#include <Accessibility.h>

Inheritance diagram for IntaRNA::Accessibility:

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Collaboration diagram for IntaRNA::Accessibility:

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

virtual	~Accessibility ()

virtual E_type	getED (const size_t from, const size_t to) const =0

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

virtual void	writeBinary (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 Attributes
static const E_type	ED_UPPER_BOUND
	upper bound for all ED return values

Protected Member Functions
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

Protected Attributes
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

Friends
std::ostream &	operator<< (std::ostream &out, const Accessibility &acc)

Detailed Description

Abstract interface that represents accessibility data for a given RNA sequence.

TODO : init function to trigger accessibility computation for a certain region

Author: Martin Mann 2014

Constructor & Destructor Documentation

◆ Accessibility()

IntaRNA::Accessibility::Accessibility	(	const RnaSequence &	sequence,
		const size_t	maxLength,
		const AccessibilityConstraint *const	accConstr
	)

inline

Construction

Parameters

sequence	the sequence the accessibility data belongs to
maxLength	the maximal length of accessible regions (>0) to be considered. 0 defaults to the full sequence's length, otherwise is is internally set to min(maxLength,seq.length).
accConstr	optional accessibility constraint

◆ ~Accessibility()

IntaRNA::Accessibility::~Accessibility ( )

inlinevirtual

destruction

Member Function Documentation

◆ checkIndices()

void IntaRNA::Accessibility::checkIndices	(	const size_t	from,
		const size_t	to
	)		const

inlineprotectedvirtual

Checks the given indices to be in the range 0 <= from <= to < seq.length and throws a std::runtime_error if the constraint is not met.

Parameters

from	the start index of the regions
to	the end index of the regions

Exceptions

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

◆ decomposeByMaxED() [1/2]

IndexRangeList IntaRNA::Accessibility::decomposeByMaxED	(	const size_t	maxRangeLength,
		const size_t	winSize,
		const size_t	minRangeLength
	)		const

Identifies regions of high accessibility by decomposing the sequence range at positions with lowest accessibility (highest ED value). This is done recursively, i.e. ranges that exceed the maxRegionLength are further decomposed (using their local max ED value) until the resulting subregions are below the given maxRangeLength.

Parameters

maxRangeLength	the maximal length of a resulting highly accessible sequence region
winSize	the ED window size to be used to identify low accessible regions. The center index of the identified window is used as split point for decomposition. Has to be greater than 0 and smaller than maxRangeLength, i.e in (0,maxRangeLength)
minRangeLength	the minimal length of a resulting sequence region

Returns: the list of index ranges of highly accessible regions of the sequence

◆ decomposeByMaxED() [2/2]

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

Decomposes a given range list into subranges that contain only positions where the position-wise ED value is below or equal to a given threshold, since any interaction site enclosing this positions has a higher ED.

Parameters

ranges	INOUT the list of ranges to decompose
maxED	the maximal ED threshold (inclusive)
minRangeLength	the minimal length of a resulting sequence region

◆ getAccConstraint()

const AccessibilityConstraint & IntaRNA::Accessibility::getAccConstraint ( ) const

inlinevirtual

Access to the globally enforced accessibility constraint. Here '.' denotes unconstrained positions and 'x' positions that have to be unstructured. Regions covering constrained positions will result in ED_UPPER_BOUND accessibility values.

Returns: the global accessibility constraint applied

Reimplemented in IntaRNA::ReverseAccessibility.

◆ getED()

virtual E_type IntaRNA::Accessibility::getED	(	const size_t	from,
		const size_t	to
	)		const

pure virtual

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

Implemented in IntaRNA::AccessibilityBasePair, IntaRNA::AccessibilityDisabled, IntaRNA::AccessibilityFromStream, IntaRNA::AccessibilityVrna, and IntaRNA::ReverseAccessibility.

◆ getMaxLength()

size_t IntaRNA::Accessibility::getMaxLength ( ) const

inlinevirtual

Access to the maximal length of accessible regions (>0) to be considered.

Returns: the maximal length of accessible regions considered

Reimplemented in IntaRNA::AccessibilityFromStream.

◆ getSequence()

const RnaSequence & IntaRNA::Accessibility::getSequence ( ) const

inlinevirtual

Access to the RnaSequence this accessibility values are accounting for.

Returns: the underlying sequence for this accessibility object.

Reimplemented in IntaRNA::ReverseAccessibility.

◆ writeBinary() [1/2]

virtual void IntaRNA::Accessibility::writeBinary ( std::ostream & out ) const

virtual

Write a native Boost binary archive of exact ED values, including the extra interval length needed for dangling ends. Works for every subclass. Compression is supplied by the stream (e.g. newOutputStream("file.agz")).

Parameters

out	binary output stream

Exceptions

std::exception on invalid ED values or output failure

Reimplemented in IntaRNA::AccessibilityFromStream, and IntaRNA::AccessibilityVrna.

◆ writeBinary() [2/2]

void IntaRNA::Accessibility::writeBinary	(	std::ostream &	out,
		const UpperBandedMatrix< E_type > *	matrix
	)		const

protected

Write an archive using stored ED rows when available. Non-empty constraints use getED() to preserve any masking applied by the subclass.

Parameters

out	binary output stream
matrix	non-owning matrix with the same unconstrained ED values as getED(), or nullptr to gather values through getED(); used only during this call

◆ writeRNAplfold_ED_text()

void IntaRNA::Accessibility::writeRNAplfold_ED_text ( std::ostream & out ) const

inline

Writes the ED values in RNAplfold style to stream.

Parameters

out	the output stream to write to

◆ writeRNAplfold_Pu_text()

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

inline

Writes the ED values as unpaired probabilities in RNAplfold style to stream.

Parameters

out	the output stream to write to
RT	the scaled temperature value to be used for conversion of ED to Pu : Pu = exp( -ED/RT )

◆ writeRNAplfold_text()

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

protected

Writes the ED values as unpaired probabilities in RNAplfold style to stream.

Parameters

out	the output stream to write to
RT	the scaled temperature value to be used for conversion of ED to Pu : Pu = exp( -ED/RT )
writeProbs	(true) write unpaired probabilities; (false) write ED

Friends And Related Symbol Documentation

◆ operator<<

std::ostream & operator<<	(	std::ostream &	out,
		const Accessibility &	acc
	)

friend

Prints the accessibility values to stream as upper triangular matrix

Parameters

out	the ostream to write to
acc	the Accessibility object to add

Returns: the altered stream out

Member Data Documentation

◆ accConstraint

AccessibilityConstraint IntaRNA::Accessibility::accConstraint

protected

accessibility constraint

◆ ED_UPPER_BOUND

const E_type IntaRNA::Accessibility::ED_UPPER_BOUND

static

upper bound for all ED return values

◆ maxLength

const size_t IntaRNA::Accessibility::maxLength

protected

the maximal length of an unpaired regions to be considered

◆ seq

const RnaSequence& IntaRNA::Accessibility::seq

protected

the RNA sequence the accessibilities correspond to

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

src/IntaRNA/Accessibility.h

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Accessibility()

◆ ~Accessibility()

Member Function Documentation

◆ checkIndices()

◆ decomposeByMaxED() [1/2]

◆ decomposeByMaxED() [2/2]

◆ getAccConstraint()

◆ getED()

◆ getMaxLength()

◆ getSequence()

◆ writeBinary() [1/2]

◆ writeBinary() [2/2]

◆ writeRNAplfold_ED_text()

◆ writeRNAplfold_Pu_text()

◆ writeRNAplfold_text()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ accConstraint

◆ ED_UPPER_BOUND

◆ maxLength

◆ seq