#include <HelixHandler.h>

Inheritance diagram for IntaRNA::HelixHandler:

[legend]

Public Member Functions
	HelixHandler ()

virtual	~HelixHandler ()

virtual const HelixConstraint &	getConstraint () const =0

virtual const InteractionEnergy &	getInteractionEnergy () const =0

virtual size_t	fillHelix (const size_t i1, const size_t j1, const size_t i2, const size_t j2)=0

virtual size_t	fillHelixSeed (const size_t i1, const size_t j1, const size_t i2, const size_t j2)=0

virtual void	traceBackHelix (Interaction &interaction, const size_t i1, const size_t i2)=0

virtual void	traceBackHelixSeed (Interaction &interaction, const size_t i1, const size_t i2)=0

virtual E_type	getHelixE (const size_t i1, const size_t i2) const =0

virtual E_type	getHelixSeedE (const size_t i1, const size_t i2) const =0

virtual size_t	getHelixLength1 (const size_t i1, const size_t i2) const =0

virtual size_t	getHelixLength2 (const size_t i1, const size_t i2) const =0

virtual size_t	getHelixSeedLength1 (const size_t i1, const size_t i2) const =0

virtual size_t	getHelixSeedLength2 (const size_t i1, const size_t i2) const =0

virtual void	setSeedHandler (SeedHandler &seedHandler)=0

Static Public Member Functions
static HelixHandler *	getHelixHandler (const InteractionEnergy &energy, const HelixConstraint &helixConstraint, SeedHandler *const seedHandler=NULL)

Detailed Description

Abstract interface to provide helix interaction information If SeedHandler is provided, also helices containing seeds will be computed

Constructor & Destructor Documentation

◆ HelixHandler()

IntaRNA::HelixHandler::HelixHandler ( )

inline

Construction

Parameters

energy	the energy function to be used for helix prediction
helixConstraint	the helix constraint to be applied

◆ ~HelixHandler()

IntaRNA::HelixHandler::~HelixHandler ( )

inlinevirtual

destruction

Member Function Documentation

◆ fillHelix()

virtual size_t IntaRNA::HelixHandler::fillHelix	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2
	)

pure virtual

Computes the helix information for the given interval boundaries

Parameters

i1	the first index of seq1 that might interact
j1	the last index of seq1 that might interact
i2	the first index of seq2 that might interact
j2	the last index of seq2 that might interact

Returns: the number of potential helix interactions

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ fillHelixSeed()

virtual size_t IntaRNA::HelixHandler::fillHelixSeed	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2
	)

pure virtual

Computes the helix information for the given interval boundaries for helices containing a seed

Parameters

i1	the first index of seq1 that might interact
j1	the last index of seq1 that might interact
i2	the first index of seq2 that might interact
j2	the last index of seq2 that might interact

Returns: the number of potential helix interactions

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ getConstraint()

virtual const HelixConstraint & IntaRNA::HelixHandler::getConstraint ( ) const

pure virtual

Access to the underlying helix constraint

Returns: the used helix constraint

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ getHelixE()

virtual E_type IntaRNA::HelixHandler::getHelixE	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

Access to the mfe of any helix with left-most base pair (i1,i2)

Parameters

i1	the left most interacting base of seq1
i2	the left most interacting base of seq2

Returns: the mfe of any helix starting at (i1,i2) or E_INF if none possible

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ getHelixHandler()

static HelixHandler * IntaRNA::HelixHandler::getHelixHandler	(	const InteractionEnergy &	energy,
		const HelixConstraint &	helixConstraint,
		SeedHandler *const	seedHandler = `NULL`
	)

static

Provides a newly allocated helixHandler according to the user defined parameters

Parameters

energy	the interaction energy handler to be used
helixConstraint	the helixConstraint to be used

Returns: the newly allocated HelixHandler object

◆ getHelixLength1()

virtual size_t IntaRNA::HelixHandler::getHelixLength1	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

Access to the length in seq1 of the mfe helix with left-most base pair (i1,i2)

Parameters

i1	the left most interacting base of seq1
i2	the left most interacting base of seq2

Returns: the length in seq1 of the mfe helix starting at (i1,i2) or 0 if none possible

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ getHelixLength2()

virtual size_t IntaRNA::HelixHandler::getHelixLength2	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

Access to the length in seq2 of the mfe helix with left-most base pair (i1,i2)

Parameters

i1	the left most interacting base of seq1
i2	the left most interacting base of seq2

Returns: the length in seq2 of the mfe helix starting at (i1,i2) or 0 if none possible

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ getHelixSeedE()

virtual E_type IntaRNA::HelixHandler::getHelixSeedE	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

Access to the mfe of any helix with left-most base pair (i1,i2)

Parameters

i1	the left most interacting base of seq1
i2	the left most interaction base of seq2

Returns: the mfe of any helix starting at (i1,i2) or E_INF if none possible

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ getHelixSeedLength1()

virtual size_t IntaRNA::HelixHandler::getHelixSeedLength1	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

Access to the length in seq1 of the mfe helix with left-most base pair (i1,i2) containing a seed

Parameters

i1	the left most interacting base of seq1
i2	the left most interacting base of seq2

Returns: the length in seq1 of the mfe helix starting at (i1,i2) or 0 if none possible

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ getHelixSeedLength2()

virtual size_t IntaRNA::HelixHandler::getHelixSeedLength2	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

Access to the length in seq2 of the mfe helix with left-most base pair (i1,i2) containing a seed

Parameters

i1	the left most interacting base of seq1
i2	the left most interacting base of seq2

Returns: the length in seq2 of the mfe helix starting at (i1,i2) or 0 if none possible

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ getInteractionEnergy()

virtual const InteractionEnergy & IntaRNA::HelixHandler::getInteractionEnergy ( ) const

pure virtual

Access to the underlying interaction energy function

Returns: the used energy function

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ setSeedHandler()

virtual void IntaRNA::HelixHandler::setSeedHandler ( SeedHandler & seedHandler )

pure virtual

Set the seedHandler used in the helixHandlerSeed computation

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ traceBackHelix()

virtual void IntaRNA::HelixHandler::traceBackHelix	(	Interaction &	interaction,
		const size_t	i1,
		const size_t	i2
	)

pure virtual

Identifies the base pairs of the mfe helix interaction starting at i1,i2 and writes them to the provided container

NOTE: the left- and right-most base pair is excluded!

Parameters

interaction	the container to add the base pairs too
i1	the start of the helix in seq1
i2	the start of the helix in seq2

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerNoBulgeMax, and IntaRNA::HelixHandlerUnpaired.

◆ traceBackHelixSeed()

virtual void IntaRNA::HelixHandler::traceBackHelixSeed	(	Interaction &	interaction,
		const size_t	i1,
		const size_t	i2
	)

pure virtual

Identifies the base pairs of the mfe helix interaction, containing a seed, starting at i1,i2 and writes them to the provided container

NOTE: the left- and right-most base pair is excluded!

Parameters

interaction	the container to add the base pairs too
i1	the start of the helix in seq1
i2	the start of the helix in seq2

Implemented in IntaRNA::HelixHandlerIdxOffset, IntaRNA::HelixHandlerUnpaired, and IntaRNA::HelixHandlerNoBulgeMax.

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

src/IntaRNA/HelixHandler.h

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ HelixHandler()

◆ ~HelixHandler()

Member Function Documentation

◆ fillHelix()

◆ fillHelixSeed()

◆ getConstraint()

◆ getHelixE()

◆ getHelixHandler()

◆ getHelixLength1()

◆ getHelixLength2()

◆ getHelixSeedE()

◆ getHelixSeedLength1()

◆ getHelixSeedLength2()

◆ getInteractionEnergy()

◆ setSeedHandler()

◆ traceBackHelix()

◆ traceBackHelixSeed()