IntaRNA::PredictorSeedExtensionKinetic Class Reference

#include <PredictorSeedExtensionKinetic.h>

Inheritance diagram for IntaRNA::PredictorSeedExtensionKinetic:

Collaboration diagram for IntaRNA::PredictorSeedExtensionKinetic:

Public Member Functions
	PredictorSeedExtensionKinetic (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker, SeedHandler *seedHandler, const char score='A')
virtual	~PredictorSeedExtensionKinetic ()
void	predict (const IndexRange &r1=IndexRange(0, RnaSequence::lastPos), const IndexRange &r2=IndexRange(0, RnaSequence::lastPos)) override
Public Member Functions inherited from IntaRNA::PredictorMfe
	PredictorMfe (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker)
virtual	~PredictorMfe ()
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	traceBack (Interaction &interaction) override
void	getNextBest (Interaction &interaction) override
Protected Member Functions inherited from IntaRNA::PredictorMfe
virtual void	initOptima ()
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)
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 ()
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)

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
Protected Attributes inherited from IntaRNA::PredictorMfe
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

Detailed Description

Deterministic, strictly downhill extension of every feasible seed.

At each step both ends compete using the complete interaction-energy difference, including accessibility, terminal penalties and both weighted dangling ends. Score A uses this difference directly; B divides by 1+s1+s2; C (C1) divides by 1+2*max(s1,s2). These are heuristic move rankings, not physical rates or a calibrated folding-time model. Only negative energy differences are accepted, including for the normalized scores.

Extensions always add one stacked pair or two stacked pairs, including across a loop. Seeds and their energies are trusted as supplied by the seed handler, even when an explicit seed contains lonely pairs. Ties prefer left, smaller s1+s2, smaller s1, then the single-pair move. Every valid visited prefix is eligible for normal MFE/suboptimal reporting; traceback reproduces the actual greedy path. Equilibrium partition-function output is unsupported.

Candidate enumeration uses the active energy model and separate loop/span limits for both RNAs. Every feasible move is evaluated with its complete energy change.

Constructor & Destructor Documentation

PredictorSeedExtensionKinetic()

IntaRNA::PredictorSeedExtensionKinetic::PredictorSeedExtensionKinetic	(	const InteractionEnergy &	energy,
		OutputHandler &	output,
		PredictionTracker *	predTracker,
		SeedHandler *	seedHandler,
		const char	score = 'A'
	)

Constructs a predictor, taking ownership of tracker and seed handler.

Parameters

energy	energy model, which must outlive this predictor
output	output handler, which must outlive this predictor
predTracker	owned tracker, or NULL
seedHandler	owned, non-NULL seed handler
score	move ranking: A, B, or C (the C1 formula)

Exceptions

std::invalid_argument

for a NULL seed handler, unknown score or output requiring an equilibrium partition function

~PredictorSeedExtensionKinetic()

virtual IntaRNA::PredictorSeedExtensionKinetic::~PredictorSeedExtensionKinetic ( )

virtual

Frees the owned seed handler and prediction tracker.

Member Function Documentation

getNextBest()

void IntaRNA::PredictorSeedExtensionKinetic::getNextBest ( Interaction &  interaction )

overrideprotectedvirtual

Finds the best cached prefix disjoint from already reported intervals.

Parameters

interaction

current report, replaced by the next report or E_INF

Reimplemented from IntaRNA::PredictorMfe.

predict()

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

overridevirtual

Extends all feasible seeds within inclusive, zero-based sequence ranges. Sequence 2 uses the reversed indexing of the energy model. Repeated calls reset all trajectories, cached output and index offsets.

Parameters

r1	permitted range in sequence 1
r2	permitted range in reversed sequence 2

Exceptions

std::invalid_argument

for an invalid or empty input range

Implements IntaRNA::Predictor.

traceBack()

void IntaRNA::PredictorSeedExtensionKinetic::traceBack ( Interaction &  interaction )

overrideprotectedvirtual

Restores the exact stored greedy path and annotates its contained seeds.

Parameters

interaction

interaction boundaries to expand

Implements IntaRNA::PredictorMfe.

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

• src/IntaRNA/PredictorSeedExtensionKinetic.h