IntaRNA::SeedHandlerNoBulge Class Reference

#include <SeedHandlerNoBulge.h>

Inheritance diagram for IntaRNA::SeedHandlerNoBulge:

Collaboration diagram for IntaRNA::SeedHandlerNoBulge:

Public Member Functions
	SeedHandlerNoBulge (const InteractionEnergy &energy, const SeedConstraint &seedConstraint)
virtual	~SeedHandlerNoBulge ()
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 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
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 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 Types
typedef std::vector< E_type >	StackingEnergyList
	container to store stacking energies of seed base pairs
typedef boost::unordered_map< Interaction::BasePair, E_type, Interaction::BasePair::Hash >	SeedHash
	container type for sparse seed information

Protected Member Functions
void	storeSeed (const size_t j1, const size_t j2, const StackingEnergyList &bpE)

Protected Attributes
SeedHash	seedForLeftEnd
	container to store seeds' hybridization energies
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 seed interaction information for each intermolecular index combination (= left end of seed) for perfectly stacked seeds only, ie. seed contain no bulges.

Member Typedef Documentation

SeedHash

typedef boost::unordered_map< Interaction::BasePair, E_type, Interaction::BasePair::Hash > IntaRNA::SeedHandlerNoBulge::SeedHash

protected

container type for sparse seed information

StackingEnergyList

typedef std::vector<E_type> IntaRNA::SeedHandlerNoBulge::StackingEnergyList

protected

container to store stacking energies of seed base pairs

Constructor & Destructor Documentation

SeedHandlerNoBulge()

IntaRNA::SeedHandlerNoBulge::SeedHandlerNoBulge ( 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

~SeedHandlerNoBulge()

IntaRNA::SeedHandlerNoBulge::~SeedHandlerNoBulge ( )

inlinevirtual

destruction

Member Function Documentation

fillSeed()

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

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

Implements IntaRNA::SeedHandler.

getSeedE()

E_type IntaRNA::SeedHandlerNoBulge::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.

getSeedLength1()

size_t IntaRNA::SeedHandlerNoBulge::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::SeedHandlerNoBulge::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::SeedHandlerNoBulge::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.

storeSeed()

void IntaRNA::SeedHandlerNoBulge::storeSeed ( const size_t  j1, const size_t  j2, const StackingEnergyList &  bpE  )

inlineprotected

Checks and stores a given seed candidate

Parameters

j1	right-most seed position in seq1
j2	right-most seed position in seq2
bpE	list of stacking energies for this seed

traceBackSeed()

void IntaRNA::SeedHandlerNoBulge::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.

updateToNextSeed()

virtual bool IntaRNA::SeedHandlerNoBulge::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 from IntaRNA::SeedHandler.

Member Data Documentation

seedForLeftEnd

SeedHash IntaRNA::SeedHandlerNoBulge::seedForLeftEnd

protected

container to store seeds' hybridization energies

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

• src/IntaRNA/SeedHandlerNoBulge.h