#include <AccessibilityVrna.h>

Inheritance diagram for IntaRNA::AccessibilityVrna:

Collaboration diagram for IntaRNA::AccessibilityVrna:

[legend]

Public Member Functions
	AccessibilityVrna (const RnaSequence &sequence, const size_t maxLength, const AccessibilityConstraint *const accConstraint, const VrnaHandler &vrnaHandler, const size_t plFoldW=0, const double pfScale=VrnaHandler::getPfScaleDefault())

virtual	~AccessibilityVrna () override

virtual E_type	getED (const size_t from, const size_t to) const override

void	writeBinary (std::ostream &out) const override

Public Member Functions inherited from IntaRNA::Accessibility
	Accessibility (const RnaSequence &sequence, const size_t maxLength, const AccessibilityConstraint *const accConstr)

virtual	~Accessibility ()

virtual const RnaSequence &	getSequence () const

virtual size_t	getMaxLength () const

virtual const AccessibilityConstraint &	getAccConstraint () const

void	writeRNAplfold_Pu_text (std::ostream &out, const Z_type RT) const

void	writeRNAplfold_ED_text (std::ostream &out) const

IndexRangeList	decomposeByMaxED (const size_t maxRangeLength, const size_t winSize, const size_t minRangeLength) const

void	decomposeByMaxED (IndexRangeList &ranges, const E_type maxED, const size_t minRangeLength) const

Static Public Member Functions
static void	addConstraints (vrna_fold_compound_t &fold_compound, const Accessibility &acc)

Protected Types
typedef UpperBandedMatrix< E_type >	EdMatrix
	type for the ED value matrix (upper triangular matrix banded by maxLength)

Protected Member Functions
void	fillByRNAplfold (const VrnaHandler &vrnaHandler, const size_t plFoldW, const size_t plFoldL, const double pfScale)

Protected Member Functions inherited from IntaRNA::Accessibility
void	writeBinary (std::ostream &out, const UpperBandedMatrix< E_type > *matrix) const

virtual void	checkIndices (const size_t from, const size_t to) const

void	writeRNAplfold_text (std::ostream &out, const Z_type RT, const bool writeProbs) const

Static Protected Member Functions
static void	callbackForStorage (FLT_OR_DBL pr, int pr_size, int j, int max, unsigned int type, void storageRT)

Protected Attributes
EdMatrix	edValues
	the ED values for the given sequence

Protected Attributes inherited from IntaRNA::Accessibility
const RnaSequence &	seq
	the RNA sequence the accessibilities correspond to

const size_t	maxLength
	the maximal length of an unpaired regions to be considered

AccessibilityConstraint	accConstraint
	accessibility constraint

Additional Inherited Members
Static Public Attributes inherited from IntaRNA::Accessibility
static const E_type	ED_UPPER_BOUND
	upper bound for all ED return values

Detailed Description

Computes accessibility energy values for all regions using the free energies of structure ensembles based on partition function computations via the Vienna RNA package. ViennaRNA operations on independent objects are synchronized once global energy parameter loading is complete. Window folding runs in parallel when ViennaRNA was built with OpenMP support; otherwise it is serialized. Native thread callers must also configure thread-safe IntaRNA diagnostic logging.

Author: Martin Mann 2014

Member Typedef Documentation

◆ EdMatrix

typedef UpperBandedMatrix<E_type> IntaRNA::AccessibilityVrna::EdMatrix

protected

type for the ED value matrix (upper triangular matrix banded by maxLength)

Constructor & Destructor Documentation

◆ AccessibilityVrna()

IntaRNA::AccessibilityVrna::AccessibilityVrna	(	const RnaSequence &	sequence,
		const size_t	maxLength,
		const AccessibilityConstraint *const	accConstraint,
		const VrnaHandler &	vrnaHandler,
		const size_t	plFoldW = `0`,
		const double	pfScale = `VrnaHandler::getPfScaleDefault()`
	)

Construction

Parameters

sequence	the sequence the accessibility data belongs to
maxLength	the maximal window size of accessible regions to be considered. 0 defaults to the sequence's length.
accConstraint	if not NULL, accessibility constraint that enforces some regions to be unstructured both in sequence and interaction
vrnaHandler	the VRNA parameter handler to be used
plFoldW	the sliding window size to be used for plFold computations @oaram pfScale can be used to explicitly set pf_scale of VRNA partition function computation. Note: only used for values >= 1.0, all other values are ignored.

◆ ~AccessibilityVrna()

virtual IntaRNA::AccessibilityVrna::~AccessibilityVrna ( )

overridevirtual

destruction

Member Function Documentation

◆ addConstraints()

static void IntaRNA::AccessibilityVrna::addConstraints	(	vrna_fold_compound_t &	fold_compound,
		const Accessibility &	acc
	)

static

Adds constraints to the VRNA fold compound that correspond to the present AccessibilityConstraints The caller must hold VrnaHandler::getSetupMutex() during concurrent use of ViennaRNA, including preparation of SHAPE soft constraints.

Parameters

fold_compound	INOUT the object to extend
acc	the accessibility handler to get constraint information from

◆ callbackForStorage()

static void IntaRNA::AccessibilityVrna::callbackForStorage	(	FLT_OR_DBL *	pr,
		int	pr_size,
		int	j,
		int	max,
		unsigned int	type,
		void *	storageRT
	)

staticprotected

callback function used when calling vrna_probs_window()

This function will be called for each probability data set in the sliding window probability computation implementation of vrna_probs_window(). The argument type specifies the type of probability that is passed to this function.

See also: vrna_probs_window()

Parameters

pr	An array of probabilities
pr_size	The length of the probability array
j	The j-position (3'-end) of the probability intervals (indexing starting with 1)
max	The (theoretical) maximum length of the probability array
type	The type of probability that is passed to this function
storageRT	Auxiliary data: should hold a pair(AccessibilityVrna*,double RT)

◆ fillByRNAplfold()

void IntaRNA::AccessibilityVrna::fillByRNAplfold	(	const VrnaHandler &	vrnaHandler,
		const size_t	plFoldW,
		const size_t	plFoldL,
		const double	pfScale
	)

protected

Use RNAplfold-like style to fill ED-values

Parameters

vrnaHandler	the VRNA handler to be used
plFoldW	the sliding window size to be used or 0 for full length
plFoldL	the maximal base pair span to be used or 0 for plFoldW @oaram pfScale can be used to explicitly set pf_scale of VRNA partition function computation. Note: only used for values >= 1.0, all other values are ignored.

◆ getED()

E_type IntaRNA::AccessibilityVrna::getED	(	const size_t	from,
		const size_t	to
	)		const

inlineoverridevirtual

Returns the accessibility energy value for the given range in the sequence, i.e. the energy difference (ED) to make the region accessible.

Parameters

from	the start index of the regions (from <= to)
to	the end index of the regions (to < seq.length)

Returns: the ED value if (j-1+1) <= maxLength or ED_UPPER_BOUND otherwise

Exceptions

std::runtime_error in case it does not hold 0 <= from <= to < seq.length

Implements IntaRNA::Accessibility.

◆ writeBinary()

void IntaRNA::AccessibilityVrna::writeBinary ( std::ostream & out ) const

inlineoverridevirtual

Write the stored ED matrix directly, without copying rows or calling getED() for unconstrained data. Constraints retain the generic getED() path. Subclasses changing getED() semantics must also override this method.

Parameters

out	binary output stream; compression is supplied by the stream

Reimplemented from IntaRNA::Accessibility.

Member Data Documentation

◆ edValues

EdMatrix IntaRNA::AccessibilityVrna::edValues

protected

the ED values for the given sequence

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

src/IntaRNA/AccessibilityVrna.h

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ EdMatrix

Constructor & Destructor Documentation

◆ AccessibilityVrna()

◆ ~AccessibilityVrna()

Member Function Documentation

◆ addConstraints()

◆ callbackForStorage()

◆ fillByRNAplfold()

◆ getED()

◆ writeBinary()

Member Data Documentation

◆ edValues