IntaRNA::OutputHandlerText Class Reference

#include <OutputHandlerText.h>

Inheritance diagram for IntaRNA::OutputHandlerText:

Collaboration diagram for IntaRNA::OutputHandlerText:

Public Member Functions
	OutputHandlerText (const OutputConstraint &outConstraint, std::ostream &out, const InteractionEnergy &energy, const size_t flankingLength=10, const bool detailedOutput=false)
virtual	~OutputHandlerText ()
virtual void	add (const Interaction &interaction)
Public Member Functions inherited from IntaRNA::OutputHandler
	OutputHandler (const OutputConstraint &outConstraint)
virtual	~OutputHandler ()
virtual size_t	reported () const
virtual void	incrementZ (const Z_type subZ)
virtual Z_type	getZ () const
const OutputConstraint &	getOutputConstraint () const

Protected Attributes
std::ostream &	out
	the output stream to write the interaction text representation to
const InteractionEnergy &	energy
	the interaction energy handler used for the energy computations
const size_t	flankingLength
	number of flanking bases left/right of the interaction to print
const bool	detailedOutput
	whether or not detailed output has to be provided
size_t	reportedInteractions
	counter of reported interactions
Z_type	Z
	aggregated overall partition function
Protected Attributes inherited from IntaRNA::OutputHandler
const OutputConstraint	outConstraint
	the output constraints to be applied
size_t	reportedInteractions
	number of reported interactions
Z_type	Z
	overall partition function for the sequences provided in Z_energy

Additional Inherited Members
Static Public Member Functions inherited from IntaRNA::OutputHandler
static std::string	reverse (const std::string &str)

Detailed Description

Interaction output handler that writes all interactions directly to stream in a simple text format.

Author

Martin Mann 2014

Constructor & Destructor Documentation

OutputHandlerText()

IntaRNA::OutputHandlerText::OutputHandlerText	(	const OutputConstraint &	outConstraint,
		std::ostream &	out,
		const InteractionEnergy &	energy,
		const size_t	flankingLength = 10,
		const bool	detailedOutput = false
	)

Construct a simple text output handler for interaction reporting.

Parameters

outConstraint	the output constraint applied to find the reported interaction
out	the stream to write to
energy	the interaction energy object used for computation
flankingLength	maximal number of nucleotides flanking the interaction to be printed in the output
detailedOutput	if (true) detailed output is provided; normal reduced output otherwise

~OutputHandlerText()

virtual IntaRNA::OutputHandlerText::~OutputHandlerText ( )

virtual

destruction, enforces a flush on the output stream.

Member Function Documentation

add()

virtual void IntaRNA::OutputHandlerText::add ( const Interaction &  interaction )

virtual

Write a given RNA-RNA interaction in simple text format to the output stream.

Parameters

interaction

the interaction to output

Implements IntaRNA::OutputHandler.

Member Data Documentation

detailedOutput

const bool IntaRNA::OutputHandlerText::detailedOutput

protected

whether or not detailed output has to be provided

energy

const InteractionEnergy& IntaRNA::OutputHandlerText::energy

protected

the interaction energy handler used for the energy computations

flankingLength

const size_t IntaRNA::OutputHandlerText::flankingLength

protected

number of flanking bases left/right of the interaction to print

out

std::ostream& IntaRNA::OutputHandlerText::out

protected

the output stream to write the interaction text representation to

reportedInteractions

size_t IntaRNA::OutputHandler::reportedInteractions

protected

counter of reported interactions

Z

Z_type IntaRNA::OutputHandler::Z

protected

aggregated overall partition function

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

• src/IntaRNA/OutputHandlerText.h