IntaRNA::AccessibilityBasePair Class Reference

#include <AccessibilityBasePair.h>

Inheritance diagram for IntaRNA::AccessibilityBasePair:

Collaboration diagram for IntaRNA::AccessibilityBasePair:

Public Member Functions
	AccessibilityBasePair (const RnaSequence &seq, const size_t maxLength, const AccessibilityConstraint *const accConstr, const E_type basePairEnergy=Ekcal_2_E(-1.0), const Z_type RT=1, const size_t minLoopLength=3)
virtual	~AccessibilityBasePair ()
virtual E_type	getED (const size_t from, const size_t to) const
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
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

Protected Attributes
const E_type	basePairEnergy
	energy of an individual base pair
const Z_type	RT
	temperature constant for normalization
const Z_type	basePairWeight
	Boltzmann Energy weight.
const size_t	minLoopLength
	minimum length of loops
NussinovHandler::E2dMatrix	logPu
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
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

Detailed Description

Provides accessibility penalties for a Nussinov-like energy scoring where each base pair is scored by basePairEnergy independently from its structural context.

This implementation is mainly for teaching and testing purpose.

Author

Mostafa Mahmoud

Martin Mann

Constructor & Destructor Documentation

AccessibilityBasePair()

IntaRNA::AccessibilityBasePair::AccessibilityBasePair	(	const RnaSequence &	seq,
		const size_t	maxLength,
		const AccessibilityConstraint *const	accConstr,
		const E_type	basePairEnergy = Ekcal_2_E(-1.0),
		const Z_type	RT = 1,
		const size_t	minLoopLength = 3
	)

~AccessibilityBasePair()

virtual IntaRNA::AccessibilityBasePair::~AccessibilityBasePair ( )

virtual

Member Function Documentation

getED()

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

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

Implements IntaRNA::Accessibility.

Member Data Documentation

basePairEnergy

const E_type IntaRNA::AccessibilityBasePair::basePairEnergy

protected

energy of an individual base pair

basePairWeight

const Z_type IntaRNA::AccessibilityBasePair::basePairWeight

protected

Boltzmann Energy weight.

logPu

NussinovHandler::E2dMatrix IntaRNA::AccessibilityBasePair::logPu

protected

minLoopLength

const size_t IntaRNA::AccessibilityBasePair::minLoopLength

protected

minimum length of loops

RT

const Z_type IntaRNA::AccessibilityBasePair::RT

protected

temperature constant for normalization

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

• src/IntaRNA/AccessibilityBasePair.h