#include <PredictorMfeEns.h>

Inheritance diagram for IntaRNA::PredictorMfeEns:

[legend]

Collaboration diagram for IntaRNA::PredictorMfeEns:

[legend]

Classes
struct	ZPartition
	data container to encode a site with respective partition function More...

Public Member Functions
	PredictorMfeEns (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker)

virtual	~PredictorMfeEns ()

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 ()

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

Z_type	getZall () const

Protected Member Functions
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 ()

virtual void	traceBack (Interaction &interaction)

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)

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
std::unordered_map< Interaction::Boundary, Z_type, Interaction::Boundary::Hash >	Z_partition
	map storing the partition of Zall for all considered interaction sites

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
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

Generic Predictor interface for ensemble-based MFE interaction computation

Author: Martin Raden

Constructor & Destructor Documentation

◆ PredictorMfeEns()

IntaRNA::PredictorMfeEns::PredictorMfeEns	(	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.

◆ ~PredictorMfeEns()

virtual IntaRNA::PredictorMfeEns::~PredictorMfeEns ( )

virtual

Member Function Documentation

◆ initZ()

virtual void IntaRNA::PredictorMfeEns::initZ ( )

protectedvirtual

Initializes the hybridization partition functions. Will be called by predict().

◆ reportOptima()

virtual void IntaRNA::PredictorMfeEns::reportOptima ( )

protectedvirtual

Calls for the stored Z_partition information updateOptima() before calling reportOptima() from its super class.

Reimplemented from IntaRNA::PredictorMfe.

◆ traceBack()

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

protectedvirtual

Reports interaction boundaries only (no base pair tracking)

Parameters

interaction the interaction to be traced

Implements IntaRNA::PredictorMfe.

Reimplemented in IntaRNA::PredictorMfeEns2dSeedExtension, and IntaRNA::PredictorMfeEnsSeedOnly.

◆ updateCompleteZ()

void IntaRNA::PredictorMfeEns::updateCompleteZ	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2,
		const Z_type	partFunct,
		const bool	isHybridZ
	)

protected

Consumes a complete partition for one interaction boundary. Exact 2D prediction finalizes each boundary once and therefore does not need to retain it until reportOptima(). The virtual updateZ() hook is called so subclasses can observe or alter the update; overrides that delegate to the base implementation inherit streaming. Tracker-enabled predictions retain the partition so their established callback timing and ordering stay intact.

◆ updateZ()

virtual void IntaRNA::PredictorMfeEns::updateZ	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2,
		const Z_type	partFunct,
		const bool	isHybridZ
	)

protectedvirtual

Updates the local hybridization partition functions as well as Zall.

Note: avoid other Zall updates via updateOptima(.., incrementZall=false)!

Note: if called multiple time for the same boundaries then the reported partition functions have to represent disjoint interaction sets!

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
partFunct	the partition function of the interaction
isHybridZ	whether or not the given Z is only covering hybridization energy terms (init+loops) or the total interaction energy

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

◆ predTracker

PredictionTracker* IntaRNA::Predictor::predTracker

protected

access to the prediction tracker of the super class

◆ updateZisComplete

bool IntaRNA::PredictorMfeEns::updateZisComplete

protected

whether updateZ() currently receives one complete boundary partition

◆ Z_partition

std::unordered_map<Interaction::Boundary, Z_type, Interaction::Boundary::Hash> IntaRNA::PredictorMfeEns::Z_partition

protected

map storing the partition of Zall for all considered interaction sites

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

src/IntaRNA/PredictorMfeEns.h

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PredictorMfeEns()

◆ ~PredictorMfeEns()

Member Function Documentation

◆ initZ()

◆ reportOptima()

◆ traceBack()

◆ updateCompleteZ()

◆ updateZ()

Member Data Documentation

◆ energy

◆ output

◆ predTracker

◆ updateZisComplete

◆ Z_partition