#include <PredictorMfe.h>

Inheritance diagram for IntaRNA::PredictorMfe:

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Collaboration diagram for IntaRNA::PredictorMfe:

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Classes
class	BestInteraction

Public Member Functions
	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 ()

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

Z_type	getZall () const

Protected Types
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
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	traceBack (Interaction &interaction)=0

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)

virtual void	reportOptima () override

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
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

Generic Predictor interface for MFE interaction computation to avoid code redundancy

Author: Martin Mann

Member Typedef Documentation

◆ BestInteractionE

typedef BestInteraction<E_type> IntaRNA::PredictorMfe::BestInteractionE

protected

BestInteraction that stores an energy value.

◆ BestInteractionZ

typedef BestInteraction<Z_type> IntaRNA::PredictorMfe::BestInteractionZ

protected

BestInteraction that stores a partition function value.

◆ HashIdx2E

typedef boost::unordered_map< Interaction::BasePair, BestInteractionE, Interaction::BasePair::Hash > IntaRNA::PredictorMfe::HashIdx2E

protected

hash to map index pairs to BestInteractionE entries

◆ InteractionList

typedef std::list<Interaction> IntaRNA::PredictorMfe::InteractionList

protected

list of interactions

Constructor & Destructor Documentation

◆ PredictorMfe()

IntaRNA::PredictorMfe::PredictorMfe	(	const InteractionEnergy &	energy,
		OutputHandler &	output,
		PredictionTracker *	predTracker
	)

Construction call the super constructor

Parameters

energy	the interaction energy handler
output	the output handler to report optimal 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.

◆ ~PredictorMfe()

virtual IntaRNA::PredictorMfe::~PredictorMfe ( )

overridevirtual

Member Function Documentation

◆ getNextBest()

virtual void IntaRNA::PredictorMfe::getNextBest ( Interaction & curBest )

protectedvirtual

Identifies the next best interaction with an energy equal to or higher than the given interaction. The new interaction will not overlap any index range stored in reportedInteractions.

Parameters

curBest IN/OUT the current best interaction to be replaced with one of equal or higher energy not overlapping with any reported interaction so far; an interaction with energy E_INF is set, if there is no better interaction left

Reimplemented in IntaRNA::PredictorMfe2dHelixBlockHeuristic, IntaRNA::PredictorMfe2dHelixBlockHeuristicSeed, IntaRNA::PredictorMfe2dHeuristic, IntaRNA::PredictorMfe2dHeuristicSeed, and IntaRNA::PredictorSeedExtensionKinetic.

◆ initOptima()

virtual void IntaRNA::PredictorMfe::initOptima ( )

overrideprotectedvirtual

Initializes the global energy minimum storage

Implements IntaRNA::Predictor.

◆ initSeedCandidates()

void IntaRNA::PredictorMfe::initSeedCandidates ( )

protected

Initialize local selection, or use a caller's shared regional collector.

◆ isValidOutputSite()

bool IntaRNA::PredictorMfe::isValidOutputSite	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2
	)		const

protected

Checks terminal GU and accessibility constraints for a complete site. Recursion cells may be useful extensions without being valid output sites.

Parameters

i1	inclusive start in sequence 1, relative to the energy offset
j1	inclusive end in sequence 1, relative to the energy offset
i2	inclusive start in reversed sequence 2, relative to its offset
j2	inclusive end in reversed sequence 2, relative to its offset

Returns: whether both terminal pairs and ED penalties satisfy output limits

◆ predictPerSeed()

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

protectedvirtual

Predict independently with each admitted seed, preserving this mode's recurrences and qualifying traceback. Statistics/trackers use one ordinary prediction; seed-specific passes do not contribute to them.

Parameters

r1	target region in original coordinates
r2	reversed-query region in original coordinates
seeds	owned seed wrapper of this predictor
factory	constructs this predictor type, owning the supplied tracker and seed adapter; children have per-seed selection disabled

Returns: true if positive-quota prediction was handled completely

Exceptions

std::logic_error if a custom predictor subclass does not override this hook to supply a factory preserving its custom recurrences

◆ reportOptima()

virtual void IntaRNA::PredictorMfe::reportOptima ( )

overrideprotectedvirtual

Calls for the stored mfe and suboptimal solutions traceBack(i) and pushes the according interactions to the output handler. For non-overlapping interaction enumeration, getNextBest() is called iteratively.

Implements IntaRNA::Predictor.

Reimplemented in IntaRNA::PredictorMfeEns.

◆ traceBack()

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

protectedpure virtual

Fills a given interaction (boundaries given) with the according hybridizing base pairs. Note, the

Parameters

interaction IN/OUT the interaction to fill

Implemented in IntaRNA::PredictorMfe2d, IntaRNA::PredictorMfe2dHelixBlockHeuristic, IntaRNA::PredictorMfe2dHelixBlockHeuristicSeed, IntaRNA::PredictorMfe2dHeuristic, IntaRNA::PredictorMfe2dHeuristicSeed, IntaRNA::PredictorMfe2dSeed, IntaRNA::PredictorMfe2dSeedExtension, IntaRNA::PredictorMfe2dSeedExtensionRIblast, IntaRNA::PredictorMfeEns, IntaRNA::PredictorMfeEns2dSeedExtension, IntaRNA::PredictorMfeEnsSeedOnly, IntaRNA::PredictorMfeSeedOnly, and IntaRNA::PredictorSeedExtensionKinetic.

◆ updateMfe4leftEnd()

virtual void IntaRNA::PredictorMfe::updateMfe4leftEnd	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2,
		const Interaction &	curInteraction
	)

protectedvirtual

Updates the mfe4leftEnd data container.

Overwrite, if no update is to be done.

Parameters

i1	interaction start in seq1
j1	interaction end in seq1
i2	interaction start in seq2
i2	interaction end in seq2
curInteraction	the interaction information to be used for update

Reimplemented in IntaRNA::PredictorMfe2dHelixBlockHeuristic, and IntaRNA::PredictorMfe2dHeuristic.

◆ updateOptima()

virtual void IntaRNA::PredictorMfe::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
	)

overrideprotectedvirtual

updates the global optimum to be the mfe interaction 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
energy	the energy of the interaction
isHybridE	whether or not the given energy is only the hybridization energy (init+loops) or the total interaction energy
incrementZall	whether or not Zall is to be incremented (if needed)

Implements IntaRNA::Predictor.

Member Data Documentation

◆ energy

InteractionEnergyIdxOffset IntaRNA::Predictor::energy

protected

access to the interaction energy handler of the super class

◆ mfe4leftEnd

HashIdx2E IntaRNA::PredictorMfe::mfe4leftEnd

protected

if non-overlapping output is required, this data structure is filled to find non-overlapping interactions

◆ mfeInteractions

InteractionList IntaRNA::PredictorMfe::mfeInteractions

protected

mfe interaction boundaries

◆ output

OutputHandler& IntaRNA::Predictor::output

protected

access to the output handler of the super class

◆ ownedSeedCandidates

std::unique_ptr<OutputHandlerSeedCandidates> IntaRNA::PredictorMfe::ownedSeedCandidates

protected

Local collector for API callers that do not provide a regional collector.

◆ perSeedPass

bool IntaRNA::PredictorMfe::perSeedPass = false

protected

Enforce complete-site spans before ranking a seed-constrained child pass.

◆ predTracker

PredictionTracker* IntaRNA::Predictor::predTracker

protected

access to the prediction tracker of the super class

◆ reportedInteractions

std::pair< IndexRangeList, IndexRangeList > IntaRNA::PredictorMfe::reportedInteractions

protected

index ranges of reported interactions to identify non-overlapping interactions (first = seq1, second = seq2) NOTE: the indices for seq2 are reversed

◆ seedCandidates

OutputHandlerSeedCandidates* IntaRNA::PredictorMfe::seedCandidates = nullptr

protected

Active collector; null on the unchanged default path.

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

src/IntaRNA/PredictorMfe.h

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ BestInteractionE

◆ BestInteractionZ

◆ HashIdx2E

◆ InteractionList

Constructor & Destructor Documentation

◆ PredictorMfe()

◆ ~PredictorMfe()

Member Function Documentation

◆ getNextBest()

◆ initOptima()

◆ initSeedCandidates()

◆ isValidOutputSite()

◆ predictPerSeed()

◆ reportOptima()

◆ traceBack()

◆ updateMfe4leftEnd()

◆ updateOptima()

Member Data Documentation

◆ energy

◆ mfe4leftEnd

◆ mfeInteractions

◆ output

◆ ownedSeedCandidates

◆ perSeedPass

◆ predTracker

◆ reportedInteractions

◆ seedCandidates