#include <PredictionTrackerProfileSpotProb.h>

Inheritance diagram for IntaRNA::PredictionTrackerProfileSpotProb:

Collaboration diagram for IntaRNA::PredictionTrackerProfileSpotProb:

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Public Member Functions
	PredictionTrackerProfileSpotProb (const InteractionEnergy &energy, const std::string &seq1streamName, const std::string &seq2streamName, const std::string &NA_string="NA", const std::string &sep=";")

	PredictionTrackerProfileSpotProb (const InteractionEnergy &energy, std::ostream seq1stream, std::ostream seq2stream, const std::string &NA_string="NA", const std::string &sep=";")

virtual	~PredictionTrackerProfileSpotProb ()

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 std::vector< Z_type >	ZProfile
	container definition for partition function profile data

Static Protected Member Functions
static void	updateProfile (ZProfile &profile, const size_t i, const size_t j, const Z_type boltzmannWeight)

template<typename ZProfileIterator >
static void	writeProfile (std::ostream &out, const ZProfileIterator &begin, const ZProfileIterator &end, const Z_type overallZ, const RnaSequence &rna, 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 *	seq1stream
	if non-NULL, the stream to write the spotProb-profile for seq1 to

std::ostream *	seq2stream
	if non-NULL, the stream to write the spotProb-profile for seq2 to

const std::string	NA_string
	the output string representation if a value is not available for profile output

const std::string	sep
	the output string representation of a column separator

ZProfile	seq1Z
	the position-wise partition function values for seq1

ZProfile	seq2Z
	the position-wise partition function values for seq2

Z_type	overallZ
	the overall partition function to be used for normalization

Detailed Description

Collects for each sequence position the partition function of any interaction enclosing this position.

The profile(s) of this information (normalized by the overall partitions function; ie the spot interaction probability) is written to stream on destruction.

Member Typedef Documentation

◆ ZProfile

typedef std::vector<Z_type> IntaRNA::PredictionTrackerProfileSpotProb::ZProfile

protected

container definition for partition function profile data

Constructor & Destructor Documentation

◆ PredictionTrackerProfileSpotProb() [1/2]

IntaRNA::PredictionTrackerProfileSpotProb::PredictionTrackerProfileSpotProb	(	const InteractionEnergy &	energy,
		const std::string &	seq1streamName,
		const std::string &	seq2streamName,
		const std::string &	NA_string = `"NA"`,
		const std::string &	sep = `";"`
	)

Constructs a PredictionTracker that collects for each positions of a sequence the partition function and thus spot probability of any interaction enclosing this position.

Parameters

energy	the energy function used for energy calculation
seq1streamName	the stream name where the profile data for seq1 is to be written to. use STDOUT/STDERR for the respective stream. Otherwise, an according file is created; if empty, no data for seq1 is collected
seq2streamName	the stream name where the profile data for seq2 is to be written to. use STDOUT/STDERR for the respective stream. Otherwise, an according file is created; if empty, no data for seq2 is collected
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

◆ PredictionTrackerProfileSpotProb() [2/2]

IntaRNA::PredictionTrackerProfileSpotProb::PredictionTrackerProfileSpotProb	(	const InteractionEnergy &	energy,
		std::ostream *	seq1stream,
		std::ostream *	seq2stream,
		const std::string &	NA_string = `"NA"`,
		const std::string &	sep = `";"`
	)

Constructs an PredictionTracker that collected for each positions of a sequence the partition function and thus spot probability of any interaction covering this position.

Parameters

energy	the energy function used
seq1stream	if non-NULL, the stream where the profile data for seq1 is to be written to; if NULL, no data for seq1 is collected
seq2stream	if non-NULL, the stream where the profile data for seq2 is to be written to; if NULL, no data for seq2 is collected
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

◆ ~PredictionTrackerProfileSpotProb()

virtual IntaRNA::PredictionTrackerProfileSpotProb::~PredictionTrackerProfileSpotProb ( )

virtual

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

Member Function Documentation

◆ updateOptimumCalled()

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

virtual

Updates the profile 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.

◆ updateProfile()

static void IntaRNA::PredictionTrackerProfileSpotProb::updateProfile	(	ZProfile &	profile,
		const size_t	i,
		const size_t	j,
		const Z_type	boltzmannWeight
	)

staticprotected

Updates a given partition function profile if not empty.

Parameters

profile	the partition function profile to update
i	the first index to update (inclusive)
j	the last index to update (inclusive)
boltzmannWeight	the Boltzmann weight to be used for the update

◆ writeProfile()

template<typename ZProfileIterator >

void IntaRNA::PredictionTrackerProfileSpotProb::writeProfile	(	std::ostream &	out,
		const ZProfileIterator &	begin,
		const ZProfileIterator &	end,
		const Z_type	overallZ,
		const RnaSequence &	rna,
		const std::string &	NA_string,
		const std::string &	sep
	)

inlinestaticprotected

Writes profile data to stream.

Parameters

out	the output stream to write to
begin	the begin iterator of the partition function data to write
end	the end iterator (exclusive) of the Z data to write
overallZ	the overall partition function to be used for normalization
rna	the RNA the data is about
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::PredictionTrackerProfileSpotProb::deleteStreamsOnDestruction

protected

whether or not the streams are to be deleted on destruction

◆ energy

const InteractionEnergy& IntaRNA::PredictionTrackerProfileSpotProb::energy

protected

energy handler used for predictions

◆ NA_string

const std::string IntaRNA::PredictionTrackerProfileSpotProb::NA_string

protected

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

◆ overallZ

Z_type IntaRNA::PredictionTrackerProfileSpotProb::overallZ

protected

the overall partition function to be used for normalization

◆ sep

const std::string IntaRNA::PredictionTrackerProfileSpotProb::sep

protected

the output string representation of a column separator

◆ seq1stream

std::ostream* IntaRNA::PredictionTrackerProfileSpotProb::seq1stream

protected

if non-NULL, the stream to write the spotProb-profile for seq1 to

◆ seq1Z

ZProfile IntaRNA::PredictionTrackerProfileSpotProb::seq1Z

protected

the position-wise partition function values for seq1

◆ seq2stream

std::ostream* IntaRNA::PredictionTrackerProfileSpotProb::seq2stream

protected

if non-NULL, the stream to write the spotProb-profile for seq2 to

◆ seq2Z

ZProfile IntaRNA::PredictionTrackerProfileSpotProb::seq2Z

protected

the position-wise partition function values for seq2

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

src/IntaRNA/PredictionTrackerProfileSpotProb.h

Public Member Functions

Protected Types

Static Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ ZProfile

Constructor & Destructor Documentation

◆ PredictionTrackerProfileSpotProb() [1/2]

◆ PredictionTrackerProfileSpotProb() [2/2]

◆ ~PredictionTrackerProfileSpotProb()

Member Function Documentation

◆ updateOptimumCalled()

◆ updateProfile()

◆ writeProfile()

Member Data Documentation

◆ deleteStreamsOnDestruction

◆ energy

◆ NA_string

◆ overallZ

◆ sep

◆ seq1stream

◆ seq1Z

◆ seq2stream

◆ seq2Z