IntaRNA::PredictorEvalOnly Class Reference

#include <PredictorEvalOnly.h>

Inheritance diagram for IntaRNA::PredictorEvalOnly:

Collaboration diagram for IntaRNA::PredictorEvalOnly:

Public Member Functions
	PredictorEvalOnly (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker, const std::vector< Interaction > &interactions)
void	predict (const IndexRange &r1=IndexRange(0, RnaSequence::lastPos), const IndexRange &r2=IndexRange(0, RnaSequence::lastPos)) override
Public Member Functions inherited from IntaRNA::Predictor
	Predictor (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker)
virtual	~Predictor ()
Z_type	getZall () const

Static Public Member Functions
static std::vector< Interaction >	parseInteractions (const std::string &encoding, const RnaSequence &target, const RnaSequence &query)
Static Public Member Functions inherited from IntaRNA::Predictor
static size_t	getMaxInteractionWidth (const size_t w, const size_t maxLoopSize)

Protected Member Functions
void	initOptima () override
	reset the partition function before each evaluation
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
	record an evaluated energy for the partition function and tracker
void	reportOptima () override
	forward the partition function and all evaluated structures to output
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
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

Evaluates predefined, nested intermolecular base pairs without searching. Prediction ranges and output filters are ignored. Identical structures are counted once; Zall and trackers describe only the supplied structures.

Constructor & Destructor Documentation

PredictorEvalOnly()

IntaRNA::PredictorEvalOnly::PredictorEvalOnly	(	const InteractionEnergy &	energy,
		OutputHandler &	output,
		PredictionTracker *	predTracker,
		const std::vector< Interaction > &	interactions
	)

Copies and validates the structures, discarding input energies and seeds.

Parameters

energy	the energy model; it and its sequences must outlive this object
output	the reporting destination, which must outlive this object
predTracker	optional tracker owned by this predictor
interactions	nonempty list with ascending target/descending query base-pair indices in the original, zero-based sequence coordinates

Exceptions

std::invalid_argument

for empty, incompatible or invalid structures

Member Function Documentation

initOptima()

void IntaRNA::PredictorEvalOnly::initOptima ( )

overrideprotectedvirtual

reset the partition function before each evaluation

Implements IntaRNA::Predictor.

parseInteractions()

static std::vector< Interaction > IntaRNA::PredictorEvalOnly::parseInteractions ( const std::string &  encoding, const RnaSequence &  target, const RnaSequence &  query  )

static

Parses a colon-separated list of hybridDB (start1dotbar1&start2dotbar2) encodings, including full-length encodings with flanking dots. Pairing bars are matched antiparallel. Starts use each sequence's input/output indexing.

Parameters

encoding	one or more nonempty encodings, each containing a base pair
target	the first sequence; must outlive the returned interactions
query	the second sequence in its original 5'-3' orientation

Returns

validated interactions referencing the provided sequences

Exceptions

std::invalid_argument

for malformed, out-of-bounds, unbalanced or non-complementary structures

predict()

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

overridevirtual

Evaluates all structures using initiation, loop, accessibility, dangling-end, terminal-pair and energy-shift contributions from the selected model.

Parameters

r1	ignored; every supplied interaction is evaluated
r2	ignored; every supplied interaction is evaluated

Exceptions

std::runtime_error

if the model cannot assign a finite energy

Implements IntaRNA::Predictor.

reportOptima()

void IntaRNA::PredictorEvalOnly::reportOptima ( )

overrideprotectedvirtual

forward the partition function and all evaluated structures to output

Implements IntaRNA::Predictor.

updateOptima()

void IntaRNA::PredictorEvalOnly::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

record an evaluated energy for the partition function and tracker

Implements IntaRNA::Predictor.

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

• src/IntaRNA/PredictorEvalOnly.h