#include <HelixHandlerNoBulgeMax.h>

Inheritance diagram for IntaRNA::HelixHandlerNoBulgeMax:

Collaboration diagram for IntaRNA::HelixHandlerNoBulgeMax:

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Public Types
typedef std::pair< E_type, size_t >	HelixData
	type used to store helix information (energy and length)

typedef boost::unordered_map< Interaction::BasePair, HelixData, Interaction::BasePair::Hash >	HelixHash

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

virtual	~HelixHandlerNoBulgeMax ()

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, 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

void	setSeedHandler (SeedHandler &seedHandler)

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

virtual	~HelixHandler ()

Protected Types
typedef HelixHash::key_type	BP
	shortening typedef

Protected Member Functions
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

Protected Attributes
const InteractionEnergy &	energy
	the used energy function

const HelixConstraint &	helixConstraint
	the helix constraint to be applied

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

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

SeedHandler *	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 maximal canonical helix information that is based on stacked base pairs only.

Author: Martin Raden

Member Typedef Documentation

◆ BP

typedef HelixHash::key_type IntaRNA::HelixHandlerNoBulgeMax::BP

protected

shortening typedef

◆ HelixData

typedef std::pair<E_type, size_t> IntaRNA::HelixHandlerNoBulgeMax::HelixData

type used to store helix information (energy and length)

◆ HelixHash

typedef boost::unordered_map< Interaction::BasePair, HelixData, Interaction::BasePair::Hash > IntaRNA::HelixHandlerNoBulgeMax::HelixHash

container type for sparse helix information for a given left-most base pair (i1,i2) it holds both the energy (first) as well as the length of the helix

Constructor & Destructor Documentation

◆ HelixHandlerNoBulgeMax()

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

inline

Constructor

Parameters

energy the energy function to be used

◆ ~HelixHandlerNoBulgeMax()

IntaRNA::HelixHandlerNoBulgeMax::~HelixHandlerNoBulgeMax ( )

inlinevirtual

destructor

Member Function Documentation

◆ decodeHelixSeedLength1()

size_t IntaRNA::HelixHandlerNoBulgeMax::decodeHelixSeedLength1 ( 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

◆ decodeHelixSeedLength2()

size_t IntaRNA::HelixHandlerNoBulgeMax::decodeHelixSeedLength2 ( 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

◆ encodeHelixSeedLength()

size_t IntaRNA::HelixHandlerNoBulgeMax::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::HelixHandlerNoBulgeMax::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: number of valid helices

Implements IntaRNA::HelixHandler.

◆ fillHelixSeed()

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

virtual

Compute the helix matrix, containing a seed, 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.

◆ getConstraint()

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

inlinevirtual

Access to the underlying helix constraint

Returns: the used helix constraint

Implements IntaRNA::HelixHandler.

◆ getHelixE()

E_type IntaRNA::HelixHandlerNoBulgeMax::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 or return 0 if bp is 0 or 1 (used in helixHandlerSeed computation to avoid too many conditions)

Implements IntaRNA::HelixHandler.

◆ getHelixLength1()

size_t IntaRNA::HelixHandlerNoBulgeMax::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.

◆ getHelixLength2()

size_t IntaRNA::HelixHandlerNoBulgeMax::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.

◆ getHelixSeedE()

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

inlinevirtual

Access to the mfe of any helix, containing a seed, 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.

◆ getHelixSeedLength1()

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

inlinevirtual

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

Implements IntaRNA::HelixHandler.

◆ getHelixSeedLength2()

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

inlinevirtual

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

Implements IntaRNA::HelixHandler.

◆ getInteractionEnergy()

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

inlinevirtual

Access to the underlying interaction energy function

Returns: the used energy function

Implements IntaRNA::HelixHandler.

◆ setSeedHandler()

void IntaRNA::HelixHandlerNoBulgeMax::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()

virtual void IntaRNA::HelixHandlerNoBulgeMax::traceBackHelix	(	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.

◆ traceBackHelixSeed()

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

virtual

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

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::HelixHandlerNoBulgeMax::energy

protected

the used energy function

◆ helix

HelixHash IntaRNA::HelixHandlerNoBulgeMax::helix

protected

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

◆ helixConstraint

const HelixConstraint& IntaRNA::HelixHandlerNoBulgeMax::helixConstraint

protected

the helix constraint to be applied

◆ helixSeed

HelixHash IntaRNA::HelixHandlerNoBulgeMax::helixSeed

protected

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

◆ seedHandler

SeedHandler* IntaRNA::HelixHandlerNoBulgeMax::seedHandler

protected

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

src/IntaRNA/HelixHandlerNoBulgeMax.h

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ BP

◆ HelixData

◆ HelixHash

Constructor & Destructor Documentation

◆ HelixHandlerNoBulgeMax()

◆ ~HelixHandlerNoBulgeMax()

Member Function Documentation

◆ decodeHelixSeedLength1()

◆ decodeHelixSeedLength2()

◆ encodeHelixSeedLength()

◆ fillHelix()

◆ fillHelixSeed()

◆ getConstraint()

◆ getHelixE()

◆ getHelixLength1()

◆ getHelixLength2()

◆ getHelixSeedE()

◆ getHelixSeedLength1()

◆ getHelixSeedLength2()

◆ getInteractionEnergy()

◆ setSeedHandler()

◆ traceBackHelix()

◆ traceBackHelixSeed()

Member Data Documentation

◆ energy

◆ helix

◆ helixConstraint

◆ helixSeed

◆ seedHandler