#include <SeedHandlerMfe.h>

Inheritance diagram for IntaRNA::SeedHandlerMfe:

Collaboration diagram for IntaRNA::SeedHandlerMfe:

[legend]

Public Types
typedef boost::multi_array< E_type, 5 >	SeedRecMatrix

typedef boost::array< SeedRecMatrix::index, 5 >	SeedIndex

typedef Matrix< std::pair< E_type, size_t > >	SeedMatrix

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

virtual	~SeedHandlerMfe ()

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

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

virtual	~SeedHandler ()

virtual const SeedConstraint &	getConstraint () const

virtual const InteractionEnergy &	getInteractionEnergy () const

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 Member Functions
E_type	getSeedE (const size_t i1, const size_t i2, const size_t bpInbetween, const size_t u1, const size_t u2) const

void	setSeedE (const size_t i1, const size_t i2, const size_t bpInbetween, const size_t u1, const size_t u2, const E_type E)

size_t	encodeSeedLength (const size_t l1, const size_t l2) const

size_t	decodeSeedLength1 (const size_t code) const

size_t	decodeSeedLength2 (const size_t code) const

void	traceBackSeed (Interaction &interaction, const size_t i1, const size_t i2, const size_t bp, const size_t u1, const size_t u2) const

Protected Attributes
SeedRecMatrix	seedE_rec

SeedMatrix	seed

size_t	offset1
	offset for seq1 indices for the current (restricted) matrices

size_t	offset2
	offset for seq2 indices for the current (restricted) matrices

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

const SeedConstraint &	seedConstraint
	the seed constraint to be applied

Detailed Description

Handler to provide mfe seed interaction information for each intermolecular index combination (= left end of seed).

Member Typedef Documentation

◆ SeedIndex

typedef boost::array<SeedRecMatrix::index, 5> IntaRNA::SeedHandlerMfe::SeedIndex

defines the seed data {{ i1, i2, bpInbetween, u1, u2 }} to access elements of the SeedRecMatrix

◆ SeedMatrix

typedef Matrix< std::pair<E_type, size_t> > IntaRNA::SeedHandlerMfe::SeedMatrix

matrix to store the seed information for each seed left side (i1,i2); it holds both the energy (first) as well as the length of the seed using the length combination using encodeSeedLength()

◆ SeedRecMatrix

typedef boost::multi_array<E_type,5> IntaRNA::SeedHandlerMfe::SeedRecMatrix

5D matrix type to hold the mfe energies for seed interactions of the ranges i1..(i1+bp+u1-1) with i2..(i2+bp+u2-1), with i1,i2 = the start index of the seed in seq1/2 bp = the number of base pairs within the seed bpInbetween = the number of base pairs enclosed by left and right base pair, ie. == (bp-2) u1/u2 = the number of unpaired positions within the seed, using the index [i1][i2][bpInbetween][u1][u2] or a SeedIndex object

Constructor & Destructor Documentation

◆ SeedHandlerMfe()

IntaRNA::SeedHandlerMfe::SeedHandlerMfe	(	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

◆ ~SeedHandlerMfe()

IntaRNA::SeedHandlerMfe::~SeedHandlerMfe ( )

inlinevirtual

destruction

Member Function Documentation

◆ decodeSeedLength1()

size_t IntaRNA::SeedHandlerMfe::decodeSeedLength1 ( const size_t code ) const

inlineprotected

Decodes the length of the seed within sequence 1 from an encoding generated with encodeSeedLength()

Parameters

code	the lengths encoding

Returns: the length of the seed in seq1

◆ decodeSeedLength2()

size_t IntaRNA::SeedHandlerMfe::decodeSeedLength2 ( const size_t code ) const

inlineprotected

Decodes the length of the seed within sequence 2 from an encoding generated with encodeSeedLength()

Parameters

code	the lengths encoding

Returns: the length of the seed in seq2

◆ encodeSeedLength()

size_t IntaRNA::SeedHandlerMfe::encodeSeedLength	(	const size_t	l1,
		const size_t	l2
	)		const

inlineprotected

Encodes the seed lengths into one number

Parameters

l1	the length of the seed in seq1
l2	the length of the seed in seq2

Returns: the combined encoding = (l1 + l2*(max_l1+1))

◆ fillSeed()

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

virtual

Computes the seed matrix 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

Implements IntaRNA::SeedHandler.

◆ getSeedE() [1/2]

E_type IntaRNA::SeedHandlerMfe::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)

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.

◆ getSeedE() [2/2]

E_type IntaRNA::SeedHandlerMfe::getSeedE	(	const size_t	i1,
		const size_t	i2,
		const size_t	bpInbetween,
		const size_t	u1,
		const size_t	u2
	)		const

inlineprotected

Provides the seed energy during recursion.

Parameters

i1	the seed left end in seq 1
i2	the seed left end in seq 2
bpInbetween	the number of seed base pairs enclosed by the left- and right-most base pair, ie. bpSeed-2
u1	the number of unpaired bases within seq 1
u2	the number of unpaired bases within seq 2

Returns: the energy of the according (sub)seed

◆ getSeedLength1()

size_t IntaRNA::SeedHandlerMfe::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)

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::SeedHandlerMfe::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)

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.

◆ isSeedBound()

bool IntaRNA::SeedHandlerMfe::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.

◆ setSeedE()

void IntaRNA::SeedHandlerMfe::setSeedE	(	const size_t	i1,
		const size_t	i2,
		const size_t	bpInbetween,
		const size_t	u1,
		const size_t	u2,
		const E_type	E
	)

inlineprotected

Fills the seed energy during recursion.

NOTE: internally a ring-list data structure is used which reuses memory instead of allocating mem for all possible parameter combinations. Thus, you have to call the method in appropriate order depending on your seed recursion.

Parameters

i1	the seed left end in seq 1
i2	the seed left end in seq 2
bpInbetween	the number of seed base pairs enclosed by the left- and right-most base pair, ie. bpSeed-2
u1	the number of unpaired bases within seq 1
u2	the number of unpaired bases within seq 2
E	the energy value to be set

◆ traceBackSeed() [1/2]

void IntaRNA::SeedHandlerMfe::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!

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.

◆ traceBackSeed() [2/2]

void IntaRNA::SeedHandlerMfe::traceBackSeed	(	Interaction &	interaction,
		const size_t	i1,
		const size_t	i2,
		const size_t	bp,
		const size_t	u1,
		const size_t	u2
	)		const

protected

Fills a given interaction with the according hybridizing base pairs of the provided seed interaction (excluding the right-most seed base pair)

Parameters

interaction	IN/OUT the interaction to fill
i1	the seed left end in seq 1 (index including offset)
i2	the seed left end in seq 2 (index including offset)
bp	the number of base pairs (bp+2) within the seed so far
u1	the number of unpaired bases within seq 1
u2	the number of unpaired bases within seq 2

Member Data Documentation

◆ offset1

size_t IntaRNA::SeedHandlerMfe::offset1

protected

offset for seq1 indices for the current (restricted) matrices

◆ offset2

size_t IntaRNA::SeedHandlerMfe::offset2

protected

offset for seq2 indices for the current (restricted) matrices

◆ seed

SeedMatrix IntaRNA::SeedHandlerMfe::seed

protected

the seed mfe information for seeds starting at (i1,i2) TODO replace with sparse data structure

◆ seedE_rec

SeedRecMatrix IntaRNA::SeedHandlerMfe::seedE_rec

protected

the recursion data for the computation of a seed interaction i1..(i1+bpInbetween+u1-1) with i2..(i2+bpInbetween+u2-1) using the indexing [i1][i2][bpInbetween][u1][u2]

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

src/IntaRNA/SeedHandlerMfe.h

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ SeedIndex

◆ SeedMatrix

◆ SeedRecMatrix

Constructor & Destructor Documentation

◆ SeedHandlerMfe()

◆ ~SeedHandlerMfe()

Member Function Documentation

◆ decodeSeedLength1()

◆ decodeSeedLength2()

◆ encodeSeedLength()

◆ fillSeed()

◆ getSeedE() [1/2]

◆ getSeedE() [2/2]

◆ getSeedLength1()

◆ getSeedLength2()

◆ isSeedBound()

◆ setSeedE()

◆ traceBackSeed() [1/2]

◆ traceBackSeed() [2/2]

Member Data Documentation

◆ offset1

◆ offset2

◆ seed

◆ seedE_rec