#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, BasePairProbabilities *pairProbabilities=nullptr)

virtual	~PredictorMfeEns2dSeedExtension () 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	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)

virtual void	prepareStackSeedExtensions (size_t n, size_t m, const StackSeedDomain &seeds)

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

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_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) 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
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)

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). Stack-only seeds use a seed-avoiding left extension and an unconstrained right extension at the first completed seed, counting each interaction once. Gapped seeds retain the legacy extension implementation.

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,
		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; must outlive predictions and remain pending until all disjoint regions have succeeded
seedHandler	the seed handler to be used

◆ ~PredictorMfeEns2dSeedExtension()

virtual IntaRNA::PredictorMfeEns2dSeedExtension::~PredictorMfeEns2dSeedExtension ( )

overridevirtual

data cleanup

Member Function Documentation

◆ addExtensionProbabilityRoot()

void IntaRNA::PredictorMfeEns2dSeedExtension::addExtensionProbabilityRoot	(	size_t	i1,
		size_t	j1,
		size_t	i2,
		size_t	j2,
		Z_type	partZ,
		bool	left,
		bool	right
	)

protected

Add one accepted left/seed/right objective to the optional reverse trace. All coordinates are local, with seed boundaries in increasing DP order.

Parameters

left	whether the left matrix is a factor (otherwise use initiation)
right	whether the right matrix is a factor

◆ addSeedPartition()

void IntaRNA::PredictorMfeEns2dSeedExtension::addSeedPartition	(	Interaction::BasePair	seed,
		Interaction::BasePair	left,
		Interaction::BasePair	right,
		Z_type	hybridZ
	)

protected

Retain an anchor-specific site ensemble before full-site aggregation.

Parameters

seed	local anchor start, sequence 2 reversed
left	local left site boundary
right	local right site boundary
hybridZ	partition assigned to this left-most seed, including initiation

◆ beginExtensionProbabilitySeed()

void IntaRNA::PredictorMfeEns2dSeedExtension::beginExtensionProbabilitySeed	(	size_t	i1,
		size_t	i2
	)

protected

Store the current anchor seed's actual pairs, including its endpoints.

◆ commitExtensionProbabilities()

void IntaRNA::PredictorMfeEns2dSeedExtension::commitExtensionProbabilities ( )

protected

Validate and atomically commit this region in original sequence order.

◆ exactBoundaryWeight()

virtual Z_type IntaRNA::PredictorMfeEns2dSeedExtension::exactBoundaryWeight	(	size_t	i1,
		size_t	j1,
		size_t	i2,
		size_t	j2
	)		const

protectedvirtual

Shared forward/outside objective coefficient. Override here for supported reweighting; return zero for forbidden boundaries. Coordinates are local.

Returns: complete boundary Boltzmann factor (ED, dangles, ends, energyAdd)

◆ extensionSeedPrefix()

std::vector< Interaction::BasePair > IntaRNA::PredictorMfeEns2dSeedExtension::extensionSeedPrefix	(	size_t	i1,
		size_t	i2,
		size_t	before
	)		const

protected

Actual seed pairs strictly before the given local target coordinate.

◆ 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

◆ finishExtensionProbabilitySeed()

void IntaRNA::PredictorMfeEns2dSeedExtension::finishExtensionProbabilitySeed ( )

protected

Reverse both extension traces and accumulate actual pair numerators.

◆ 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

◆ initExtensionProbabilities()

void IntaRNA::PredictorMfeEns2dSeedExtension::initExtensionProbabilities	(	size_t	n,
		size_t	m
	)

protected

Begin a regional trace; no allocation if no probability sink was requested.

◆ predict()

virtual void IntaRNA::PredictorMfeEns2dSeedExtension::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

Implements IntaRNA::Predictor.

Reimplemented in IntaRNA::PredictorMfeEns2dHeuristicSeedExtension.

◆ predictStackSeeds()

void IntaRNA::PredictorMfeEns2dSeedExtension::predictStackSeeds	(	const IndexRange &	r1,
		const IndexRange &	r2
	)

protected

Run the selected disjoint stack-seed partition backend.

◆ prepareStackSeedExtensions()

virtual void IntaRNA::PredictorMfeEns2dSeedExtension::prepareStackSeedExtensions	(	size_t	n,
		size_t	m,
		const StackSeedDomain &	seeds
	)

protectedvirtual

Prepare optional heuristic right endpoints for the admitted stack seeds.

Parameters

n	first active range length
m	second active range length
seeds	contained seeds used by the partition recurrence

Reimplemented in IntaRNA::PredictorMfeEns2dHeuristicSeedExtension.

◆ printMatrix()

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

protected

◆ stackSeedRightSelector()

virtual std::function< Interaction::BasePair(Interaction::BasePair, Interaction::BasePair)> IntaRNA::PredictorMfeEns2dSeedExtension::stackSeedRightSelector ( ) const

protectedvirtual

Select one right endpoint per anchor for the heuristic retained ensemble. An empty function requests the full exact ensemble. Nonempty selectors use local increasing coordinates and receive the anchor's first and last pair.

Returns: selector shared by the forward and outside recurrences

Reimplemented in IntaRNA::PredictorMfeEns2dHeuristicSeedExtension.

◆ traceBack()

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

overrideprotectedvirtual

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

◆ extensionProbabilityTrace

std::unique_ptr<ExtensionProbabilityTrace> IntaRNA::PredictorMfeEns2dSeedExtension::extensionProbabilityTrace

protected

◆ 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

◆ pairProbabilities

BasePairProbabilities* IntaRNA::PredictorMfeEns2dSeedExtension::pairProbabilities

protected

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

◆ 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

◆ addExtensionProbabilityRoot()

◆ addSeedPartition()

◆ beginExtensionProbabilitySeed()

◆ commitExtensionProbabilities()

◆ exactBoundaryWeight()

◆ extensionSeedPrefix()

◆ fillHybridZ_left()

◆ fillHybridZ_right()

◆ finishExtensionProbabilitySeed()

◆ getNonOverlappingEnergy()

◆ initExtensionProbabilities()

◆ predict()

◆ predictStackSeeds()

◆ prepareStackSeedExtensions()

◆ printMatrix()

◆ stackSeedRightSelector()

◆ traceBack()

Member Data Documentation

◆ energy

◆ extensionProbabilityTrace

◆ hybridZ_left

◆ hybridZ_right

◆ output

◆ pairProbabilities

◆ seedHandler