#include <PredictorMfe2dHeuristicSeed.h>

Inheritance diagram for IntaRNA::PredictorMfe2dHeuristicSeed:

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Collaboration diagram for IntaRNA::PredictorMfe2dHeuristicSeed:

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Public Member Functions
	PredictorMfe2dHeuristicSeed (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker predTracker, SeedHandler seedHandler)

virtual	~PredictorMfe2dHeuristicSeed ()

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

Public Member Functions inherited from IntaRNA::PredictorMfe2dHeuristic
	PredictorMfe2dHeuristic (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker)

virtual	~PredictorMfe2dHeuristic ()

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
virtual void	traceBack (Interaction &interaction)

virtual void	fillHybridE ()

virtual void	getNextBest (Interaction &curBest)

Protected Member Functions inherited from IntaRNA::PredictorMfe2dHeuristic
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::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	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)

Protected Attributes
E2dMatrix	hybridE_seed
	the best hybridization energy including a seed for start i1,i2

SeedHandlerIdxOffset	seedHandler
	handler to generate and access seed information with idx offset

InteractionEnergyIdxOffset	energy
	access to the interaction energy handler of the super class

OutputHandler &	output
	access to the output handler of the super class

std::pair< IndexRangeList, IndexRangeList >	reportedInteractions
	access to the list of reported interaction ranges of the super class

E2dMatrix	hybridE

Protected Attributes inherited from IntaRNA::PredictorMfe2dHeuristic
E2dMatrix	hybridE
	energy of all interaction hybrids starting in i1,i2

InteractionEnergyIdxOffset	energy
	access to the interaction energy handler of the super class

OutputHandler &	output
	access to the output handler of the super class

std::pair< IndexRangeList, IndexRangeList >	reportedInteractions
	access to the list of reported interaction ranges of the super class

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

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::PredictorMfe2dHeuristic
typedef Matrix< BestInteractionE >	E2dMatrix
	matrix type to hold the mfe energies and boundaries 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

Memory efficient interaction predictor that uses both qualitative heuristics (interactions have to have a seed interaction) and performance heuristics (not all possible interactions considered)

To this end, for each interaction start i1,i2 only the optimal right side interaction with boundaries j1,j2 is considered in the recursion instead of all possible interaction ranges.

This yields a quadratic time and space complexity.

Author: Martin Mann

Constructor & Destructor Documentation

◆ PredictorMfe2dHeuristicSeed()

IntaRNA::PredictorMfe2dHeuristicSeed::PredictorMfe2dHeuristicSeed	(	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 applied

◆ ~PredictorMfe2dHeuristicSeed()

virtual IntaRNA::PredictorMfe2dHeuristicSeed::~PredictorMfe2dHeuristicSeed ( )

virtual

Member Function Documentation

◆ fillHybridE()

virtual void IntaRNA::PredictorMfe2dHeuristicSeed::fillHybridE ( )

protectedvirtual

Computes all entries of both hybridE matrices and reports all valid interactions via updateOptima()

Reimplemented from IntaRNA::PredictorMfe2dHeuristic.

◆ getNextBest()

virtual void IntaRNA::PredictorMfe2dHeuristicSeed::getNextBest ( Interaction & curBest )

protectedvirtual

Identifies the next best interaction (containing a seed) 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 from IntaRNA::PredictorMfe2dHeuristic.

◆ predict()

virtual void IntaRNA::PredictorMfe2dHeuristicSeed::predict	(	const IndexRange &	r1 = `IndexRange(0, RnaSequence::lastPos)`,
		const IndexRange &	r2 = `IndexRange(0, RnaSequence::lastPos)`
	)

virtual

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.

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::PredictorMfe2dHeuristic.

◆ traceBack()

virtual void IntaRNA::PredictorMfe2dHeuristicSeed::traceBack ( Interaction & interaction )

protectedvirtual

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

Parameters

interaction IN/OUT the interaction to fill

Reimplemented from IntaRNA::PredictorMfe2dHeuristic.

Member Data Documentation

◆ energy

InteractionEnergyIdxOffset IntaRNA::Predictor::energy

protected

access to the interaction energy handler of the super class

◆ hybridE

E2dMatrix IntaRNA::PredictorMfe2dHeuristic::hybridE

protected

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

◆ hybridE_seed

E2dMatrix IntaRNA::PredictorMfe2dHeuristicSeed::hybridE_seed

protected

the best hybridization energy including a seed for start i1,i2

◆ output

OutputHandler& IntaRNA::Predictor::output

protected

access to the output handler of the super class

◆ reportedInteractions

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

protected

access to the list of reported interaction ranges of the super class

◆ seedHandler

SeedHandlerIdxOffset IntaRNA::PredictorMfe2dHeuristicSeed::seedHandler

protected

handler to generate and access seed information with idx offset

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

src/IntaRNA/PredictorMfe2dHeuristicSeed.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PredictorMfe2dHeuristicSeed()

◆ ~PredictorMfe2dHeuristicSeed()

Member Function Documentation

◆ fillHybridE()

◆ getNextBest()

◆ predict()

◆ traceBack()

Member Data Documentation

◆ energy

◆ hybridE

◆ hybridE_seed

◆ output

◆ reportedInteractions

◆ seedHandler