#include <PredictorMfe2dSeedExtensionRIblast.h>

Inheritance diagram for IntaRNA::PredictorMfe2dSeedExtensionRIblast:

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Collaboration diagram for IntaRNA::PredictorMfe2dSeedExtensionRIblast:

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Classes
struct	ExtendedSeed

Public Member Functions
	PredictorMfe2dSeedExtensionRIblast (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker predTracker, SeedHandler seedHandler)

virtual	~PredictorMfe2dSeedExtensionRIblast ()

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

Public Member Functions inherited from IntaRNA::PredictorMfe2d
	PredictorMfe2d (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker)

virtual	~PredictorMfe2d ()

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

Public Attributes
const int	parallelDropOutLength = 5

const int	thoroughDropOutLength = 16

Protected Types
typedef PredictorMfe2d::E2dMatrix	E2dMatrix
	matrix type to hold the mfe energies for interaction site starts

Protected Types inherited from IntaRNA::PredictorMfe2d
typedef Matrix< E_type >	E2dMatrix
	matrix type to hold the mfe energies 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
virtual void	parallelExtension (ExtendedSeed &seed, const size_t max_extension1, size_t max_extension2)

void	fillHybridE_left (const size_t j1, const size_t j2)

void	fillHybridE_right (const size_t i1, const size_t i2)

virtual void	traceBack (Interaction &interaction)

void	printMatrix (const E2dMatrix &matrix)

Protected Member Functions inherited from IntaRNA::PredictorMfe2d
virtual void	fillHybridE (const size_t j1, const size_t j2, const size_t i1init, const size_t i2init, const bool callUpdateOptima)

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	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 ()

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)

E2dMatrix	hybridE_left
	energy of all interaction hybrids that start on the left side of the seed

E2dMatrix	hybridE_right
	energy of all interaction hybrids that start on the right side of the seed

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::PredictorMfe2d
E2dMatrix	hybridE_pq

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::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)

Detailed Description

Implements seed-based space-efficient interaction prediction following the ideas introduced for the RIblast approach (doi: 10.1093/bioinformatics/btx287).

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).

Author: Frank Gelhausen; Martin Raden

Member Typedef Documentation

◆ E2dMatrix

typedef PredictorMfe2d::E2dMatrix IntaRNA::PredictorMfe2dSeedExtensionRIblast::E2dMatrix

protected

matrix type to hold the mfe energies for interaction site starts

Constructor & Destructor Documentation

◆ PredictorMfe2dSeedExtensionRIblast()

IntaRNA::PredictorMfe2dSeedExtensionRIblast::PredictorMfe2dSeedExtensionRIblast	(	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

◆ ~PredictorMfe2dSeedExtensionRIblast()

virtual IntaRNA::PredictorMfe2dSeedExtensionRIblast::~PredictorMfe2dSeedExtensionRIblast ( )

virtual

data cleanup

Member Function Documentation

◆ fillHybridE_left()

void IntaRNA::PredictorMfe2dSeedExtensionRIblast::fillHybridE_left	(	const size_t	j1,
		const size_t	j2
	)

protected

Computes all entries of the hybridE matrix for interactions starting in i1 and i2 and report all valid interactions to updateOptima()

Parameters

j1	start of the interaction within seq 1
j2	start of the interaction within seq 2

◆ fillHybridE_right()

void IntaRNA::PredictorMfe2dSeedExtensionRIblast::fillHybridE_right	(	const size_t	i1,
		const size_t	i2
	)

protected

Computes all entries of the hybridE matrix for interactions starting in i1 and i2 and report all valid interactions to updateOptima()

Parameters

i1	end of the interaction within seq 1
i2	end of the interaction within seq 2

◆ parallelExtension()

virtual void IntaRNA::PredictorMfe2dSeedExtensionRIblast::parallelExtension	(	ExtendedSeed &	seed,
		const size_t	max_extension1,
		size_t	max_extension2
	)

protectedvirtual

linearly extends given seed to left and right until energy stops improving

Parameters

seed
max_extension1
max_extension2

◆ predict()

virtual void IntaRNA::PredictorMfe2dSeedExtensionRIblast::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.

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

Reimplemented from IntaRNA::PredictorMfe2d.

◆ printMatrix()

void IntaRNA::PredictorMfe2dSeedExtensionRIblast::printMatrix ( const E2dMatrix & matrix )

inlineprotected

◆ traceBack()

virtual void IntaRNA::PredictorMfe2dSeedExtensionRIblast::traceBack ( Interaction & interaction )

protectedvirtual

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::PredictorMfe2d.

Member Data Documentation

◆ energy

InteractionEnergyIdxOffset IntaRNA::Predictor::energy

protected

access to the interaction energy handler of the super class

◆ hybridE_left

E2dMatrix IntaRNA::PredictorMfe2dSeedExtensionRIblast::hybridE_left

protected

energy of all interaction hybrids that start on the left side of the seed

◆ hybridE_right

E2dMatrix IntaRNA::PredictorMfe2dSeedExtensionRIblast::hybridE_right

protected

energy of all interaction hybrids that start on the right side of the seed

◆ output

OutputHandler& IntaRNA::Predictor::output

protected

access to the output handler of the super class

◆ parallelDropOutLength

const int IntaRNA::PredictorMfe2dSeedExtensionRIblast::parallelDropOutLength = 5

◆ seedHandler

SeedHandlerIdxOffset IntaRNA::PredictorMfe2dSeedExtensionRIblast::seedHandler

protected

the seed handler (with idx offset)

◆ thoroughDropOutLength

const int IntaRNA::PredictorMfe2dSeedExtensionRIblast::thoroughDropOutLength = 16

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

src/IntaRNA/PredictorMfe2dSeedExtensionRIblast.h

Classes

Public Member Functions

Public Attributes

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ E2dMatrix

Constructor & Destructor Documentation

◆ PredictorMfe2dSeedExtensionRIblast()

◆ ~PredictorMfe2dSeedExtensionRIblast()

Member Function Documentation

◆ fillHybridE_left()

◆ fillHybridE_right()

◆ parallelExtension()

◆ predict()

◆ printMatrix()

◆ traceBack()

Member Data Documentation

◆ energy

◆ hybridE_left

◆ hybridE_right

◆ output

◆ parallelDropOutLength

◆ seedHandler

◆ thoroughDropOutLength