#include <HelixHandlerUnpaired.h>

Inheritance diagram for IntaRNA::HelixHandlerUnpaired:

Collaboration diagram for IntaRNA::HelixHandlerUnpaired:

[legend]

Public Types
typedef boost::multi_array< std::pair< E_type, size_t >, 3 >	HelixRecMatrix

typedef boost::array< HelixRecMatrix::index, 3 >	HelixIndex

typedef Matrix< std::tuple< E_type, size_t, size_t > >	HelixMatrix

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

Public Member Functions
	HelixHandlerUnpaired (const InteractionEnergy &energy, const HelixConstraint &helixConstraint, SeedHandler *const seedHandler=NULL)

virtual	~HelixHandlerUnpaired ()

virtual const HelixConstraint &	getConstraint () const

virtual const InteractionEnergy &	getInteractionEnergy () 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	getHelixLength1 (const size_t i1, const size_t i2, const size_t bp) const

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

void	setSeedHandler (SeedHandler &seedHandler)

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

virtual	~HelixHandler ()

Protected Member Functions
size_t	getBestBP (const size_t i1, const size_t i2) const

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

void	setHelixPair (const size_t i1, const size_t i2, const size_t bp, const E_type E, const size_t length)

size_t	encodeHelixLength (const size_t l1, const size_t l2) const

size_t	decodeHelixLength1 (const size_t code) const

size_t	decodeHelixLength2 (const size_t code) const

size_t	encodeHelixSeedLength (const size_t l1, const size_t l2) const

size_t	decodeHelixSeedLength1 (const size_t code) const

size_t	decodeHelixSeedLength2 (const size_t code) const

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

Protected Attributes
const InteractionEnergy &	energy
	the used energy function

const HelixConstraint &	helixConstraint
	the helix constraint to be applied

HelixRecMatrix	helixE_rec

HelixMatrix	helix
	the helix mfe information for helix starting at (i1, i2)

HelixSeedMatrix	helixSeed
	the helix mfe information for helix with seed starting at (i1, i2)

size_t	offset1
	offset for seq1 indices for the current matrices

size_t	offset2
	offset for seq2 indices for the current matrices

SeedHandler *	seedHandler
	used seedHandler

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

Handler to provide helix interaction information that allows for minor interior loops with a constraint maximal number of unpaired bases (per loop)

Author: Rick Gelhausen

Member Typedef Documentation

◆ HelixIndex

typedef boost::array<HelixRecMatrix::index, 3> IntaRNA::HelixHandlerUnpaired::HelixIndex

defines the helix data {{ i1, i2, bp }} to acces elements of the HelixRecMatrix

◆ HelixMatrix

typedef Matrix< std::tuple<E_type, size_t, size_t> > IntaRNA::HelixHandlerUnpaired::HelixMatrix

matrix to store the helix information for each helix left side (i1, i2) it holds both the energy (first) as well as the length of the helix using the length combination of encodeHelixLength() The third entry is the bestBP, i.e. the optimal number of bases for this left boundary

◆ HelixRecMatrix

typedef boost::multi_array<std::pair<E_type, size_t>,3> IntaRNA::HelixHandlerUnpaired::HelixRecMatrix

3D matrix type to hold the mfe energies for helix interactions of the ranges i1..(i1+bpMax-1) and i2..(i2+bpMax-1), with i1,i2 = the start index of the helix in seq1/2 bp = the maximal number of base pairs within the helix (>=bpMin) using the index [i1][i2][bp] or a HelixIndex object

◆ HelixSeedMatrix

typedef Matrix< std::pair<E_type, size_t> > IntaRNA::HelixHandlerUnpaired::HelixSeedMatrix

Constructor & Destructor Documentation

◆ HelixHandlerUnpaired()

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

inline

Constructor

Parameters

energy the energy function to be used

◆ ~HelixHandlerUnpaired()

IntaRNA::HelixHandlerUnpaired::~HelixHandlerUnpaired ( )

inlinevirtual

destructor

Member Function Documentation

◆ decodeHelixLength1()

size_t IntaRNA::HelixHandlerUnpaired::decodeHelixLength1 ( const size_t code ) const

inlineprotected

Decodes the length of the helix within sequence 1 from an encoding generated with encodeHelixLength()

Parameters

code	the lengths encoding

Returns: the length of the helix in seq1

◆ decodeHelixLength2()

size_t IntaRNA::HelixHandlerUnpaired::decodeHelixLength2 ( const size_t code ) const

inlineprotected

Decodes the length of the helix within sequence 2 from an encoding generated with encodeHelixLength()

Parameters

code	the lengths encoding

Returns: the length of the helix in seq2

◆ decodeHelixSeedLength1()

size_t IntaRNA::HelixHandlerUnpaired::decodeHelixSeedLength1 ( const size_t code ) const

inlineprotected

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

Parameters

code	the lengths encoding

Returns: the length of the seed in seq1

◆ decodeHelixSeedLength2()

size_t IntaRNA::HelixHandlerUnpaired::decodeHelixSeedLength2 ( const size_t code ) const

inlineprotected

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

Parameters

code	the lengths encoding

Returns: the length of the seed in seq2

◆ encodeHelixLength()

size_t IntaRNA::HelixHandlerUnpaired::encodeHelixLength	(	const size_t	l1,
		const size_t	l2
	)		const

inlineprotected

Encodes the helix lengths into one number

Parameters

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

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

◆ encodeHelixSeedLength()

size_t IntaRNA::HelixHandlerUnpaired::encodeHelixSeedLength	(	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))

◆ fillHelix()

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

virtual

Compute the helix 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

Implements IntaRNA::HelixHandler.

◆ fillHelixSeed()

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

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

Implements IntaRNA::HelixHandler.

◆ getBestBP()

size_t IntaRNA::HelixHandlerUnpaired::getBestBP	(	const size_t	i1,
		const size_t	i2
	)		const

inlineprotected

Parameters

i1	the helix left end in seq 1 (index including offset)
i2	the helix left end in seq 2 (index including offset)

Returns: get optimal number of bases for this left boundary

◆ getConstraint()

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

inlinevirtual

Access to the underlying helix constraint

Returns: the used helix constraint

Implements IntaRNA::HelixHandler.

◆ getHelixE() [1/2]

E_type IntaRNA::HelixHandlerUnpaired::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)

Parameters

i1	the left most interaction 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

Implements IntaRNA::HelixHandler.

◆ getHelixE() [2/2]

E_type IntaRNA::HelixHandlerUnpaired::getHelixE	(	const size_t	i1,
		const size_t	i2,
		const size_t	bp
	)

inlineprotected

Provides the helix energy during recursion

Parameters

i1	the helix left end in seq 1 (index including offset)
i2	the helix left end in seq 2 (index including offset)
bp	the number of base pairs
u1	the number of unpaired bases within seq 1
u2	the number of unpaired bases within seq 2

Returns: the energy of the according helix

◆ getHelixLength1() [1/2]

size_t IntaRNA::HelixHandlerUnpaired::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)

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

Implements IntaRNA::HelixHandler.

◆ getHelixLength1() [2/2]

size_t IntaRNA::HelixHandlerUnpaired::getHelixLength1	(	const size_t	i1,
		const size_t	i2,
		const size_t	bp
	)		const

inlinevirtual

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
bp	the number of base pairs allowed

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

◆ getHelixLength2() [1/2]

size_t IntaRNA::HelixHandlerUnpaired::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)

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

Implements IntaRNA::HelixHandler.

◆ getHelixLength2() [2/2]

size_t IntaRNA::HelixHandlerUnpaired::getHelixLength2	(	const size_t	i1,
		const size_t	i2,
		const size_t	bp
	)		const

inlinevirtual

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
bp	the number of base pairs allowed

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

◆ getHelixSeedE()

E_type IntaRNA::HelixHandlerUnpaired::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)

Parameters

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

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

Implements IntaRNA::HelixHandler.

◆ getHelixSeedLength1()

size_t IntaRNA::HelixHandlerUnpaired::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

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

Implements IntaRNA::HelixHandler.

◆ getHelixSeedLength2()

size_t IntaRNA::HelixHandlerUnpaired::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

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

Implements IntaRNA::HelixHandler.

◆ getInteractionEnergy()

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

inlinevirtual

Access to the underlying interaction energy function

Returns: the used energy function

Implements IntaRNA::HelixHandler.

◆ setHelixPair()

void IntaRNA::HelixHandlerUnpaired::setHelixPair	(	const size_t	i1,
		const size_t	i2,
		const size_t	bp,
		const E_type	E,
		const size_t	length
	)

inlineprotected

Fills the helix energy during recursion

Parameters

i1	the helix left end in seq 1 (index including offset)
i2	the helix left end in seq 2 (index including offset)
bp	the number of base pairs
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

◆ setSeedHandler()

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

inlinevirtual

Set the seedHandler in order to compute helixSeed

Parameters

seedHandler seedHandler to be used in the helix computation

Implements IntaRNA::HelixHandler.

◆ traceBackHelix() [1/2]

void IntaRNA::HelixHandlerUnpaired::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!

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.

◆ traceBackHelix() [2/2]

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

protected

Fills a given interaction with the according hybridizing base pairs of the provided helix interaction

Parameters

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

◆ traceBackHelixSeed()

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

virtual

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!

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

◆ energy

const InteractionEnergy& IntaRNA::HelixHandlerUnpaired::energy

protected

the used energy function

◆ helix

HelixMatrix IntaRNA::HelixHandlerUnpaired::helix

protected

the helix mfe information for helix starting at (i1, i2)

◆ helixConstraint

const HelixConstraint& IntaRNA::HelixHandlerUnpaired::helixConstraint

protected

the helix constraint to be applied

◆ helixE_rec

HelixRecMatrix IntaRNA::HelixHandlerUnpaired::helixE_rec

protected

the recursion data for the computation of a helix interaction bp: the number of bases i1..(i1+bp-1) and i2..(i2+bp-1) using the indexing [i1][i2][bp]

◆ helixSeed

HelixSeedMatrix IntaRNA::HelixHandlerUnpaired::helixSeed

protected

the helix mfe information for helix with seed starting at (i1, i2)

◆ offset1

size_t IntaRNA::HelixHandlerUnpaired::offset1

protected

offset for seq1 indices for the current matrices

◆ offset2

size_t IntaRNA::HelixHandlerUnpaired::offset2

protected

offset for seq2 indices for the current matrices

◆ seedHandler

SeedHandler* IntaRNA::HelixHandlerUnpaired::seedHandler

protected

used seedHandler

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

src/IntaRNA/HelixHandlerUnpaired.h

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ HelixIndex

◆ HelixMatrix

◆ HelixRecMatrix

◆ HelixSeedMatrix

Constructor & Destructor Documentation

◆ HelixHandlerUnpaired()

◆ ~HelixHandlerUnpaired()

Member Function Documentation

◆ decodeHelixLength1()

◆ decodeHelixLength2()

◆ decodeHelixSeedLength1()

◆ decodeHelixSeedLength2()

◆ encodeHelixLength()

◆ encodeHelixSeedLength()

◆ fillHelix()

◆ fillHelixSeed()

◆ getBestBP()

◆ getConstraint()

◆ getHelixE() [1/2]

◆ getHelixE() [2/2]

◆ getHelixLength1() [1/2]

◆ getHelixLength1() [2/2]

◆ getHelixLength2() [1/2]

◆ getHelixLength2() [2/2]

◆ getHelixSeedE()

◆ getHelixSeedLength1()

◆ getHelixSeedLength2()

◆ getInteractionEnergy()

◆ setHelixPair()

◆ setSeedHandler()

◆ traceBackHelix() [1/2]

◆ traceBackHelix() [2/2]

◆ traceBackHelixSeed()

Member Data Documentation

◆ energy

◆ helix

◆ helixConstraint

◆ helixE_rec

◆ helixSeed

◆ offset1

◆ offset2

◆ seedHandler