#include <SeedHandler.h>

Inheritance diagram for IntaRNA::SeedHandler:

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Collaboration diagram for IntaRNA::SeedHandler:

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Public Member Functions
	SeedHandler (const InteractionEnergy &energy, const SeedConstraint &seedConstraint)

virtual	~SeedHandler ()

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)=0

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

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

virtual bool	isSeedBound (const size_t i1, const size_t i2) const =0

virtual size_t	getSeedLength1 (const size_t i1, const size_t i2) const =0

virtual size_t	getSeedLength2 (const size_t i1, const size_t i2) const =0

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

Protected Attributes
const InteractionEnergy &	energy
	the used energy function

const SeedConstraint &	seedConstraint
	the seed constraint to be applied

Detailed Description

Abstract interface to provide seed interaction information

Constructor & Destructor Documentation

◆ SeedHandler()

IntaRNA::SeedHandler::SeedHandler	(	const InteractionEnergy &	energy,
		const SeedConstraint &	seedConstraint
	)

inline

Construction

Parameters

energy	the energy function to be used for seed prediction
seedConstraint	the seed constraint to be applied

◆ ~SeedHandler()

IntaRNA::SeedHandler::~SeedHandler ( )

inlinevirtual

destruction

Member Function Documentation

◆ addSeeds()

virtual void IntaRNA::SeedHandler::addSeeds ( Interaction & i ) const

virtual

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 in IntaRNA::SeedHandlerIdxOffset.

◆ areLoopOverlapping()

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

virtual

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 in IntaRNA::SeedHandlerIdxOffset.

◆ fillSeed()

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

pure virtual

Computes the seed 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 seed interactions

Implemented in IntaRNA::SeedHandlerExplicit, IntaRNA::SeedHandlerIdxOffset, IntaRNA::SeedHandlerMfe, and IntaRNA::SeedHandlerNoBulge.

◆ getConstraint()

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

inlinevirtual

Access to the underlying seed constraint

Returns: the used seed constraint

Reimplemented in IntaRNA::SeedHandlerIdxOffset.

◆ getInteractionEnergy()

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

inlinevirtual

Access to the underlying interaction energy function

Returns: the used energy function

Reimplemented in IntaRNA::SeedHandlerIdxOffset.

◆ getSeedE()

virtual E_type IntaRNA::SeedHandler::getSeedE	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

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

Implemented in IntaRNA::SeedHandlerExplicit, IntaRNA::SeedHandlerIdxOffset, IntaRNA::SeedHandlerMfe, and IntaRNA::SeedHandlerNoBulge.

◆ getSeedLength1()

virtual size_t IntaRNA::SeedHandler::getSeedLength1	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

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

Implemented in IntaRNA::SeedHandlerExplicit, IntaRNA::SeedHandlerIdxOffset, IntaRNA::SeedHandlerMfe, and IntaRNA::SeedHandlerNoBulge.

◆ getSeedLength2()

virtual size_t IntaRNA::SeedHandler::getSeedLength2	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

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

Implemented in IntaRNA::SeedHandlerExplicit, IntaRNA::SeedHandlerIdxOffset, IntaRNA::SeedHandlerMfe, and IntaRNA::SeedHandlerNoBulge.

◆ isFeasibleSeedBasePair()

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

virtual

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 in IntaRNA::SeedHandlerIdxOffset.

◆ isSeedBound()

virtual bool IntaRNA::SeedHandler::isSeedBound	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

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

Implemented in IntaRNA::SeedHandlerExplicit, IntaRNA::SeedHandlerIdxOffset, IntaRNA::SeedHandlerMfe, and IntaRNA::SeedHandlerNoBulge.

◆ traceBackSeed()

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

pure virtual

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!

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

Implemented in IntaRNA::SeedHandlerExplicit, IntaRNA::SeedHandlerIdxOffset, IntaRNA::SeedHandlerMfe, and IntaRNA::SeedHandlerNoBulge.

◆ updateToNextSeed()

virtual bool IntaRNA::SeedHandler::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

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 in IntaRNA::SeedHandlerExplicit, IntaRNA::SeedHandlerIdxOffset, and IntaRNA::SeedHandlerNoBulge.

Member Data Documentation

◆ energy

const InteractionEnergy& IntaRNA::SeedHandler::energy

protected

the used energy function

◆ seedConstraint

const SeedConstraint& IntaRNA::SeedHandler::seedConstraint

protected

the seed constraint to be applied

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

src/IntaRNA/SeedHandler.h

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SeedHandler()

◆ ~SeedHandler()

Member Function Documentation

◆ addSeeds()

◆ areLoopOverlapping()

◆ fillSeed()

◆ getConstraint()

◆ getInteractionEnergy()

◆ getSeedE()

◆ getSeedLength1()

◆ getSeedLength2()

◆ isFeasibleSeedBasePair()

◆ isSeedBound()

◆ traceBackSeed()

◆ updateToNextSeed()

Member Data Documentation

◆ energy

◆ seedConstraint