IntaRNA Namespace Reference

Namespaces
namespace	matrix_detail

Classes
class	Accessibility
class	AccessibilityArchive
class	AccessibilityBasePair
class	AccessibilityConstraint
class	AccessibilityDisabled
class	AccessibilityFromStream
class	AccessibilityVrna
class	HelixConstraint
class	HelixHandler
class	HelixHandlerIdxOffset
class	HelixHandlerNoBulgeMax
class	HelixHandlerUnpaired
class	IndexRange
class	IndexRangeList
class	Interaction
class	InteractionEnergy
class	InteractionEnergyBasePair
class	InteractionEnergyIdxOffset
class	InteractionEnergyVrna
class	InteractionRange
class	Matrix
class	NussinovHandler
class	OutputConstraint
class	OutputHandler
class	OutputHandlerCsv
class	OutputHandlerEnsemble
class	OutputHandlerHub
class	OutputHandlerInteractionList
class	OutputHandlerText
class	OutputStreamHandler
class	OutputStreamHandlerSortedCsv
class	PredictionTracker
class	PredictionTrackerHub
class	PredictionTrackerPairMinE
class	PredictionTrackerProfileMinE
class	PredictionTrackerProfileSpotProb
class	PredictionTrackerSpotProb
class	PredictionTrackerSpotProbAll
class	Predictor
class	PredictorEvalOnly
class	PredictorMfe
class	PredictorMfe2d
class	PredictorMfe2dHelixBlockHeuristic
class	PredictorMfe2dHelixBlockHeuristicSeed
class	PredictorMfe2dHeuristic
class	PredictorMfe2dHeuristicSeed
class	PredictorMfe2dHeuristicSeedExtension
class	PredictorMfe2dSeed
class	PredictorMfe2dSeedExtension
class	PredictorMfe2dSeedExtensionRIblast
class	PredictorMfeEns
class	PredictorMfeEns2d
class	PredictorMfeEns2dHeuristic
class	PredictorMfeEns2dHeuristicSeedExtension
class	PredictorMfeEns2dSeedExtension
class	PredictorMfeEnsSeedOnly
class	PredictorMfeSeedOnly
class	PredictorSeedExtensionKinetic
class	ReverseAccessibility
class	RnaSequence
class	SeedConstraint
class	SeedHandler
class	SeedHandlerExplicit
class	SeedHandlerIdxOffset
class	SeedHandlerMfe
class	SeedHandlerNoBulge
class	UpperBandedMatrix
class	UpperTriangularMatrix
class	VrnaHandler

Typedefs
typedef float	E_kcal_type
	type for energy values in kcal/mol units for in-/output only
typedef int	E_type
	type for energy values (energy + accessibility [ED]) (internally)
typedef double	Z_type
	type for probabilities, RT and Boltzmann values

Functions
std::ostream &	operator<< (std::ostream &out, const AccessibilityConstraint &c)
std::ostream *	newOutputStream (const std::string &outName)
void	deleteOutputStream (std::ostream *&outStream)
std::istream *	newInputStream (const std::string &inName)
void	deleteInputStream (std::istream *&inStream)
std::ostream &	operator<< (std::ostream &out, const HelixConstraint &c)
std::ostream &	operator<< (std::ostream &out, const IndexRangeList &l)
std::ostream &	operator<< (std::ostream &out, const RnaSequence &rna)
std::ostream &	operator<< (std::ostream &out, const SeedConstraint &c)

Variables
const E_type	E_INF = (std::numeric_limits<E_type>::max() / 8) + 1
const E_type	E_MAX = E_INF / 2
const Z_type	Z_INF = std::numeric_limits<Z_type>::infinity()

Typedef Documentation

E_kcal_type

typedef float IntaRNA::E_kcal_type

type for energy values in kcal/mol units for in-/output only

E_type

typedef int IntaRNA::E_type

type for energy values (energy + accessibility [ED]) (internally)

Z_type

typedef double IntaRNA::Z_type

type for probabilities, RT and Boltzmann values

Function Documentation

deleteInputStream()

void IntaRNA::deleteInputStream

(

std::istream *&

inStream

)

Deletes an input stream pointer returned by newInputStream() and sets it to NULL. If it is a file stream, it is closed before deletion. If it is pointing to std::cin, only the pointer is reset to NULL.

Parameters

inStream

the pointer to the input stream to delete; will be set to NULL

deleteOutputStream()

void IntaRNA::deleteOutputStream

(

std::ostream *&

outStream

)

Deletes an output stream pointer returned by newOutputStream() and sets it to NULL. If it is a file stream, it is closed before deletion. If it is pointing to std::cout or std::cerr, only the pointer is reset to NULL.

Parameters

outStream

the pointer to the output stream to delete; will be set to NULL

newInputStream()

std::istream * IntaRNA::newInputStream

(

const std::string &

inName

)

Returns an open input stream for the given input name, i.e.

• & std::cin : if inName == STDIN
• new std::fstream( inName ) : else inName non-empty

If the filename ends in '.gz' or '.agz', gzip compression and binary input is enabled.

Parameters

inName

the name of the input to open. use STDIN for the respective input stream or otherwise a filename to be created.

Returns

the open input stream, or NULL in error case

newOutputStream()

std::ostream * IntaRNA::newOutputStream

(

const std::string &

outName

)

Returns an open output stream for the given output name, i.e.

• & std::cout : if outName == STDOUT
• & std::cerr : if outName == STDERR
• new std::fstream( outName ) : else if outName non-empty

If the filename ends in '.gz' or '.agz', gzip compression and binary output is enabled.

Parameters

outName

the name of the output to open. use STDOUT/STDERR for the respective output stream or otherwise a filename to be created.

Returns

the open output stream, or NULL in error case

operator<<() [1/5]

std::ostream & IntaRNA::operator<< ( std::ostream &  out, const AccessibilityConstraint &  c  )

inline

Prints the accessibility constraint in range-based encoding to stream

Parameters

out	the ostream to write to
c	the AccessibilityConstraint object to add

Returns

the altered stream out

operator<<() [2/5]

std::ostream & IntaRNA::operator<< ( std::ostream &  out, const HelixConstraint &  c  )

inline

Prints the helix constraint details to stream

Parameters

out	the ostream to write to
c	the object to add

Returns

the altered stream out

operator<<() [3/5]

std::ostream & IntaRNA::operator<< ( std::ostream &  out, const IndexRangeList &  l  )

inline

Prints the boundaries of the list's ranges to stream

Parameters

out	the ostream to write to
l	the IndexRangeList object to add

Returns

the altered stream out

operator<<() [4/5]

std::ostream & IntaRNA::operator<< ( std::ostream &  out, const RnaSequence &  rna  )

inline

prints the sequence id and the sequence to stream

Parameters

out	the ostream to write to
rna	the RnaSequence object to add

Returns

the altered stream out

operator<<() [5/5]

std::ostream & IntaRNA::operator<< ( std::ostream &  out, const SeedConstraint &  c  )

inline

Prints the seed constraint details to stream

Parameters

out	the ostream to write to
c	the object to add

Returns

the altered stream out

Variable Documentation

E_INF

const E_type IntaRNA::E_INF = (std::numeric_limits<E_type>::max() / 8) + 1

E_MAX

const E_type IntaRNA::E_MAX = E_INF / 2

Z_INF

const Z_type IntaRNA::Z_INF = std::numeric_limits<Z_type>::infinity()