#include <PredictorMfeEns2dHeuristicSeedExtension.h>

Inheritance diagram for IntaRNA::PredictorMfeEns2dHeuristicSeedExtension:

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Collaboration diagram for IntaRNA::PredictorMfeEns2dHeuristicSeedExtension:

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Public Member Functions
	PredictorMfeEns2dHeuristicSeedExtension (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker predTracker, SeedHandler seedHandler, BasePairProbabilities *pairProbabilities=nullptr)

virtual	~PredictorMfeEns2dHeuristicSeedExtension () 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::PredictorMfeEns2dSeedExtension
	PredictorMfeEns2dSeedExtension (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker predTracker, SeedHandler seedHandler, BasePairProbabilities *pairProbabilities=nullptr)

virtual	~PredictorMfeEns2dSeedExtension () 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 Member Functions
void	prepareStackSeedExtensions (size_t n, size_t m, const StackSeedDomain &seeds) override

std::function< Interaction::BasePair(Interaction::BasePair, Interaction::BasePair)>	stackSeedRightSelector () const override

virtual void	updateOptRightZ (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const E_type hybridE)

virtual void	fillHybridZ_right (const size_t i1, const size_t i2, const size_t si1, const size_t si2)

virtual void	fillHybridZ_left (const size_t j1, const size_t j2) override

Protected Member Functions inherited from IntaRNA::PredictorMfeEns2dSeedExtension
void	addSeedPartition (Interaction::BasePair seed, Interaction::BasePair left, Interaction::BasePair right, Z_type hybridZ)

virtual Z_type	exactBoundaryWeight (size_t i1, size_t j1, size_t i2, size_t j2) const

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

void	initExtensionProbabilities (size_t n, size_t m)

void	beginExtensionProbabilitySeed (size_t i1, size_t i2)

void	addExtensionProbabilityRoot (size_t i1, size_t j1, size_t i2, size_t j2, Z_type partZ, bool left, bool right)

void	finishExtensionProbabilitySeed ()

void	commitExtensionProbabilities ()

std::vector< Interaction::BasePair >	extensionSeedPrefix (size_t i1, size_t i2, size_t before) const

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

virtual void	traceBack (Interaction &interaction) override

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
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

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
bool	selectingStackSeedRight = false
	Only rank right extensions while preparing canonical stack-seed choices.

std::unordered_map< Interaction::BasePair, Interaction::BasePair, Interaction::BasePair::Hash >	stackSeedRight
	Preferred local endpoint keyed by the local first pair of each seed.

Z_type	E_right_opt = E_INF
	optimal energy of the right extension

size_t	j1opt
	boundaries of the right extension with the optimal energy

size_t	j2opt

SeedHandlerIdxOffset	seedHandler
	the seed handler (with idx offset)

Z2dMatrix	hybridZ_left

Z2dMatrix	hybridZ_right

Protected Attributes inherited from IntaRNA::PredictorMfeEns2dSeedExtension
std::unique_ptr< ExtensionProbabilityTrace >	extensionProbabilityTrace

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

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

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)

Protected Types inherited from IntaRNA::PredictorMfeEns2dSeedExtension
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

Detailed Description

Implements heuristic, 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). Stack-only seeds share the exact predictor's left-most anchor tables. The first completed seed uniquely owns each chain, equivalently the left-most seed after removing containing occurrences. Retain its one-sided extensions and the left extensions ending at its preferred right endpoint. Pair probabilities describe this retained ensemble.

Author: Frank Gelhausen; Martin Raden

Constructor & Destructor Documentation

◆ PredictorMfeEns2dHeuristicSeedExtension()

IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::PredictorMfeEns2dHeuristicSeedExtension	(	const InteractionEnergy &	energy,
		OutputHandler &	output,
		PredictionTracker *	predTracker,
		SeedHandler *	seedHandler,
		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 this approximate ensemble
seedHandler	the seed handler to be used

◆ ~PredictorMfeEns2dHeuristicSeedExtension()

virtual IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::~PredictorMfeEns2dHeuristicSeedExtension ( )

overridevirtual

data cleanup

Member Function Documentation

◆ fillHybridZ_left()

virtual void IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::fillHybridZ_left	(	const size_t	j1,
		const size_t	j2
	)

overrideprotectedvirtual

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 from IntaRNA::PredictorMfeEns2dSeedExtension.

◆ fillHybridZ_right()

virtual void IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::fillHybridZ_right	(	const size_t	i1,
		const size_t	i2,
		const size_t	si1,
		const size_t	si2
	)

protectedvirtual

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

Parameters

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

◆ predict()

virtual void IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::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.

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

Reimplemented from IntaRNA::PredictorMfeEns2dSeedExtension.

◆ prepareStackSeedExtensions()

void IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::prepareStackSeedExtensions	(	size_t	n,
		size_t	m,
		const StackSeedDomain &	seeds
	)

overrideprotectedvirtual

Freeze one preferred right endpoint for each admitted stack anchor. The existing virtual right-extension hooks determine the choice; partition contributions are deferred to the shared left-most-anchor recurrence.

Parameters

n	first active range length
m	second active range length
seeds	contained stack occurrences in the active range

Reimplemented from IntaRNA::PredictorMfeEns2dSeedExtension.

◆ stackSeedRightSelector()

std::function< Interaction::BasePair(Interaction::BasePair, Interaction::BasePair)> IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::stackSeedRightSelector ( ) const

overrideprotectedvirtual

Returns: the frozen right-endpoint selector for the approximate ensemble

Reimplemented from IntaRNA::PredictorMfeEns2dSeedExtension.

◆ updateOptRightZ()

void IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::updateOptRightZ	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2,
		const E_type	hybridE
	)

inlineprotectedvirtual

updates E_right_opt, j1opt, and j2opt if needed

Parameters

i1	the index of the first sequence interacting with i2
j1	the index of the first sequence interacting with j2
i2	the index of the second sequence interacting with i1
j2	the index of the second sequence interacting with j1
hybridE	ensemble energy of the hybridization

Member Data Documentation

◆ E_right_opt

Z_type IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::E_right_opt = E_INF

protected

optimal energy of the right extension

◆ hybridZ_left

Z2dMatrix IntaRNA::PredictorMfeEns2dSeedExtension::hybridZ_left

protected

energy of all interaction hybrids that end in position p (seq1) and q (seq2) and do not necessarily contain a seed interaction

◆ hybridZ_right

Z2dMatrix IntaRNA::PredictorMfeEns2dSeedExtension::hybridZ_right

protected

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

◆ j1opt

size_t IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::j1opt

protected

boundaries of the right extension with the optimal energy

◆ j2opt

size_t IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::j2opt

protected

◆ seedHandler

SeedHandlerIdxOffset IntaRNA::PredictorMfeEns2dSeedExtension::seedHandler

protected

the seed handler (with idx offset)

◆ selectingStackSeedRight

bool IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::selectingStackSeedRight = false

protected

Only rank right extensions while preparing canonical stack-seed choices.

◆ stackSeedRight

std::unordered_map<Interaction::BasePair,Interaction::BasePair,Interaction::BasePair::Hash> IntaRNA::PredictorMfeEns2dHeuristicSeedExtension::stackSeedRight

protected

Preferred local endpoint keyed by the local first pair of each seed.

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

src/IntaRNA/PredictorMfeEns2dHeuristicSeedExtension.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PredictorMfeEns2dHeuristicSeedExtension()

◆ ~PredictorMfeEns2dHeuristicSeedExtension()

Member Function Documentation

◆ fillHybridZ_left()

◆ fillHybridZ_right()

◆ predict()

◆ prepareStackSeedExtensions()

◆ stackSeedRightSelector()

◆ updateOptRightZ()

Member Data Documentation

◆ E_right_opt

◆ hybridZ_left

◆ hybridZ_right

◆ j1opt

◆ j2opt

◆ seedHandler

◆ selectingStackSeedRight

◆ stackSeedRight