParams &params, bool inLoopProbs)
	Computes the McCaskill matrices and keeps them accessible (alifold) More...

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_
	DP matrix data structures of VRNA's McCaskill algorithm.
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_
	minimum free energy structure (if computed)

Detailed Description

Implementation of RnaEnsemble.

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

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

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