#include <HelixHandlerIdxOffset.h>

Inheritance diagram for IntaRNA::HelixHandlerIdxOffset:

Collaboration diagram for IntaRNA::HelixHandlerIdxOffset:

[legend]

Public Member Functions
	HelixHandlerIdxOffset (HelixHandler *helixHandler)

virtual	~HelixHandlerIdxOffset ()

virtual const InteractionEnergy &	getInteractionEnergy () const

size_t	getOffset1 () const

void	setOffset1 (size_t offset1)

size_t	getOffset2 () const

void	setOffset2 (size_t offset2)

virtual const HelixConstraint &	getConstraint () const

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

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

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

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

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

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

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

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

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

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

virtual void	setSeedHandler (SeedHandler &seedHandler)

Public Member Functions inherited from IntaRNA::HelixHandler
	HelixHandler ()

virtual	~HelixHandler ()

Protected Attributes
HelixHandler *	helixHandlerOriginal
	the index shifted helixHandler

HelixConstraint	helixConstraintOffset
	the index shifted helix constraint

SeedHandlerIdxOffset *	seedHandlerIdxOffset

size_t	idxOffset1
	offset for indices in seq1

size_t	idxOffset2
	offset for indices in seq2

Additional Inherited Members
Static Public Member Functions inherited from IntaRNA::HelixHandler
static HelixHandler *	getHelixHandler (const InteractionEnergy &energy, const HelixConstraint &helixConstraint, SeedHandler *const seedHandler=NULL)

Detailed Description

Wrapper around a HelixHandler object where indices are shifted by a given positive offset (shifted towards infinity). This is useful for local interaction computations.

Author: Rick Gelhausen

Constructor & Destructor Documentation

◆ HelixHandlerIdxOffset()

IntaRNA::HelixHandlerIdxOffset::HelixHandlerIdxOffset ( HelixHandler * helixHandler )

inline

Construction

◆ ~HelixHandlerIdxOffset()

IntaRNA::HelixHandlerIdxOffset::~HelixHandlerIdxOffset ( )

inlinevirtual

destruction

Member Function Documentation

◆ fillHelix()

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

inlinevirtual

Computes the helix matrix for the given interval boundaries

Note, the indices are shifted by an offset for computation.

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: number of possible helix interactions

Implements IntaRNA::HelixHandler.

◆ fillHelixSeed()

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

inlinevirtual

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

Note, the indices are shifted by an offset for computation.

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

Implements IntaRNA::HelixHandler.

◆ getConstraint()

const HelixConstraint & IntaRNA::HelixHandlerIdxOffset::getConstraint ( ) const

inlinevirtual

Access to the underlying helix constraint

Returns: the used helix constraint

Implements IntaRNA::HelixHandler.

◆ getHelixE()

E_type IntaRNA::HelixHandlerIdxOffset::getHelixE	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

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

Note, the indices are shifted by an offset for computation

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

Implements IntaRNA::HelixHandler.

◆ getHelixLength1()

size_t IntaRNA::HelixHandlerIdxOffset::getHelixLength1	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

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

Note, the indices are shifted by an offset for computation.

Parameters

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

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

Implements IntaRNA::HelixHandler.

◆ getHelixLength2()

size_t IntaRNA::HelixHandlerIdxOffset::getHelixLength2	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

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

Note, the indices are shifted by an offset for computation.

Parameters

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

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

Implements IntaRNA::HelixHandler.

◆ getHelixSeedE()

E_type IntaRNA::HelixHandlerIdxOffset::getHelixSeedE	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

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

Note, the indices are shifted by an offset for computation

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

Implements IntaRNA::HelixHandler.

◆ getHelixSeedLength1()

size_t IntaRNA::HelixHandlerIdxOffset::getHelixSeedLength1	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

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

Note, the indices are shifted by an offset for computation.

Parameters

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

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

Implements IntaRNA::HelixHandler.

◆ getHelixSeedLength2()

size_t IntaRNA::HelixHandlerIdxOffset::getHelixSeedLength2	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

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

Note, the indices are shifted by an offset for computation.

Parameters

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

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

Implements IntaRNA::HelixHandler.

◆ getInteractionEnergy()

const InteractionEnergy & IntaRNA::HelixHandlerIdxOffset::getInteractionEnergy ( ) const

inlinevirtual

Access to the underlying interaction energy function

Returns: the used energy function

Implements IntaRNA::HelixHandler.

◆ getOffset1()

size_t IntaRNA::HelixHandlerIdxOffset::getOffset1 ( ) const

inline

Access to the currently used index offset for sequence 1

Returns: the index offset for sequence 1 used

◆ getOffset2()

size_t IntaRNA::HelixHandlerIdxOffset::getOffset2 ( ) const

inline

Access to the currently used index offset for sequence 2

Returns: the index offset for sequence 2 used

◆ setOffset1()

void IntaRNA::HelixHandlerIdxOffset::setOffset1 ( size_t offset1 )

inline

Sets the index offset to be used for sequence 1

Parameters

offset1 the index offset for sequence 1 to be used

◆ setOffset2()

void IntaRNA::HelixHandlerIdxOffset::setOffset2 ( size_t offset2 )

inline

Sets the index offset to be used for sequence 2

Parameters

offset2 the index offset for sequence 2 to be used

◆ setSeedHandler()

void IntaRNA::HelixHandlerIdxOffset::setSeedHandler ( SeedHandler & seedHandler )

inlinevirtual

Check whether the given seedHandler is of type SeedHandlerIdxOffset Set the seedHandler of helixHandlerOriginal

Parameters

seedHandler the seedHandler with offset

Implements IntaRNA::HelixHandler.

◆ traceBackHelix()

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

inlinevirtual

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

NOTE: the right most base pair is excluded!

Note, the indices are shifted by an offset for computation.

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

Implements IntaRNA::HelixHandler.

◆ traceBackHelixSeed()

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

inlinevirtual

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 indices are shifted by an offset for computation.

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

Implements IntaRNA::HelixHandler.

Member Data Documentation

◆ helixConstraintOffset

HelixConstraint IntaRNA::HelixHandlerIdxOffset::helixConstraintOffset

protected

the index shifted helix constraint

◆ helixHandlerOriginal

HelixHandler* IntaRNA::HelixHandlerIdxOffset::helixHandlerOriginal

protected

the index shifted helixHandler

◆ idxOffset1

size_t IntaRNA::HelixHandlerIdxOffset::idxOffset1

protected

offset for indices in seq1

◆ idxOffset2

size_t IntaRNA::HelixHandlerIdxOffset::idxOffset2

protected

offset for indices in seq2

◆ seedHandlerIdxOffset

SeedHandlerIdxOffset* IntaRNA::HelixHandlerIdxOffset::seedHandlerIdxOffset

protected

the seedHandler with offset Note: (might be needed later)

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

src/IntaRNA/HelixHandlerIdxOffset.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ HelixHandlerIdxOffset()

◆ ~HelixHandlerIdxOffset()

Member Function Documentation

◆ fillHelix()

◆ fillHelixSeed()

◆ getConstraint()

◆ getHelixE()

◆ getHelixLength1()

◆ getHelixLength2()

◆ getHelixSeedE()

◆ getHelixSeedLength1()

◆ getHelixSeedLength2()

◆ getInteractionEnergy()

◆ getOffset1()

◆ getOffset2()

◆ setOffset1()

◆ setOffset2()

◆ setSeedHandler()

◆ traceBackHelix()

◆ traceBackHelixSeed()

Member Data Documentation

◆ helixConstraintOffset

◆ helixHandlerOriginal

◆ idxOffset1

◆ idxOffset2

◆ seedHandlerIdxOffset