#include <PredictorMfeEns2dSeedExtension.h>

Inheritance diagram for IntaRNA::PredictorMfeEns2dSeedExtension:

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Collaboration diagram for IntaRNA::PredictorMfeEns2dSeedExtension:

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Public Member Functions
	PredictorMfeEns2dSeedExtension (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker predTracker, SeedHandler seedHandler)

virtual	~PredictorMfeEns2dSeedExtension ()

virtual void	predict (const IndexRange &r1=IndexRange(0, RnaSequence::lastPos), const IndexRange &r2=IndexRange(0, RnaSequence::lastPos))

Public Member Functions inherited from IntaRNA::PredictorMfeEns
	PredictorMfeEns (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker)

virtual	~PredictorMfeEns ()

Public Member Functions inherited from IntaRNA::PredictorMfe
	PredictorMfe (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker)

virtual	~PredictorMfe ()

Public Member Functions inherited from IntaRNA::Predictor
	Predictor (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker)

virtual	~Predictor ()

Z_type	getZall () const

Protected Types
typedef Matrix< Z_type >	Z2dMatrix
	matrix type to hold the partition functions for interaction site starts

Protected Types inherited from IntaRNA::PredictorMfe
typedef BestInteraction< E_type >	BestInteractionE
	BestInteraction that stores an energy value.

typedef BestInteraction< Z_type >	BestInteractionZ
	BestInteraction that stores a partition function value.

typedef std::list< Interaction >	InteractionList
	list of interactions

typedef boost::unordered_map< Interaction::BasePair, BestInteractionE, Interaction::BasePair::Hash >	HashIdx2E
	hash to map index pairs to BestInteractionE entries

Protected Member Functions
virtual void	fillHybridZ_left (const size_t j1, const size_t j2)

virtual void	fillHybridZ_right (const size_t i1, const size_t i2)

virtual void	traceBack (Interaction &interaction)

virtual E_type	getNonOverlappingEnergy (const size_t si1, const size_t si2, const size_t sj1, const size_t sj2)

void	printMatrix (const Z2dMatrix &matrix)

Protected Member Functions inherited from IntaRNA::PredictorMfeEns
virtual void	initZ ()

virtual void	updateZ (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const Z_type partFunct, const bool isHybridZ)

void	updateCompleteZ (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const Z_type partFunct, const bool isHybridZ)

virtual void	reportOptima ()

Protected Member Functions inherited from IntaRNA::PredictorMfe
virtual void	initOptima ()

bool	isValidOutputSite (const size_t i1, const size_t j1, const size_t i2, const size_t j2) const

virtual void	updateOptima (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const E_type energy, const bool isHybridE, const bool incrementZall)

virtual void	getNextBest (Interaction &curBest)

virtual void	updateMfe4leftEnd (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const Interaction &curInteraction)

Protected Member Functions inherited from IntaRNA::Predictor
virtual void	updateZall (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const E_type energy, const bool isHybridE)

void	incrementZall (const Z_type partZ)

Protected Attributes
Z2dMatrix	hybridZ_left
	partition function of all interaction hybrids that start on the left side of the seed including E_init

SeedHandlerIdxOffset	seedHandler
	the seed handler (with idx offset)

Z2dMatrix	hybridZ_right
	partition function of all interaction hybrids that start on the right side of the seed excluding E_init

InteractionEnergyIdxOffset	energy
	access to the interaction energy handler of the super class

OutputHandler &	output
	access to the output handler of the super class

Protected Attributes inherited from IntaRNA::PredictorMfeEns
std::unordered_map< Interaction::Boundary, Z_type, Interaction::Boundary::Hash >	Z_partition
	map storing the partition of Zall for all considered interaction sites

bool	updateZisComplete
	whether updateZ() currently receives one complete boundary partition

InteractionEnergyIdxOffset	energy
	access to the interaction energy handler of the super class

OutputHandler &	output
	access to the output handler of the super class

PredictionTracker *	predTracker
	access to the prediction tracker of the super class

Protected Attributes inherited from IntaRNA::PredictorMfe
InteractionList	mfeInteractions
	mfe interaction boundaries

HashIdx2E	mfe4leftEnd

std::pair< IndexRangeList, IndexRangeList >	reportedInteractions

InteractionEnergyIdxOffset	energy
	access to the interaction energy handler of the super class

OutputHandler &	output
	access to the output handler of the super class

PredictionTracker *	predTracker
	access to the prediction tracker of the super class

Protected Attributes inherited from IntaRNA::Predictor
InteractionEnergyIdxOffset	energy
	energy computation handler

OutputHandler &	output
	interaction output handler

PredictionTracker *	predTracker
	prediction tracker to be used

Z_type	Zall

Additional Inherited Members
Static Public Member Functions inherited from IntaRNA::Predictor
static size_t	getMaxInteractionWidth (const size_t w, const size_t maxLoopSize)

Detailed Description

Implements seed-based space-efficient interaction prediction based on minimizing ensemble free energy of interaction sites.

Note, for each seed start (i1,i2) only the mfe seed is considered for the overall interaction computation instead of considering all possible seeds starting at (i1,i2).

Author: Frank Gelhausen; Martin Raden

Member Typedef Documentation

◆ Z2dMatrix

typedef Matrix<Z_type> IntaRNA::PredictorMfeEns2dSeedExtension::Z2dMatrix

protected

matrix type to hold the partition functions for interaction site starts

Constructor & Destructor Documentation

◆ PredictorMfeEns2dSeedExtension()

IntaRNA::PredictorMfeEns2dSeedExtension::PredictorMfeEns2dSeedExtension	(	const InteractionEnergy &	energy,
		OutputHandler &	output,
		PredictionTracker *	predTracker,
		SeedHandler *	seedHandler
	)

Constructs a predictor and stores the energy and output handler

Parameters

energy	the interaction energy handler
output	the output handler to report mfe interactions to
predTracker	the prediction tracker to be used or NULL if no tracking is to be done; if non-NULL, the tracker gets deleted on this->destruction.
seedHandler	the seed handler to be used

◆ ~PredictorMfeEns2dSeedExtension()

virtual IntaRNA::PredictorMfeEns2dSeedExtension::~PredictorMfeEns2dSeedExtension ( )

virtual

data cleanup

Member Function Documentation

◆ fillHybridZ_left()

virtual void IntaRNA::PredictorMfeEns2dSeedExtension::fillHybridZ_left	(	const size_t	j1,
		const size_t	j2
	)

protectedvirtual

Computes all entries of the hybridE matrix for interactions ending in p=j1 and q=j2 and report all valid interactions to updateOptima()

Parameters

j1	end of the interaction within seq 1
j2	end of the interaction within seq 2

Reimplemented in IntaRNA::PredictorMfeEns2dHeuristicSeedExtension.

◆ fillHybridZ_right()

virtual void IntaRNA::PredictorMfeEns2dSeedExtension::fillHybridZ_right	(	const size_t	i1,
		const size_t	i2
	)

protectedvirtual

Computes all entries of the hybridE matrix for interactions starting in i1 and i2 and report all valid interactions to updateOptima()

Note: (i1,i2) have to be complementary (right-most base pair of seed)

Parameters

i1	end of the interaction within seq 1
i2	end of the interaction within seq 2

◆ getNonOverlappingEnergy()

virtual E_type IntaRNA::PredictorMfeEns2dSeedExtension::getNonOverlappingEnergy	(	const size_t	si1,
		const size_t	si2,
		const size_t	sj1,
		const size_t	sj2
	)

protectedvirtual

Returns the hybridization energy of the non overlapping part of seeds starting at si and sj

Parameters

si1	the index of seed1 in the first sequence
si2	the index of seed1 in the second sequence
sj1	the index of seed2 in the first sequence
sj2	the index of seed2 in the second sequence

◆ predict()

virtual void IntaRNA::PredictorMfeEns2dSeedExtension::predict	(	const IndexRange &	r1 = `IndexRange(0, RnaSequence::lastPos)`,
		const IndexRange &	r2 = `IndexRange(0, RnaSequence::lastPos)`
	)

virtual

Computes the mfe for the given sequence ranges (i1-j1) in the first sequence and (i2-j2) in the second sequence and reports it to the output handler.

Each considered interaction contains a seed according to the seed handler constraints.

Parameters

r1	the index range of the first sequence interacting with r2
r2	the index range of the second sequence interacting with r1

Implements IntaRNA::Predictor.

Reimplemented in IntaRNA::PredictorMfeEns2dHeuristicSeedExtension.

◆ printMatrix()

void IntaRNA::PredictorMfeEns2dSeedExtension::printMatrix ( const Z2dMatrix & matrix )

protected

◆ traceBack()

virtual void IntaRNA::PredictorMfeEns2dSeedExtension::traceBack ( Interaction & interaction )

protectedvirtual

adds seed information and calls traceBack() of super class

Parameters

interaction IN/OUT the interaction to fill

Reimplemented from IntaRNA::PredictorMfeEns.

Member Data Documentation

◆ energy

InteractionEnergyIdxOffset IntaRNA::Predictor::energy

protected

access to the interaction energy handler of the super class

◆ hybridZ_left

Z2dMatrix IntaRNA::PredictorMfeEns2dSeedExtension::hybridZ_left

protected

partition function of all interaction hybrids that start on the left side of the seed including E_init

◆ hybridZ_right

Z2dMatrix IntaRNA::PredictorMfeEns2dSeedExtension::hybridZ_right

protected

partition function of all interaction hybrids that start on the right side of the seed excluding E_init

◆ output

OutputHandler& IntaRNA::Predictor::output

protected

access to the output handler of the super class

◆ seedHandler

SeedHandlerIdxOffset IntaRNA::PredictorMfeEns2dSeedExtension::seedHandler

protected

the seed handler (with idx offset)

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

src/IntaRNA/PredictorMfeEns2dSeedExtension.h

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Z2dMatrix

Constructor & Destructor Documentation

◆ PredictorMfeEns2dSeedExtension()

◆ ~PredictorMfeEns2dSeedExtension()

Member Function Documentation

◆ fillHybridZ_left()

◆ fillHybridZ_right()

◆ getNonOverlappingEnergy()

◆ predict()

◆ printMatrix()

◆ traceBack()

Member Data Documentation

◆ energy

◆ hybridZ_left

◆ hybridZ_right

◆ output

◆ seedHandler