IntaRNA::PredictionTrackerPairMinE Class Reference

#include <PredictionTrackerPairMinE.h>

Inheritance diagram for IntaRNA::PredictionTrackerPairMinE:

Collaboration diagram for IntaRNA::PredictionTrackerPairMinE:

Public Member Functions
	PredictionTrackerPairMinE (const InteractionEnergy &energy, const std::string &streamName, const std::string &E_INF_string="NA", const std::string &sep=";")
	PredictionTrackerPairMinE (const InteractionEnergy &energy, std::ostream *outStream, const std::string &E_INF_string="NA", const std::string &sep=";")
virtual	~PredictionTrackerPairMinE ()
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< E_type >	E2dMatrix
	matrix type to hold the mfe energies and boundaries for interaction site starts

Static Protected Member Functions
static void	writeData (std::ostream &out, const E2dMatrix &pairMinE, const InteractionEnergy &energy, const std::string &E_INF_string, const std::string &sep_string)

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	E_INF_string
	the output string representation of E_INF values in the profile output
const std::string	sep_string
	the output string representation of column separators
E2dMatrix	pairMinE
	the index-pair-wise minimal energy values

Detailed Description

Collects for each intermolecular index pair the minimal energy of any interaction covering this pair (even if not forming a base pair).

The pair data is written to stream on destruction.

Member Typedef Documentation

E2dMatrix

typedef Matrix<E_type> IntaRNA::PredictionTrackerPairMinE::E2dMatrix

protected

matrix type to hold the mfe energies and boundaries for interaction site starts

Constructor & Destructor Documentation

PredictionTrackerPairMinE() [1/2]

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

Constructs a PredictionTracker that collected for index pair of two sequences the minimal energy of any interaction covering this position.

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)
E_INF_string	the output string representation of E_INF values in the profile output
sep	the column separator to be used in profile output

PredictionTrackerPairMinE() [2/2]

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

Constructs a PredictionTracker that collected for index pair of two sequences the minimal energy of any interaction covering this position.

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)
E_INF_string	the output string representation of E_INF values in the profile output
sep	the column separator to be used in profile output

~PredictionTrackerPairMinE()

virtual IntaRNA::PredictionTrackerPairMinE::~PredictionTrackerPairMinE ( )

virtual

destruction: write the pair information to the according stream.

Member Function Documentation

updateOptimumCalled()

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

virtual

Updates the minE 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::PredictionTrackerPairMinE::writeData ( std::ostream &  out, const E2dMatrix &  pairMinE, const InteractionEnergy &  energy, const std::string &  E_INF_string, const std::string &  sep_string  )

staticprotected

Writes minE data to stream.

Parameters

out	the output stream to write to
pairMinE	the minE data to write
energy	the energy function used
E_INF_string	the string to be used for E_INF entries
sep_string	the output string representation of column separators

Member Data Documentation

deleteStreamsOnDestruction

const bool IntaRNA::PredictionTrackerPairMinE::deleteStreamsOnDestruction

protected

whether or not the streams are to be deleted on destruction

E_INF_string

const std::string IntaRNA::PredictionTrackerPairMinE::E_INF_string

protected

the output string representation of E_INF values in the profile output

energy

const InteractionEnergy& IntaRNA::PredictionTrackerPairMinE::energy

protected

energy handler used for predictions

outStream

std::ostream* IntaRNA::PredictionTrackerPairMinE::outStream

protected

the stream to write the minE-data to

pairMinE

E2dMatrix IntaRNA::PredictionTrackerPairMinE::pairMinE

protected

the index-pair-wise minimal energy values

sep_string

const std::string IntaRNA::PredictionTrackerPairMinE::sep_string

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/PredictionTrackerPairMinE.h