#include <SeedConstraint.h>

Collaboration diagram for IntaRNA::SeedConstraint:

[legend]

Public Member Functions
	SeedConstraint (const size_t bp, const size_t maxUnpairedOverall, const size_t maxUnpaired1, const size_t maxUnpaired2, const E_type maxE, const E_type maxED, const E_type maxEhybrid, const IndexRangeList &ranges1, const IndexRangeList &ranges2reversed, const std::string &explicitSeeds, const bool noGUallowed, const bool noGUendAllowed, const bool noLP)

virtual	~SeedConstraint ()

size_t	getBasePairs () const

size_t	getMaxUnpairedOverall () const

size_t	getMaxUnpaired1 () const

size_t	getMaxUnpaired2 () const

E_type	getMaxE () const

E_type	getMaxED () const

E_type	getMaxEhybrid () const

size_t	getMaxLength1 () const

size_t	getMaxLength2 () const

bool	isGUallowed () const

bool	isGUendAllowed () const

bool	isLpAllowed () const

const IndexRangeList &	getRanges1 () const

const IndexRangeList &	getRanges2 () const

const std::string &	getExplicitSeeds () const

IndexRangeList &	getRanges1 ()

IndexRangeList &	getRanges2 ()

std::string &	getExplicitSeeds ()

Protected Attributes
size_t	bp
	the number of base pairs to be present in a seed

size_t	maxUnpairedOverall
	the overall summed maximally allowed number of unpaired bases in a seed

size_t	maxUnpaired1
	the maximally allowed number of unpaired bases in seed seq1

size_t	maxUnpaired2
	the maximally allowed number of unpaired bases in seed seq2

E_type	maxE
	the maximal energy allowed for a seed

E_type	maxED
	the maximal ED value (per sequence) allowed for a seed

E_type	maxEhybrid
	the maximal hybridization energy (incl E_init) allowed for a seed

IndexRangeList	ranges1
	the index ranges of seq1 to be searched for seeds

IndexRangeList	ranges2
	the index ranges of seq2 to be searched for seeds

std::string	explicitSeeds
	the string encoding of the explicit seed interactions to be used

bool	bpGUallowed
	whether or not GU base pairs are allowed within seeds

bool	bpGUendAllowed
	whether or not GU base pairs are allowed at seed ends

bool	lpAllowed
	whether or not lonely base pairs are allowed

Friends
std::ostream &	operator<< (std::ostream &out, const SeedConstraint &c)

Detailed Description

Encodes seed constraints to be used for interaction prediction.

Author: Martin Mann

Constructor & Destructor Documentation

◆ SeedConstraint()

IntaRNA::SeedConstraint::SeedConstraint	(	const size_t	bp,
		const size_t	maxUnpairedOverall,
		const size_t	maxUnpaired1,
		const size_t	maxUnpaired2,
		const E_type	maxE,
		const E_type	maxED,
		const E_type	maxEhybrid,
		const IndexRangeList &	ranges1,
		const IndexRangeList &	ranges2reversed,
		const std::string &	explicitSeeds,
		const bool	noGUallowed,
		const bool	noGUendAllowed,
		const bool	noLP
	)

inline

Construction

Parameters

bp	of base pairs a seed has to have (>= 2)
maxUnpairedOverall	the maximal (summed) number of unpaired bases within both seq1 and seq2 allowed within a seed
maxUnpaired1	the maximal number of unpaired bases within seq1 allowed within a seed
maxUnpaired2	the maximal number of unpaired bases within seq2 allowed within a seed
maxE	maximal energy a seed is allowed to have
maxED	maximal ED value a seed is allowed to have for each subsequence
maxE	maximal hybridization energy (including E_init) a seed is allowed to have
ranges1	the index ranges of seq1 to be searched for seeds
ranges2reversed	the index reversed ranges of seq2 to be searched for seeds
explicitSeeds	the encodings of explicit seed interactions to be used
noGUallowed	whether or not GU base pairs are allowed within seeds
noGUendAllowed	whether or not GU base pairs are allowed at the ends of seeds
noLP	whether or not lonely base pairs are allowed

◆ ~SeedConstraint()

IntaRNA::SeedConstraint::~SeedConstraint ( )

inlinevirtual

Member Function Documentation

◆ getBasePairs()

size_t IntaRNA::SeedConstraint::getBasePairs ( ) const

inline

Provides the number of base pairs to be present within a seed

Returns: the number of base pairs a seed has to have

◆ getExplicitSeeds() [1/2]

std::string & IntaRNA::SeedConstraint::getExplicitSeeds ( )

inline

Access to the explicit seed encodings to be used for prediction.

Returns: the provided explicit seed encodings

◆ getExplicitSeeds() [2/2]

const std::string & IntaRNA::SeedConstraint::getExplicitSeeds ( ) const

inline

Access to the explicit seed encodings to be used for prediction.

Returns: the provided explicit seed encodings

◆ getMaxE()

E_type IntaRNA::SeedConstraint::getMaxE ( ) const

inline

Provides the maximally allowed energy for seeds to be considered

Returns: the maximally allowed energy for a seed

◆ getMaxED()

E_type IntaRNA::SeedConstraint::getMaxED ( ) const

inline

Provides the maximally allowed ED value for each seed subsequence to be considered

Returns: the maximally allowed ED value (per sequence) for a seed

◆ getMaxEhybrid()

E_type IntaRNA::SeedConstraint::getMaxEhybrid ( ) const

inline

Provides the maximally allowed hybridization energy (including E_init) for seeds to be considered

Returns: the maximally allowed hybridization energy for a seed

◆ getMaxLength1()

size_t IntaRNA::SeedConstraint::getMaxLength1 ( ) const

inline

Provides the maximal length of the seed in seq1

Returns: the maximal length of the seed in seq1

◆ getMaxLength2()

size_t IntaRNA::SeedConstraint::getMaxLength2 ( ) const

inline

Provides the maximal length of the seed in seq2

Returns: the maximal length of the seed in seq2

◆ getMaxUnpaired1()

size_t IntaRNA::SeedConstraint::getMaxUnpaired1 ( ) const

inline

Provides the maximal number of unpaired bases within the first sequence within a seed

Returns: the maximal number of unpaired bases within the first sequence a seed is allowed to have

◆ getMaxUnpaired2()

size_t IntaRNA::SeedConstraint::getMaxUnpaired2 ( ) const

inline

Provides the maximal number of unpaired bases within the second sequence within a seed

Returns: the maximal number of unpaired bases within the second sequence a seed is allowed to have

◆ getMaxUnpairedOverall()

size_t IntaRNA::SeedConstraint::getMaxUnpairedOverall ( ) const

inline

Provides the overall maximal number of unpaired bases within a seed

Returns: the overall maximal number of unpaired bases within a seed is allowed to have

◆ getRanges1() [1/2]

IndexRangeList & IntaRNA::SeedConstraint::getRanges1 ( )

inline

Index ranges in seq1 to be searched for seeds or empty if all indices are to be considered.

Returns: index ranges to be searched or empty list if all indices relevant

◆ getRanges1() [2/2]

const IndexRangeList & IntaRNA::SeedConstraint::getRanges1 ( ) const

inline

Index ranges in seq1 to be searched for seeds or empty if all indices are to be considered.

Returns: index ranges to be searched or empty list if all indices relevant

◆ getRanges2() [1/2]

IndexRangeList & IntaRNA::SeedConstraint::getRanges2 ( )

inline

Index ranges in seq2 to be searched for seeds or empty if all indices are to be considered.

Returns: index ranges to be searched or empty list if all indices relevant

◆ getRanges2() [2/2]

const IndexRangeList & IntaRNA::SeedConstraint::getRanges2 ( ) const

inline

Index ranges in seq2 to be searched for seeds or empty if all indices are to be considered.

Returns: index ranges to be searched or empty list if all indices relevant

◆ isGUallowed()

bool IntaRNA::SeedConstraint::isGUallowed ( ) const

inline

Whether or not GU base pairs are allowed within seeds

Returns: true if GU base pairs are allowed; false otherwise

◆ isGUendAllowed()

bool IntaRNA::SeedConstraint::isGUendAllowed ( ) const

inline

Whether or not GU base pairs are allowed at seed ends

Returns: true if GU base pairs are allowed at seed ends; false otherwise

◆ isLpAllowed()

bool IntaRNA::SeedConstraint::isLpAllowed ( ) const

inline

Whether or not lonely base pairs are allowed

Returns: true if lonely base pairs are allowed; false otherwise

Friends And Related Symbol Documentation

◆ operator<<

std::ostream & operator<<	(	std::ostream &	out,
		const SeedConstraint &	c
	)

friend

Prints the seed constraint details to stream

Parameters

out	the ostream to write to
c	the object to add

Returns: the altered stream out

Member Data Documentation

◆ bp

size_t IntaRNA::SeedConstraint::bp

protected

the number of base pairs to be present in a seed

◆ bpGUallowed

bool IntaRNA::SeedConstraint::bpGUallowed

protected

whether or not GU base pairs are allowed within seeds

◆ bpGUendAllowed

bool IntaRNA::SeedConstraint::bpGUendAllowed

protected

whether or not GU base pairs are allowed at seed ends

◆ explicitSeeds

std::string IntaRNA::SeedConstraint::explicitSeeds

protected

the string encoding of the explicit seed interactions to be used

◆ lpAllowed

bool IntaRNA::SeedConstraint::lpAllowed

protected

whether or not lonely base pairs are allowed

◆ maxE

E_type IntaRNA::SeedConstraint::maxE

protected

the maximal energy allowed for a seed

◆ maxED

E_type IntaRNA::SeedConstraint::maxED

protected

the maximal ED value (per sequence) allowed for a seed

◆ maxEhybrid

E_type IntaRNA::SeedConstraint::maxEhybrid

protected

the maximal hybridization energy (incl E_init) allowed for a seed

◆ maxUnpaired1

size_t IntaRNA::SeedConstraint::maxUnpaired1

protected

the maximally allowed number of unpaired bases in seed seq1

◆ maxUnpaired2

size_t IntaRNA::SeedConstraint::maxUnpaired2

protected

the maximally allowed number of unpaired bases in seed seq2

◆ maxUnpairedOverall

size_t IntaRNA::SeedConstraint::maxUnpairedOverall

protected

the overall summed maximally allowed number of unpaired bases in a seed

◆ ranges1

IndexRangeList IntaRNA::SeedConstraint::ranges1

protected

the index ranges of seq1 to be searched for seeds

◆ ranges2

IndexRangeList IntaRNA::SeedConstraint::ranges2

protected

the index ranges of seq2 to be searched for seeds

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

src/IntaRNA/SeedConstraint.h

Public Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ SeedConstraint()

◆ ~SeedConstraint()

Member Function Documentation

◆ getBasePairs()

◆ getExplicitSeeds() [1/2]

◆ getExplicitSeeds() [2/2]

◆ getMaxE()

◆ getMaxED()

◆ getMaxEhybrid()

◆ getMaxLength1()

◆ getMaxLength2()

◆ getMaxUnpaired1()

◆ getMaxUnpaired2()

◆ getMaxUnpairedOverall()

◆ getRanges1() [1/2]

◆ getRanges1() [2/2]

◆ getRanges2() [1/2]

◆ getRanges2() [2/2]

◆ isGUallowed()

◆ isGUendAllowed()

◆ isLpAllowed()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ bp

◆ bpGUallowed

◆ bpGUendAllowed

◆ explicitSeeds

◆ lpAllowed

◆ maxE

◆ maxED

◆ maxEhybrid

◆ maxUnpaired1

◆ maxUnpaired2

◆ maxUnpairedOverall

◆ ranges1

◆ ranges2