IntaRNA::PredictionTrackerSpotProb Class Reference

#include <PredictionTrackerSpotProb.h>

Inheritance diagram for IntaRNA::PredictionTrackerSpotProb:

Collaboration diagram for IntaRNA::PredictionTrackerSpotProb:

Classes
class	Spot

Public Member Functions
	PredictionTrackerSpotProb (const InteractionEnergy &energy, const std::string &spots, const std::string &outStreamName, const std::string &sep=";")
	PredictionTrackerSpotProb (const InteractionEnergy &energy, const std::string &spots, std::ostream &outStream, const std::string &sep=";")
virtual	~PredictionTrackerSpotProb ()
virtual void	updateOptimumCalled (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const E_type energy)
Public Member Functions inherited from IntaRNA::PredictionTracker
	PredictionTracker ()
virtual	~PredictionTracker ()

Static Public Attributes
static const std::string	str_spot
	regex string encoding of a single spot string encoding
static const boost::regex	regexSpotString
	regex to match a valid list of spot encodings

Protected Member Functions
Spot	fromString (std::string &&spotString)

Protected Attributes
const InteractionEnergy &	energy
	energy handler used for predictions
std::ostream *	outStream
	the stream to write the probabilities to
const bool	deleteOutStream
	whether or not outStream is to be deleted on destruction
std::vector< Spot >	spots
	tracking information for each spot
const std::string	sep
	the output column separator to be used
Z_type	noSpotZ
	partition function of all interaction not covering a tracked spot
Z_type	overallZ
	overall partition function of all reported interactions

Detailed Description

Computes probability estimations that a given set of interaction spots are covered by an interaction. Furthermore it computes the probability that none of the targeted spots is covered by an interaction.

The information is written to stream on destruction.

Constructor & Destructor Documentation

PredictionTrackerSpotProb() [1/2]

IntaRNA::PredictionTrackerSpotProb::PredictionTrackerSpotProb	(	const InteractionEnergy &	energy,
		const std::string &	spots,
		const std::string &	outStreamName,
		const std::string &	sep = ";"
	)

Constructs a PredictionTracker that collects probability information for a set of interaction spots by computing the Boltzmann probability of any interaction enclosing the positions.

Parameters

energy	the energy function used for energy calculation
spots	the interaction spots to track for their probabilities
outStreamName	the stream name where the probability data is to be written to. use STDOUT/STDERR for the respective stream. Otherwise, an according file is created
sep	the column separator to be used in profile output

PredictionTrackerSpotProb() [2/2]

IntaRNA::PredictionTrackerSpotProb::PredictionTrackerSpotProb	(	const InteractionEnergy &	energy,
		const std::string &	spots,
		std::ostream &	outStream,
		const std::string &	sep = ";"
	)

Constructs a PredictionTracker that collects probability information for a set of interaction spots by computing the Boltzmann probability of any interaction enclosing the positions.

Parameters

energy	the energy function used for energy calculation
spots	the interaction spots to track for their probabilities
outStream	the stream where the probability data is to be written to.
sep	the column separator to be used in profile output

~PredictionTrackerSpotProb()

virtual IntaRNA::PredictionTrackerSpotProb::~PredictionTrackerSpotProb ( )

virtual

destruction: write the probabilities to stream.

Member Function Documentation

fromString()

Spot IntaRNA::PredictionTrackerSpotProb::fromString ( std::string &&  spotString )

protected

Creates spot information from string encoding

Parameters

spotString

the string to decode

Returns

the respective Spot object

updateOptimumCalled()

virtual void IntaRNA::PredictionTrackerSpotProb::updateOptimumCalled ( const size_t  i1, const size_t  j1, const size_t  i2, const size_t  j2, const E_type  energy  )

virtual

Updates the probability information for each Predictor.updateOptima() call.

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
energy	the overall energy of the interaction site

Implements IntaRNA::PredictionTracker.

Member Data Documentation

deleteOutStream

const bool IntaRNA::PredictionTrackerSpotProb::deleteOutStream

protected

whether or not outStream is to be deleted on destruction

energy

const InteractionEnergy& IntaRNA::PredictionTrackerSpotProb::energy

protected

energy handler used for predictions

noSpotZ

Z_type IntaRNA::PredictionTrackerSpotProb::noSpotZ

protected

partition function of all interaction not covering a tracked spot

outStream

std::ostream* IntaRNA::PredictionTrackerSpotProb::outStream

protected

the stream to write the probabilities to

overallZ

Z_type IntaRNA::PredictionTrackerSpotProb::overallZ

protected

overall partition function of all reported interactions

regexSpotString

const boost::regex IntaRNA::PredictionTrackerSpotProb::regexSpotString

static

regex to match a valid list of spot encodings

sep

const std::string IntaRNA::PredictionTrackerSpotProb::sep

protected

the output column separator to be used

spots

std::vector<Spot> IntaRNA::PredictionTrackerSpotProb::spots

protected

tracking information for each spot

str_spot

const std::string IntaRNA::PredictionTrackerSpotProb::str_spot

static

regex string encoding of a single spot string encoding

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

• src/IntaRNA/PredictionTrackerSpotProb.h