#include <PredictionTrackerProfileMinE.h>

Inheritance diagram for IntaRNA::PredictionTrackerProfileMinE:

Collaboration diagram for IntaRNA::PredictionTrackerProfileMinE:

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

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

virtual	~PredictionTrackerProfileMinE ()

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< E_type >	MinEProfile
	container definition for minE profile data

Static Protected Member Functions
static void	updateProfile (MinEProfile &profile, const size_t i, const size_t j, const E_type E)

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

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

MinEProfile	seq1minE
	the position-wise minimal energy values for seq1

MinEProfile	seq2minE
	the position-wise minimal energy values for seq2

Detailed Description

Collects for each sequence position the minimal energy of any interaction enclosing this position.

The profile(s) of this information is written to stream on destruction.

Member Typedef Documentation

◆ MinEProfile

typedef std::vector<E_type> IntaRNA::PredictionTrackerProfileMinE::MinEProfile

protected

container definition for minE profile data

Constructor & Destructor Documentation

◆ PredictionTrackerProfileMinE() [1/2]

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

Constructs a PredictionTracker that collects for each positions of a sequence the minimal energy 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
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

◆ PredictionTrackerProfileMinE() [2/2]

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

Constructs an PredictionTracker that collected for each positions of a sequence the minimal energy 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
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

◆ ~PredictionTrackerProfileMinE()

virtual IntaRNA::PredictionTrackerProfileMinE::~PredictionTrackerProfileMinE ( )

virtual

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

Member Function Documentation

◆ updateOptimumCalled()

virtual void IntaRNA::PredictionTrackerProfileMinE::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::PredictionTrackerProfileMinE::updateProfile	(	MinEProfile &	profile,
		const size_t	i,
		const size_t	j,
		const E_type	E
	)

staticprotected

Updates a given minE profile if not empty.

Parameters

profile	the minE profile to update
i	the first index to update (inclusive)
j	the last index to update (inclusive)
E	the energy to be used for the update

◆ writeProfile()

template<typename MinEProfileIterator >

void IntaRNA::PredictionTrackerProfileMinE::writeProfile	(	std::ostream &	out,
		const MinEProfileIterator &	begin,
		const MinEProfileIterator &	end,
		const RnaSequence &	rna,
		const std::string &	E_INF_string,
		const std::string &	sep_string
	)

inlinestaticprotected

Writes profile data to stream.

Parameters

out	the output stream to write to
begin	the begin iterator of the minE data to write
end	the end iterator (exclusive) of the minE data to write
rna	the RNA the data is about
E_INF_string	the string to be used for E_INF entries

Member Data Documentation

◆ deleteStreamsOnDestruction

const bool IntaRNA::PredictionTrackerProfileMinE::deleteStreamsOnDestruction

protected

whether or not the streams are to be deleted on destruction

◆ E_INF_string

const std::string IntaRNA::PredictionTrackerProfileMinE::E_INF_string

protected

the output string representation of E_INF values in the profile output

◆ energy

const InteractionEnergy& IntaRNA::PredictionTrackerProfileMinE::energy

protected

energy handler used for predictions

◆ sep_string

const std::string IntaRNA::PredictionTrackerProfileMinE::sep_string

protected

the output string representation of column separators

◆ seq1minE

MinEProfile IntaRNA::PredictionTrackerProfileMinE::seq1minE

protected

the position-wise minimal energy values for seq1

◆ seq1stream

std::ostream* IntaRNA::PredictionTrackerProfileMinE::seq1stream

protected

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

◆ seq2minE

MinEProfile IntaRNA::PredictionTrackerProfileMinE::seq2minE

protected

the position-wise minimal energy values for seq2

◆ seq2stream

std::ostream* IntaRNA::PredictionTrackerProfileMinE::seq2stream

protected

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

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

src/IntaRNA/PredictionTrackerProfileMinE.h

Public Member Functions

Protected Types

Static Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ MinEProfile

Constructor & Destructor Documentation

◆ PredictionTrackerProfileMinE() [1/2]

◆ PredictionTrackerProfileMinE() [2/2]

◆ ~PredictionTrackerProfileMinE()

Member Function Documentation

◆ updateOptimumCalled()

◆ updateProfile()

◆ writeProfile()

Member Data Documentation

◆ deleteStreamsOnDestruction

◆ E_INF_string

◆ energy

◆ sep_string

◆ seq1minE

◆ seq1stream

◆ seq2minE

◆ seq2stream