#include <PredictorMfeEnsSeedOnly.h>

Inheritance diagram for IntaRNA::PredictorMfeEnsSeedOnly:

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Collaboration diagram for IntaRNA::PredictorMfeEnsSeedOnly:

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

virtual	~PredictorMfeEnsSeedOnly () 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 Member Functions
virtual void	traceBack (Interaction &interaction) override

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
SeedHandlerIdxOffset	seedHandler
	the seed handler (with idx offset)

size_t	seedLastPos1
	last position of a seed of interest (in index-range of seedHandler)

size_t	seedLastPos2
	last position of a seed of interest (in index-range of seedHandler)

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::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

Ensemble-based prediction of seed interaction only.

Author: Martin Raden

Constructor & Destructor Documentation

◆ PredictorMfeEnsSeedOnly()

IntaRNA::PredictorMfeEnsSeedOnly::PredictorMfeEnsSeedOnly	(	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

◆ ~PredictorMfeEnsSeedOnly()

virtual IntaRNA::PredictorMfeEnsSeedOnly::~PredictorMfeEnsSeedOnly ( )

overridevirtual

data cleanup

Member Function Documentation

◆ predict()

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

overridevirtual

Computes the mfe seed 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.

◆ traceBack()

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

overrideprotectedvirtual

Fills a given interaction (boundaries given) with the according hybridizing base pairs using hybridE_seed.

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

◆ output

OutputHandler& IntaRNA::Predictor::output

protected

access to the output handler of the super class

◆ seedHandler

SeedHandlerIdxOffset IntaRNA::PredictorMfeEnsSeedOnly::seedHandler

protected

the seed handler (with idx offset)

◆ seedLastPos1

size_t IntaRNA::PredictorMfeEnsSeedOnly::seedLastPos1

protected

last position of a seed of interest (in index-range of seedHandler)

◆ seedLastPos2

size_t IntaRNA::PredictorMfeEnsSeedOnly::seedLastPos2

protected

last position of a seed of interest (in index-range of seedHandler)

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

src/IntaRNA/PredictorMfeEnsSeedOnly.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PredictorMfeEnsSeedOnly()

◆ ~PredictorMfeEnsSeedOnly()

Member Function Documentation

◆ predict()

◆ traceBack()

Member Data Documentation

◆ energy

◆ output

◆ seedHandler

◆ seedLastPos1

◆ seedLastPos2