#include <PredictorMfeEns2d.h>

Inheritance diagram for IntaRNA::PredictorMfeEns2d:

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Collaboration diagram for IntaRNA::PredictorMfeEns2d:

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Public Member Functions
	PredictorMfeEns2d (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker predTracker, BasePairProbabilities pairProbabilities=nullptr)

virtual	~PredictorMfeEns2d () override

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

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

virtual	~PredictorMfeEns () override

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

virtual	~PredictorMfe () override

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
void	predictRegion (const IndexRange &r1, const IndexRange &r2)

void	accumulatePairMasses (size_t j1, size_t j2, Z2dMatrix &outside, Z2dMatrix &masses, Z_type &denominator) const

virtual void	fillHybridZ (const size_t j1, const size_t j2, const size_t i1init, const size_t i2init, const bool callUpdateZ)

Protected Member Functions inherited from IntaRNA::PredictorMfeEns
void	updateExactCompleteZ (size_t i1, size_t j1, size_t i2, size_t j2, Z_type hybrid, Z_type coefficient)

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 () override

virtual void	traceBack (Interaction &interaction) override

Protected Member Functions inherited from IntaRNA::PredictorMfe
virtual bool	predictPerSeed (const IndexRange &r1, const IndexRange &r2, SeedHandlerIdxOffset &seeds, const std::function< Predictor (OutputHandler &, PredictionTracker , SeedHandler *)> &factory)

void	initSeedCandidates ()

virtual void	initOptima () override

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) override

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
BasePairProbabilities *	pairProbabilities
	optional sequence-pair owner, never deleted or finalized by this predictor

Z2dMatrix	hybridZ

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

const std::pair< Z_type, Z_type > *	exactContribution = nullptr
	scoped coefficient and hybrid expected by the checked complete update

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
OutputHandlerSeedCandidates *	seedCandidates = nullptr
	Active collector; null on the unchanged default path.

std::unique_ptr< OutputHandlerSeedCandidates >	ownedSeedCandidates
	Local collector for API callers that do not provide a regional collector.

bool	perSeedPass = false
	Enforce complete-site spans before ranking a seed-constrained child pass.

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

Memory efficient ensemble predictor for RNAup-like computation, i.e. full DP-implementation without seed-heuristic, using 2D matrices

Author: Martin Raden; Frank Gelhausen

Member Typedef Documentation

◆ Z2dMatrix

typedef Matrix<Z_type> IntaRNA::PredictorMfeEns2d::Z2dMatrix

protected

matrix type to hold the partition functions for interaction site starts

Constructor & Destructor Documentation

◆ PredictorMfeEns2d()

IntaRNA::PredictorMfeEns2d::PredictorMfeEns2d	(	const InteractionEnergy &	energy,
		OutputHandler &	output,
		PredictionTracker *	predTracker,
		BasePairProbabilities *	pairProbabilities = `nullptr`
	)

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.
pairProbabilities	optional non-owning sink; requires needZall and must remain pending until all disjoint regions have succeeded. Collection reverses this class's fillHybridZ recurrence; subclasses changing that recurrence must also supply their own collection.

◆ ~PredictorMfeEns2d()

virtual IntaRNA::PredictorMfeEns2d::~PredictorMfeEns2d ( )

overridevirtual

Member Function Documentation

◆ accumulatePairMasses()

void IntaRNA::PredictorMfeEns2d::accumulatePairMasses	(	size_t	j1,
		size_t	j2,
		Z2dMatrix &	outside,
		Z2dMatrix &	masses,
		Z_type &	denominator
	)		const

protected

Reverse the current fixed-right hybrid recurrence. Adjoint seeds obey the same site filters and numerical-zero tests as updateZ(). Implicit noLP stacking partners are counted in addition to the explicit DP-state pairs.

Parameters

j1	right boundary in local target coordinates
j2	right boundary in local reversed-query coordinates
outside	scratch adjoints, same dimensions as hybridZ
masses	accumulated numerators in original regional orientation
denominator	accumulated boundary contributions, checked against Zall

◆ fillHybridZ()

virtual void IntaRNA::PredictorMfeEns2d::fillHybridZ	(	const size_t	j1,
		const size_t	j2,
		const size_t	i1init,
		const size_t	i2init,
		const bool	callUpdateZ
	)

protectedvirtual

Computes all entries of the hybridE matrix for interactions ending in p=j1 and q=j2 and reports every complete boundary via updateCompleteZ(), which invokes the virtual updateZ() hook.

Parameters

j1	end of the interaction within seq 1
j2	end of the interaction within seq 2
i1init	smallest value for i1
i2init	smallest value for i2
callUpdateZ	whether or not updateCompleteZ() is to be called

◆ predict()

virtual void IntaRNA::PredictorMfeEns2d::predict	(	const IndexRange &	r1 = `IndexRange(0, RnaSequence::lastPos)`,
		const IndexRange &	r2 = `IndexRange(0, RnaSequence::lastPos)`
	)

overridevirtual

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.

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::PredictorMfeEns2dHeuristic.

◆ predictRegion()

void IntaRNA::PredictorMfeEns2d::predictRegion	(	const IndexRange &	r1,
		const IndexRange &	r2
	)

protected

Compute one region, allowing predict() to fail the sink on any exception.

Member Data Documentation

◆ energy

InteractionEnergyIdxOffset IntaRNA::Predictor::energy

protected

access to the interaction energy handler of the super class

◆ hybridZ

Z2dMatrix IntaRNA::PredictorMfeEns2d::hybridZ

protected

energy of all interaction hybrids that end in position p (seq1) and q (seq2)

◆ output

OutputHandler& IntaRNA::Predictor::output

protected

access to the output handler of the super class

◆ pairProbabilities

BasePairProbabilities* IntaRNA::PredictorMfeEns2d::pairProbabilities

protected

optional sequence-pair owner, never deleted or finalized by this predictor

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

src/IntaRNA/PredictorMfeEns2d.h

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Z2dMatrix

Constructor & Destructor Documentation

◆ PredictorMfeEns2d()

◆ ~PredictorMfeEns2d()

Member Function Documentation

◆ accumulatePairMasses()

◆ fillHybridZ()

◆ predict()

◆ predictRegion()

Member Data Documentation

◆ energy

◆ hybridZ

◆ output

◆ pairProbabilities