#include <SeedHandlerExplicit.h>

Inheritance diagram for IntaRNA::SeedHandlerExplicit:

Collaboration diagram for IntaRNA::SeedHandlerExplicit:

[legend]

Classes
class	SeedData

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

virtual	~SeedHandlerExplicit ()

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

Static Public Member Functions
static std::string	checkSeedEncoding (const std::string &seed)

static size_t	getSeedMinBP (const std::string &seedEncoding)

Protected Attributes
boost::unordered_map< Interaction::BasePair, SeedData, Interaction::BasePair::Hash >	seedForLeftEnd
	container to store

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

const SeedConstraint &	seedConstraint
	the seed constraint to be applied

Detailed Description

Enables the explicit definition of possible seed interactions.

Only the provided seeds will be considered for interaction prediction.

Constructor & Destructor Documentation

◆ SeedHandlerExplicit()

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

Construction

Parameters

energy	the energy function to be used for seed prediction
seedConstraint	the seed constraint to be applied that contains the explicit seed encodings

◆ ~SeedHandlerExplicit()

virtual IntaRNA::SeedHandlerExplicit::~SeedHandlerExplicit ( )

virtual

destruction

Member Function Documentation

◆ checkSeedEncoding()

static std::string IntaRNA::SeedHandlerExplicit::checkSeedEncoding ( const std::string & seed )

static

checks whether or not a given explicit seed encoding is valid or not

Parameters

seed	the seed encoding to check

Returns: an empty string for valid encodings; or an error description otherwise

◆ fillSeed()

virtual size_t IntaRNA::SeedHandlerExplicit::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()

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

virtual

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

Implements IntaRNA::SeedHandler.

◆ getSeedLength1()

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

virtual

Access to the length in seq1 of the 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()

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

virtual

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

Implements IntaRNA::SeedHandler.

◆ getSeedMinBP()

static size_t IntaRNA::SeedHandlerExplicit::getSeedMinBP ( const std::string & seedEncoding )

static

parses the given explicit seed encoding for the minimal number of base pairs within any of the encoded seed

Parameters

seedEncoding the explicit seed encoding to parse

Returns: the minimal number of base pairs among all encoded seeds

◆ isSeedBound()

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

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

Implements IntaRNA::SeedHandler.

◆ traceBackSeed()

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

virtual

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

NOTE: the left- and right-most base pair is 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::SeedHandlerExplicit::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

boost::unordered_map< Interaction::BasePair, SeedData, Interaction::BasePair::Hash > IntaRNA::SeedHandlerExplicit::seedForLeftEnd

protected

container to store

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

src/IntaRNA/SeedHandlerExplicit.h

Classes

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SeedHandlerExplicit()

◆ ~SeedHandlerExplicit()

Member Function Documentation

◆ checkSeedEncoding()

◆ fillSeed()

◆ getSeedE()

◆ getSeedLength1()

◆ getSeedLength2()

◆ getSeedMinBP()

◆ isSeedBound()

◆ traceBackSeed()

◆ updateToNextSeed()

Member Data Documentation

◆ seedForLeftEnd