IntaRNA::PredictionTrackerSpotProbAll Class Reference

#include <PredictionTrackerSpotProbAll.h>

Inheritance diagram for IntaRNA::PredictionTrackerSpotProbAll:

Collaboration diagram for IntaRNA::PredictionTrackerSpotProbAll:

Public Member Functions
	PredictionTrackerSpotProbAll (const InteractionEnergy &energy, const std::string &streamName, const std::string &NA_string="NA", const std::string &sep=";")
	PredictionTrackerSpotProbAll (const InteractionEnergy &energy, std::ostream *outStream, const std::string &NA_string="NA", const std::string &sep=";")
virtual	~PredictionTrackerSpotProbAll ()
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 ()

Protected Types
typedef Matrix< Z_type >	Z2dMatrix
	matrix type to hold the partition function for each index pair

Static Protected Member Functions
static void	writeData (std::ostream &out, const Z2dMatrix &pairZ, const Z_type &overallZ, const InteractionEnergy &energy, const std::string &NA_string, const std::string &sep)

Protected Attributes
const InteractionEnergy &	energy
	energy handler used for predictions
const bool	deleteStreamsOnDestruction
	whether or not the streams are to be deleted on destruction
std::ostream *	outStream
	the stream to write the minE-data to
const std::string	NA_string
	the output string representation if a value is not available for output
const std::string	sep
	the output string representation of column separators
Z_type	overallZ
	overall partition function
Z2dMatrix	pairZ
	the index-pair-wise minimal energy values

Detailed Description

Collects for each intermolecular index pair the probability that this pair is covered by an interaction.

The pair data is written to stream on destruction.

Member Typedef Documentation

Z2dMatrix

typedef Matrix<Z_type> IntaRNA::PredictionTrackerSpotProbAll::Z2dMatrix

protected

matrix type to hold the partition function for each index pair

Constructor & Destructor Documentation

PredictionTrackerSpotProbAll() [1/2]

IntaRNA::PredictionTrackerSpotProbAll::PredictionTrackerSpotProbAll	(	const InteractionEnergy &	energy,
		const std::string &	streamName,
		const std::string &	NA_string = "NA",
		const std::string &	sep = ";"
	)

Constructs a PredictionTracker that collected for each index pair of two sequences the probability to be covered by an interaction.

Note, if a filename is provided, its stream is closed on destruction of this object!

Parameters

energy	the energy function used for energy calculation
streamName	the stream name where the data is to be written to. use STDOUT/STDERR for the respective stream. Otherwise, an according file is created (has to be non-empty)
NA_string	the output string representation if a value is not available for profile output
sep	the column separator to be used in profile output

PredictionTrackerSpotProbAll() [2/2]

IntaRNA::PredictionTrackerSpotProbAll::PredictionTrackerSpotProbAll	(	const InteractionEnergy &	energy,
		std::ostream *	outStream,
		const std::string &	NA_string = "NA",
		const std::string &	sep = ";"
	)

Constructs a PredictionTracker that collected for each index pair of two sequences the probability to be covered by an interaction.

Note, the stream is NOT closed nor deleted on destruction of this object!

Parameters

energy	the energy function used
outStream	the stream where the data is to be written to (has to be non-null)
NA_string	the output string representation if a value is not available for profile output
sep	the column separator to be used in profile output

~PredictionTrackerSpotProbAll()

virtual IntaRNA::PredictionTrackerSpotProbAll::~PredictionTrackerSpotProbAll ( )

virtual

destruction: write the profile(s) to the according streams.

Member Function Documentation

updateOptimumCalled()

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

virtual

Updates the partition function 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.

writeData()

static void IntaRNA::PredictionTrackerSpotProbAll::writeData ( std::ostream &  out, const Z2dMatrix &  pairZ, const Z_type &  overallZ, const InteractionEnergy &  energy, const std::string &  NA_string, const std::string &  sep  )

staticprotected

Writes profile data to stream.

Parameters

out	the output stream to write to
pairZ	the partition function data to write
overallZ	the overall partition function for pairZ
energy	the energy function used
NA_string	the string to be used for missing entries
sep	the column separator to be used in profile output

Member Data Documentation

deleteStreamsOnDestruction

const bool IntaRNA::PredictionTrackerSpotProbAll::deleteStreamsOnDestruction

protected

whether or not the streams are to be deleted on destruction

energy

const InteractionEnergy& IntaRNA::PredictionTrackerSpotProbAll::energy

protected

energy handler used for predictions

NA_string

const std::string IntaRNA::PredictionTrackerSpotProbAll::NA_string

protected

the output string representation if a value is not available for output

outStream

std::ostream* IntaRNA::PredictionTrackerSpotProbAll::outStream

protected

the stream to write the minE-data to

overallZ

Z_type IntaRNA::PredictionTrackerSpotProbAll::overallZ

protected

overall partition function

pairZ

Z2dMatrix IntaRNA::PredictionTrackerSpotProbAll::pairZ

protected

the index-pair-wise minimal energy values

sep

const std::string IntaRNA::PredictionTrackerSpotProbAll::sep

protected

the output string representation of column separators

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

• src/IntaRNA/PredictionTrackerSpotProbAll.h