IntaRNA::OutputHandler Class Reference

#include <OutputHandler.h>

Inheritance diagram for IntaRNA::OutputHandler:

Collaboration diagram for IntaRNA::OutputHandler:

Public Member Functions
	OutputHandler (const OutputConstraint &outConstraint)
virtual	~OutputHandler ()
virtual void	add (const Interaction &interaction)=0
virtual size_t	reported () const
virtual void	incrementZ (const Z_type subZ)
virtual Z_type	getZ () const
const OutputConstraint &	getOutputConstraint () const

Static Public Member Functions
static std::string	reverse (const std::string &str)

Protected Attributes
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

Detailed Description

Defines an output and storage interface to enable different output formats for all predicted RNA-RNA interactions.

Author

Martin Mann 2014

Constructor & Destructor Documentation

OutputHandler()

IntaRNA::OutputHandler::OutputHandler ( const OutputConstraint &  outConstraint )

inline

Construction

Parameters

outConstraint

the output constraints to be heeded

~OutputHandler()

IntaRNA::OutputHandler::~OutputHandler ( )

inlinevirtual

Destruction

Member Function Documentation

add()

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

pure virtual

Adds a given RNA-RNA interaction to the storage/output.

NOTE: the given interaction object and its source object might be deleted later on. Thus, a deep copy is needed in order to make them completely independent.

Parameters

interaction	the interaction to add
outConstraint	the output constraint applied to find the reported interaction

Implemented in IntaRNA::OutputHandlerCsv, IntaRNA::OutputHandlerEnsemble, IntaRNA::OutputHandlerHub, IntaRNA::OutputHandlerInteractionList, and IntaRNA::OutputHandlerText.

getOutputConstraint()

const OutputConstraint & IntaRNA::OutputHandler::getOutputConstraint ( ) const

inline

Access to the output constraints to be applied

Returns

the OutputConstraint object to be heeded

getZ()

Z_type IntaRNA::OutputHandler::getZ ( ) const

inlinevirtual

Access to the partition function (initialized with 0) aggregated via incrementZ().

Returns

the aggregated partition function Z

Reimplemented in IntaRNA::OutputHandlerHub.

incrementZ()

void IntaRNA::OutputHandler::incrementZ ( const Z_type  subZ )

inlinevirtual

Increments the overall partition function with the given value.

Note, take care that multiple increments have to represent disjoint subsets of all interactions for the same pair of sequences, otherwise the aggregated overall partition function will be wrong!

Parameters

subZ	increment to be added to the overall partition function

Reimplemented in IntaRNA::OutputHandlerHub.

reported()

size_t IntaRNA::OutputHandler::reported ( ) const

inlinevirtual

Returns the number of reported interactions.

Returns

the number of reported interactions

Reimplemented in IntaRNA::OutputHandlerHub.

reverse()

std::string IntaRNA::OutputHandler::reverse ( const std::string &  str )

inlinestatic

returns the reversed string

Parameters

str	the string to reverse

Returns

the reversed string

Member Data Documentation

outConstraint

const OutputConstraint IntaRNA::OutputHandler::outConstraint

protected

the output constraints to be applied

reportedInteractions

size_t IntaRNA::OutputHandler::reportedInteractions

protected

number of reported interactions

Z

Z_type IntaRNA::OutputHandler::Z

protected

overall partition function for the sequences provided in Z_energy

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

• src/IntaRNA/OutputHandler.h