#include <PredictorMfeEns2dHeuristic.h>

Inheritance diagram for IntaRNA::PredictorMfeEns2dHeuristic:

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Collaboration diagram for IntaRNA::PredictorMfeEns2dHeuristic:

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Classes
struct	ProbabilityContinuation
	The selected chain owns its first pair and, optionally, its next stack pair. More...

Public Member Functions
	PredictorMfeEns2dHeuristic (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker predTracker, BasePairProbabilities pairProbabilities=nullptr)

virtual	~PredictorMfeEns2dHeuristic () 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::PredictorMfeEns2d
	PredictorMfeEns2d (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker predTracker, BasePairProbabilities pairProbabilities=nullptr)

virtual	~PredictorMfeEns2d () 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< BestInteractionZ >	Z2dMatrix
	matrix type to hold the mfe energies and boundaries for interaction site starts

Protected Types inherited from IntaRNA::PredictorMfeEns2d
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	predictRegionHeuristic (const IndexRange &r1, const IndexRange &r2)

void	recordProbabilityCandidate (size_t i1, size_t j1, size_t i2, size_t j2, Z_type hybrid, const ProbabilityContinuation &continuation)

void	commitProbabilityRegion ()

virtual void	fillHybridZ ()

Protected Member Functions inherited from IntaRNA::PredictorMfeEns2d
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
Z2dMatrix	hybridZ
	energy of all interaction hybrids starting in i1,i2

Matrix< ProbabilityContinuation >	probabilityContinuation
	Allocated only for probability output; selected continuations form a DAG.

Matrix< Z_type >	probabilityFlow
	Complete candidate weight flowing into each retained continuation.

Matrix< Z_type >	probabilityMass
	Numerators in local target/reversed-query coordinates until region commit.

Z_type	probabilityDenominator = 0
	Independently accumulated objective, required to agree exactly with Zall.

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::PredictorMfeEns2d
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 interaction predictor that uses a heuristic to find the mfe or a close-to-mfe interaction.

To this end, for each interaction start i1,i2 only the optimal right side interaction with boundaries j1,j2 is considered in the recursion instead of all possible interaction ranges.

This yields a quadratic time and space complexity. Optional pair probabilities refer to all admitted candidate chains considered by this pruning rule, with the same Zall as ordinary heuristic prediction. They approximate the unrestricted interaction ensemble. Collection adds quadratic storage and a reverse traversal of the retained continuations.

Author: Martin Raden; Frank Gelhausen

Member Typedef Documentation

◆ Z2dMatrix

typedef Matrix<BestInteractionZ> IntaRNA::PredictorMfeEns2dHeuristic::Z2dMatrix

protected

matrix type to hold the mfe energies and boundaries for interaction site starts

Constructor & Destructor Documentation

◆ PredictorMfeEns2dHeuristic()

IntaRNA::PredictorMfeEns2dHeuristic::PredictorMfeEns2dHeuristic	(	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 for probabilities of the pruned candidate ensemble; requires needZall

◆ ~PredictorMfeEns2dHeuristic()

virtual IntaRNA::PredictorMfeEns2dHeuristic::~PredictorMfeEns2dHeuristic ( )

overridevirtual

Member Function Documentation

◆ commitProbabilityRegion()

void IntaRNA::PredictorMfeEns2dHeuristic::commitProbabilityRegion ( )

protected

Propagate candidate weights through selected chains and commit this region.

◆ fillHybridZ()

virtual void IntaRNA::PredictorMfeEns2dHeuristic::fillHybridZ ( )

protectedvirtual

Computes all entries of the hybridE matrix and reports all valid interactions via updateOptima()

◆ predict()

virtual void IntaRNA::PredictorMfeEns2dHeuristic::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

Reimplemented from IntaRNA::PredictorMfeEns2d.

◆ predictRegionHeuristic()

void IntaRNA::PredictorMfeEns2dHeuristic::predictRegionHeuristic	(	const IndexRange &	r1,
		const IndexRange &	r2
	)

protected

Compute one region under predict()'s failure guard.

◆ recordProbabilityCandidate()

void IntaRNA::PredictorMfeEns2dHeuristic::recordProbabilityCandidate	(	size_t	i1,
		size_t	j1,
		size_t	i2,
		size_t	j2,
		Z_type	hybrid,
		const ProbabilityContinuation &	continuation
	)

protected

Record precisely the accepted updateZ candidate, crediting newly prepended pairs and routing its full weight to the retained child chain. Coordinates are local and the query is reversed; lastPos denotes an initial candidate.

Member Data Documentation

◆ energy

InteractionEnergyIdxOffset IntaRNA::Predictor::energy

protected

access to the interaction energy handler of the super class

◆ hybridZ

Z2dMatrix IntaRNA::PredictorMfeEns2dHeuristic::hybridZ

protected

energy of all interaction hybrids starting in i1,i2

◆ output

OutputHandler& IntaRNA::Predictor::output

protected

access to the output handler of the super class

◆ probabilityContinuation

Matrix<ProbabilityContinuation> IntaRNA::PredictorMfeEns2dHeuristic::probabilityContinuation

protected

Allocated only for probability output; selected continuations form a DAG.

◆ probabilityDenominator

Z_type IntaRNA::PredictorMfeEns2dHeuristic::probabilityDenominator = 0

protected

Independently accumulated objective, required to agree exactly with Zall.

◆ probabilityFlow

Matrix<Z_type> IntaRNA::PredictorMfeEns2dHeuristic::probabilityFlow

protected

Complete candidate weight flowing into each retained continuation.

◆ probabilityMass

Matrix<Z_type> IntaRNA::PredictorMfeEns2dHeuristic::probabilityMass

protected

Numerators in local target/reversed-query coordinates until region commit.

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

src/IntaRNA/PredictorMfeEns2dHeuristic.h

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Z2dMatrix

Constructor & Destructor Documentation

◆ PredictorMfeEns2dHeuristic()

◆ ~PredictorMfeEns2dHeuristic()

Member Function Documentation

◆ commitProbabilityRegion()

◆ fillHybridZ()

◆ predict()

◆ predictRegionHeuristic()

◆ recordProbabilityCandidate()

Member Data Documentation

◆ energy

◆ hybridZ

◆ output

◆ probabilityContinuation

◆ probabilityDenominator

◆ probabilityFlow

◆ probabilityMass