#include <Interaction.h>

Collaboration diagram for IntaRNA::Interaction:

[legend]

Classes
class	BasePair
	type of a base pair index encoding More...

class	Boundary

class	Seed

Public Types
typedef std::vector< BasePair >	PairingVec
	type of a vector encoding base pair indices that are interacting

typedef std::set< Seed >	SeedSet
	type of a vector containing seeds

Public Member Functions
	Interaction (const RnaSequence &s1, const RnaSequence &s2)

	Interaction (const Interaction &toCopy)

	Interaction (const InteractionRange &range)

virtual	~Interaction ()

bool	isValid () const

bool	isEmpty () const

void	sort ()

void	clear ()

void	setSeedRange (const BasePair bp_left, const BasePair bp_right, const E_type energy)

IndexRangeList	getSeedRanges1 () const

IndexRangeList	getSeedRanges2 () const

Interaction &	operator= (const Interaction &toCopy)

Interaction &	operator= (const InteractionRange &range)

bool	operator< (const Interaction &i) const

bool	operator== (const Interaction &i) const

Static Public Member Functions
static bool	compareEnergy (const E_type &energy, const Interaction &hasLargerE)

static std::string	dotBar (const Interaction &i, const bool fullLength=false)

static std::string	dotBracket (const Interaction &i, const char symOpen='(', const char symClose=')', const bool fullLength=false)

Public Attributes
const RnaSequence *	s1
	the first interaction partner

const RnaSequence *	s2
	the second interaction partner

PairingVec	basePairs
	interacting indices

E_type	energy
	energy of the interaction

SeedSet *	seed
	optional: seed information

Static Protected Member Functions
template<typename bpIterator >
static std::string	dotSomething (bpIterator bpBegin, const bpIterator bpEnd, const bool handleSeq1, const char bpSymbol)

Friends
std::ostream &	operator<< (std::ostream &out, const BasePair &bp)

std::ostream &	operator<< (std::ostream &out, const Boundary &b)

std::ostream &	operator<< (std::ostream &out, const Interaction &i)

Detailed Description

Data structure to describe and store an Interaction

Member Typedef Documentation

◆ PairingVec

typedef std::vector<BasePair> IntaRNA::Interaction::PairingVec

type of a vector encoding base pair indices that are interacting

◆ SeedSet

typedef std::set<Seed> IntaRNA::Interaction::SeedSet

type of a vector containing seeds

Constructor & Destructor Documentation

◆ Interaction() [1/3]

IntaRNA::Interaction::Interaction	(	const RnaSequence &	s1,
		const RnaSequence &	s2
	)

inline

construction

Parameters

s1	the sequence of the first interaction partner
s2	the sequence of the second interaction partner

◆ Interaction() [2/3]

IntaRNA::Interaction::Interaction ( const Interaction & toCopy )

inline

copy construction from interaction

Parameters

toCopy the interaction range to make this a copy of

◆ Interaction() [3/3]

IntaRNA::Interaction::Interaction ( const InteractionRange & range )

inline

construction from interaction range, ie. forming base pairs at the beginning and end of the interaction range.

NOTE: the ends have to be complementary nucleotides

Parameters

range the interaction range to be used for initialization

◆ ~Interaction()

IntaRNA::Interaction::~Interaction ( )

inlinevirtual

destruction

Member Function Documentation

◆ clear()

void IntaRNA::Interaction::clear ( )

inline

Clears all interaction information.

◆ compareEnergy()

bool IntaRNA::Interaction::compareEnergy	(	const E_type &	energy,
		const Interaction &	hasLargerE
	)

inlinestatic

Compares if an interaction has larger energy that a given value

Parameters

energy	the energy to compare to
hasLargerE	the interaction that is supposed to have larger energy

Returns: (energy < (hasLargerE.energy-precisionDelta))

◆ dotBar()

static std::string IntaRNA::Interaction::dotBar	(	const Interaction &	i,
		const bool	fullLength = `false`
	)

static

Produces a dot-bar encoding of the interaction in the form

startId1 dot-bar-1 & startId2 dot-bar-2

where dot-bar-1/2 encodes all positions of the first/second sequence enclosed by the first and last base pair of the interaction. Here, a '|' bar encodes an intermolecular base pair and a '.' dot encodes unpaired positions.

Note, within this encoding, the '&' separated parts can be swapped if needed yielding still a valid encoding (for the swapped sequences).

Parameters

i	interaction to encode
fullLength	whether or not full length base pair annotation is to be printed

Returns: the dot-bracket encoding

◆ dotBracket()

static std::string IntaRNA::Interaction::dotBracket	(	const Interaction &	i,
		const char	symOpen = `'('`,
		const char	symClose = `')'`,
		const bool	fullLength = `false`
	)

static

Produces a dot-bracket encoding of the interaction in VRNA style in the form

dot-bracket-1 & dot-bracket-2

where dot-bracket-1/2 encodes all positions of the first/second sequence enclosed by the first and last base pair of the interaction. In dot-bracket-1, a closing '(' parenthesis encodes an intermolecular base pair and a '.' dot encodes unpaired positions. In dot-bracket-2, closing ')' parentheses are used to mark base pairs.

Parameters

i	interaction to encode
symOpen	the symbol to be used for base pairs in dot-bracket-1
symClose	the symbol to be used for base pairs in dot-bracket-2
fullLength	whether or not full length base pair annotation is to be printed

Returns: the VRNA-styled dot-bracket encoding

◆ dotSomething()

template<typename bpIterator >

std::string IntaRNA::Interaction::dotSomething	(	bpIterator	bpBegin,
		const bpIterator	bpEnd,
		const bool	handleSeq1,
		const char	bpSymbol
	)

inlinestaticprotected

◆ getSeedRanges1()

IndexRangeList IntaRNA::Interaction::getSeedRanges1 ( ) const

Compiles the list of ranges in seq1 covered by seeds.

Returns: the list of ranges covered by seeds in seq1

◆ getSeedRanges2()

IndexRangeList IntaRNA::Interaction::getSeedRanges2 ( ) const

Compiles the list of ranges in seq2 covered by seeds.

Returns: the list of ranges covered by seeds in seq2

◆ isEmpty()

bool IntaRNA::Interaction::isEmpty ( ) const

inline

Checks whether or not the interaction contains no base pairs.

Returns: true if the interaction encodes no base pair; false otherwise

◆ isValid()

bool IntaRNA::Interaction::isValid ( ) const

checks whether or not the current interaction is non-empty, nested and sorted.

Returns: true if the interaction encoding is non-empty, nested and sorted; false otherwise

◆ operator<()

bool IntaRNA::Interaction::operator< ( const Interaction & i ) const

inline

Checks whether or not this interaction is considered better (smaller) than another interaction of the same sequences

Parameters

i	the interaction to compare to (for the same sequences!)

Returns: energy < i.energy || (energy == i.energy && bpLeft < i.bpLeft) || (energy == i.energy && bpLeft == i.bpLeft && bpRight < i.bpRight)

◆ operator=() [1/2]

Interaction & IntaRNA::Interaction::operator= ( const Interaction & toCopy )

Creates an interaction with one base pair for each interaction range boundary.

NOTE: the ends have to be complementary nucleotides

NOTE: the interaction energy is reset too.

Parameters

toCopy the interaction to copy

Returns: the altered object (*this)

◆ operator=() [2/2]

Interaction & IntaRNA::Interaction::operator= ( const InteractionRange & range )

Creates an interaction with one base pair for each interaction range boundary.

NOTE: the ends have to be complementary nucleotides

NOTE: the interaction energy is reset too.

Parameters

range the interaction range to copy

Returns: the altered object (*this)

◆ operator==()

bool IntaRNA::Interaction::operator== ( const Interaction & i ) const

Checks whether or not this interaction equals another

Parameters

i	the interaction to compare to (for the same sequences!)

Returns: (equal sequence pointers) && (same energy) && (same positions)

◆ setSeedRange()

void IntaRNA::Interaction::setSeedRange	(	const BasePair	bp_left,
		const BasePair	bp_right,
		const E_type	energy
	)

Sets the seedRange member according to the given data

Parameters

bp_left	left most base pair in seed
bp_right	right most base pair in seed
energy	full energy of the seed interaction

◆ sort()

void IntaRNA::Interaction::sort ( )

inline

Sorts the stored interacting base pairs.

Friends And Related Symbol Documentation

◆ operator<< [1/3]

std::ostream & operator<<	(	std::ostream &	out,
		const BasePair &	bp
	)

friend

Prints the interacting base pair to stream

Parameters

out	the ostream to write to
bp	the Interaction base pair object to add

Returns: the altered stream out

◆ operator<< [2/3]

std::ostream & operator<<	(	std::ostream &	out,
		const Boundary &	b
	)

friend

Prints the interaction boundary to stream

Parameters

out	the ostream to write to
b	the Boundary object to add

Returns: the altered stream out

◆ operator<< [3/3]

std::ostream & operator<<	(	std::ostream &	out,
		const Interaction &	i
	)

friend

Prints the interacting base pairs to stream

Parameters

out	the ostream to write to
i	the Interaction object to add

Returns: the altered stream out

Member Data Documentation

◆ basePairs

PairingVec IntaRNA::Interaction::basePairs

interacting indices

◆ energy

E_type IntaRNA::Interaction::energy

energy of the interaction

◆ s1

const RnaSequence* IntaRNA::Interaction::s1

the first interaction partner

◆ s2

const RnaSequence* IntaRNA::Interaction::s2

the second interaction partner

◆ seed

SeedSet* IntaRNA::Interaction::seed

optional: seed information

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

src/IntaRNA/Interaction.h

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Protected Member Functions

Friends

Detailed Description

Member Typedef Documentation

◆ PairingVec

◆ SeedSet

Constructor & Destructor Documentation

◆ Interaction() [1/3]

◆ Interaction() [2/3]

◆ Interaction() [3/3]

◆ ~Interaction()

Member Function Documentation

◆ clear()

◆ compareEnergy()

◆ dotBar()

◆ dotBracket()

◆ dotSomething()

◆ getSeedRanges1()

◆ getSeedRanges2()

◆ isEmpty()

◆ isValid()

◆ operator<()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setSeedRange()

◆ sort()

Friends And Related Symbol Documentation

◆ operator<< [1/3]

◆ operator<< [2/3]

◆ operator<< [3/3]

Member Data Documentation

◆ basePairs

◆ energy

◆ s1

◆ s2

◆ seed