#include <SeedHandlerIdxOffset.h>

Inheritance diagram for IntaRNA::SeedHandlerIdxOffset:

Collaboration diagram for IntaRNA::SeedHandlerIdxOffset:

[legend]

Public Member Functions
	SeedHandlerIdxOffset (SeedHandler *seedHandler, const bool deleteOnDestruction=true)

virtual	~SeedHandlerIdxOffset ()

size_t	getOffset1 () const

void	setOffset1 (size_t offset1)

size_t	getOffset2 () const

void	setOffset2 (size_t offset2)

virtual const SeedConstraint &	getConstraint () const

virtual const InteractionEnergy &	getInteractionEnergy () const

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

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

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

virtual bool	isSeedBound (const size_t i1, const size_t i2) const

virtual size_t	getSeedLength1 (const size_t i1, const size_t i2) const

virtual size_t	getSeedLength2 (const size_t i1, const size_t i2) const

virtual SeedHandler &	getOriginalSeedHandler ()

virtual bool	updateToNextSeed (size_t &i1, size_t &i2, const size_t i1min=0, const size_t i1max=RnaSequence::lastPos, const size_t i2min=0, const size_t i2max=RnaSequence::lastPos) const

virtual void	addSeeds (Interaction &i) const

virtual bool	areLoopOverlapping (const size_t i1, const size_t i2, const size_t k1, const size_t k2) const

virtual bool	isFeasibleSeedBasePair (const size_t i1, const size_t i2, const bool atEndOfSeed=false) const

Public Member Functions inherited from IntaRNA::SeedHandler
	SeedHandler (const InteractionEnergy &energy, const SeedConstraint &seedConstraint)

virtual	~SeedHandler ()

Protected Attributes
SeedHandler *	seedHandlerOriginal
	the index shifted seed handler

const bool	deleteOnDestruction
	whether or not the original seed handler is to be destroyed

SeedConstraint	seedConstraintOffset
	the index shifted seed constraint

size_t	idxOffset1
	offset for indices in seq1

size_t	idxOffset2
	offset for indices in seq2

InteractionEnergyIdxOffset	energyIdxOffset
	dedicated energy object to avoid

Protected Attributes inherited from IntaRNA::SeedHandler
const InteractionEnergy &	energy
	the used energy function

const SeedConstraint &	seedConstraint
	the seed constraint to be applied

Detailed Description

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

Author: Martin Mann

Constructor & Destructor Documentation

◆ SeedHandlerIdxOffset()

IntaRNA::SeedHandlerIdxOffset::SeedHandlerIdxOffset	(	SeedHandler *	seedHandler,
		const bool	deleteOnDestruction = `true`
	)

inline

Construction

Parameters

seedHandler	the seed handler to be wrapped
deleteOnDestruction	whether or not the seedHandler is to be deleted within the destructor

◆ ~SeedHandlerIdxOffset()

IntaRNA::SeedHandlerIdxOffset::~SeedHandlerIdxOffset ( )

inlinevirtual

destruction of this object and the wrapped seed handler

Member Function Documentation

◆ addSeeds()

void IntaRNA::SeedHandlerIdxOffset::addSeeds ( Interaction & i ) const

inlinevirtual

Adds all seeds to a given interaction that are completely covered by its base pairs.

Parameters

i	the interaction to update with indexing in global in-sequence order

Reimplemented from IntaRNA::SeedHandler.

◆ areLoopOverlapping()

bool IntaRNA::SeedHandlerIdxOffset::areLoopOverlapping	(	const size_t	i1,
		const size_t	i2,
		const size_t	k1,
		const size_t	k2
	)		const

inlinevirtual

Checks whether or not two seeds are loop overlapping, ie. given i1 < k1, the last x (>1) base pairs of seed(i1,i2) are equal to the first x base pairs of seed(k1,k2), or vice versa if k1 < i1.

Parameters

i1	the left most interacting base of seq1 of seedA
i2	the left most interacting base of seq2 of seedA
k1	the left most interacting base of seq1 of seedB
k2	the left most interacting base of seq2 of seedB

Returns: true if seedA and seedB exist and they are loop overlapping; false otherwise

Reimplemented from IntaRNA::SeedHandler.

◆ fillSeed()

size_t IntaRNA::SeedHandlerIdxOffset::fillSeed	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2
	)

inlinevirtual

Computes the seed 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 seed interactions

Implements IntaRNA::SeedHandler.

◆ getConstraint()

const SeedConstraint & IntaRNA::SeedHandlerIdxOffset::getConstraint ( ) const

inlinevirtual

Access to the underlying seed constraint

Returns: the used seed constraint

Reimplemented from IntaRNA::SeedHandler.

◆ getInteractionEnergy()

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

inlinevirtual

Access to the underlying interaction energy function

Returns: the used energy function

Reimplemented from IntaRNA::SeedHandler.

◆ getOffset1()

size_t IntaRNA::SeedHandlerIdxOffset::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::SeedHandlerIdxOffset::getOffset2 ( ) const

inline

Access to the currently used index offset for sequence 2

Returns: the index offset for sequence 2 used

◆ getOriginalSeedHandler()

SeedHandler & IntaRNA::SeedHandlerIdxOffset::getOriginalSeedHandler ( )

inlinevirtual

Access to the wrapped SeedHandler instance.

Returns: the internally used SeedHandler without offset

◆ getSeedE()

E_type IntaRNA::SeedHandlerIdxOffset::getSeedE	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

Access to the mfe of any seed 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 seed starting at (i1,i2) or E_INF if none possible

Implements IntaRNA::SeedHandler.

◆ getSeedLength1()

size_t IntaRNA::SeedHandlerIdxOffset::getSeedLength1	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

Access to the length in seq1 of the mfe seed 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 length in seq1 of the mfe seed starting at (i1,i2) or 0 if none possible

Implements IntaRNA::SeedHandler.

◆ getSeedLength2()

size_t IntaRNA::SeedHandlerIdxOffset::getSeedLength2	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

Access to the length in seq2 of the mfe seed 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 length in seq2 of the mfe seed starting at (i1,i2) or 0 if none possible

Implements IntaRNA::SeedHandler.

◆ isFeasibleSeedBasePair()

bool IntaRNA::SeedHandlerIdxOffset::isFeasibleSeedBasePair	(	const size_t	i1,
		const size_t	i2,
		const bool	atEndOfSeed = `false`
	)		const

inlinevirtual

Checks whether or not a given index pair is a valid seed base pair

Parameters

i1	the interacting base of seq1
i2	the interacting base of seq2
atEndOfSeed	whether or not the (i1,i2) form the end of a seed

Returns: true if (i1,i2) are complementary, ED(i,i) < maxED, and both i1 and i2 are in allowed regions; false otherwise

Reimplemented from IntaRNA::SeedHandler.

◆ isSeedBound()

bool IntaRNA::SeedHandlerIdxOffset::isSeedBound	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

Checks whether or not a given base pair is the left-most base pair of any seed

Parameters

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

Returns: true if (i1,i2) is the left most base pair of some seed; false otherwise

Implements IntaRNA::SeedHandler.

◆ setOffset1()

void IntaRNA::SeedHandlerIdxOffset::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::SeedHandlerIdxOffset::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

◆ traceBackSeed()

void IntaRNA::SeedHandlerIdxOffset::traceBackSeed	(	Interaction &	interaction,
		const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

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

NOTE: the left- and right-most base pairs are 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 seed in seq1
i2	the start of the seed in seq2

Implements IntaRNA::SeedHandler.

◆ updateToNextSeed()

bool IntaRNA::SeedHandlerIdxOffset::updateToNextSeed	(	size_t &	i1,
		size_t &	i2,
		const size_t	i1min = `0`,
		const size_t	i1max = `RnaSequence::lastPos`,
		const size_t	i2min = `0`,
		const size_t	i2max = `RnaSequence::lastPos`
	)		const

inlinevirtual

Replace the input variables i1 and i2 to values to within the given range that correspond to

the first seed (if the given index pair is no valid seed start or one of the indices is out of range bounds)
the next seed according to some seed order

The indices are not updated if the last seed within the range is given or no seed within the range could be found. It returns whether or not the input variables have been updated.

Note, if changed, only the seed left-most base pair is within the range but the full seed indices might exceed i1max or i2max.

Parameters

i1	seq1 seed index to be changed
i2	seq2 seed index to be changed
i1min	first position within seq1 (inclusive)
i1max	last position within seq1 (inclusive)
i2min	first position within seq2 (inclusive)
i2max	last position within seq2 (inclusive)

Returns: true if the input variables have been changed; false otherwise

Reimplemented from IntaRNA::SeedHandler.

Member Data Documentation

◆ deleteOnDestruction

const bool IntaRNA::SeedHandlerIdxOffset::deleteOnDestruction

protected

whether or not the original seed handler is to be destroyed

◆ energyIdxOffset

InteractionEnergyIdxOffset IntaRNA::SeedHandlerIdxOffset::energyIdxOffset

protected

dedicated energy object to avoid

◆ idxOffset1

size_t IntaRNA::SeedHandlerIdxOffset::idxOffset1

protected

offset for indices in seq1

◆ idxOffset2

size_t IntaRNA::SeedHandlerIdxOffset::idxOffset2

protected

offset for indices in seq2

◆ seedConstraintOffset

SeedConstraint IntaRNA::SeedHandlerIdxOffset::seedConstraintOffset

protected

the index shifted seed constraint

◆ seedHandlerOriginal

SeedHandler* IntaRNA::SeedHandlerIdxOffset::seedHandlerOriginal

protected

the index shifted seed handler

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

src/IntaRNA/SeedHandlerIdxOffset.h

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SeedHandlerIdxOffset()

◆ ~SeedHandlerIdxOffset()

Member Function Documentation

◆ addSeeds()

◆ areLoopOverlapping()

◆ fillSeed()

◆ getConstraint()

◆ getInteractionEnergy()

◆ getOffset1()

◆ getOffset2()

◆ getOriginalSeedHandler()

◆ getSeedE()

◆ getSeedLength1()

◆ getSeedLength2()

◆ isFeasibleSeedBasePair()

◆ isSeedBound()

◆ setOffset1()

◆ setOffset2()

◆ traceBackSeed()

◆ updateToNextSeed()

Member Data Documentation

◆ deleteOnDestruction

◆ energyIdxOffset

◆ idxOffset1

◆ idxOffset2

◆ seedConstraintOffset

◆ seedHandlerOriginal