IntaRNA::AccessibilityConstraint Class Reference

#include <AccessibilityConstraint.h>

Collaboration diagram for IntaRNA::AccessibilityConstraint:

Public Member Functions
	AccessibilityConstraint (const size_t length, const size_t maxBpSpan, const std::string &shapeFile, const std::string &shapeMethod, const std::string &shapeConversion)
	AccessibilityConstraint (const AccessibilityConstraint &toCopy, const bool reverseIndices=false)
	AccessibilityConstraint (const RnaSequence &seq, const std::string &dotBracket, const size_t maxBpSpan, const std::string &shapeFile, const std::string &shapeMethod, const std::string &shapeConversion)
virtual	~AccessibilityConstraint ()
bool	isMarkedBlocked (const size_t i) const
bool	isMarkedAccessible (const size_t i) const
bool	isMarkedPaired (const size_t i) const
bool	isUnconstrained (const size_t i) const
bool	isAccessible (const size_t i) const
bool	isEmpty () const
char	getVrnaDotBracket (const size_t i) const
size_t	getMaxBpSpan () const
const std::string &	getShapeFile () const
const std::string &	getShapeMethod () const
const std::string &	getShapeConversion () const
AccessibilityConstraint &	operator= (const AccessibilityConstraint &c)

Static Public Attributes
static const char	dotBracket_unconstrained
	the marker for unconstrained positions in dot-bracket notation
static const char	dotBracket_blocked
	the marker for blocked positions in dot-bracket notation
static const char	dotBracket_accessible
	the marker for accessible positions in dot-bracket notation
static const char	dotBracket_paired
	the marker for paired positions in dot-bracket notation
static const std::string	dotBracket_constraints
	collection of all allowed encoding of constraints
static const std::string	dotBracketAlphabet
	the alphabet to encode accessibility constraints in dot-bracket notation
static const std::string	regionIndexList
	regular expression that encodes a single region encoding as index list
static const boost::regex	regex
	the regular expression that marks a non-empty valid constraint encoding
static const boost::regex	regexShapeMethod
	the regular expression to be matched by shapeMethod encodings
static const boost::regex	regexShapeConversion
	the regular expression to be matched by shapeConversion encodings

Static Protected Member Functions
static void	screenDotBracket (const std::string &dotBracket, const char marker, IndexRangeList &storage)

Protected Attributes
size_t	length
	the overall sequence length this constraint is about
size_t	maxBpSpan
	the maximal base pair span to be used for accessibility computation
std::string	shapeFile
	filename of SHAPE reactivity data or empty if no SHAPE data to be used
std::string	shapeMethod
	method for converting SHAPE reactivity data to pseudo energies
std::string	shapeConversion
	method for conversion of SHAPE reactivity data to paired probabilities
IndexRangeList	blocked
	sorted list of ranges that are marked as blocked
IndexRangeList	accessible
	sorted list of ranges that are marked as accessible
IndexRangeList	paired
	sorted list of ranges that are marked as paired (intramolecular)

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

Detailed Description

Represents the constraints for accessibility computation, ie. sequence regions that are known to be blocked (not available to interaction) or for sure accessible.

These constraints are than incorporated into the computation of the accessibility (ED) values to be used for interaction prediction.

Author

Martin Mann

Constructor & Destructor Documentation

AccessibilityConstraint() [1/3]

IntaRNA::AccessibilityConstraint::AccessibilityConstraint ( const size_t  length, const size_t  maxBpSpan, const std::string &  shapeFile, const std::string &  shapeMethod, const std::string &  shapeConversion  )

inline

Empty constraint construction

Parameters

length	length of the constrained sequence
maxBpSpan	the maximal base pair span to be used for accessibility computation; set to 0 for full sequence length
shapeFile	if non-empty: name of the SHAPE reactivity data file to be used for accessibility computation
shapeMethod	if non-empty: encoding of the method to be used to convert SHAPE reactivity data to pseudo energies
shapeConversion	if non-empty: encoding of the method to be used to convert SHAPE reactivity data to pairing probabilities

AccessibilityConstraint() [2/3]

IntaRNA::AccessibilityConstraint::AccessibilityConstraint ( const AccessibilityConstraint &  toCopy, const bool  reverseIndices = false  )

inline

Copy construction

Parameters

toCopy	the constraint to copy
reverseIndices	whether or not to reverse indexing (eg to be used for ReverseAccessibility)

AccessibilityConstraint() [3/3]

IntaRNA::AccessibilityConstraint::AccessibilityConstraint	(	const RnaSequence &	seq,
		const std::string &	dotBracket,
		const size_t	maxBpSpan,
		const std::string &	shapeFile,
		const std::string &	shapeMethod,
		const std::string &	shapeConversion
	)

Constraint construction based on VRNA-like dot-bracket encoding

Parameters

seq	the constrained sequence
dotBracket	the constraint encoding in VRNA-like dot-bracket encoding
maxBpSpan	the maximal base pair span to be used for accessibility computation; set to 0 for full sequence length
shapeFile	if non-empty: name of the SHAPE reactivity data file to be used for accessibility computation
shapeMethod	if non-empty: encoding of the method to be used to convert SHAPE reactivity data to pseudo energies
shapeConversion	if non-empty: encoding of the method to be used to convert SHAPE reactivity data to pairing probabilities

~AccessibilityConstraint()

IntaRNA::AccessibilityConstraint::~AccessibilityConstraint ( )

inlinevirtual

Member Function Documentation

getMaxBpSpan()

size_t IntaRNA::AccessibilityConstraint::getMaxBpSpan ( ) const

inline

Provides the maximal base pair span to be considered for accessibility computation.

Returns

the maximal base pair span for accessibility computation

getShapeConversion()

const std::string & IntaRNA::AccessibilityConstraint::getShapeConversion ( ) const

inline

Get method how to convert SHAPE reactivity data to pairing probabilities.

Returns

the encoding or an empty string if no SHAPE data available

getShapeFile()

const std::string & IntaRNA::AccessibilityConstraint::getShapeFile ( ) const

inline

Get filename from where to read SHAPE reactivity data.

Returns

the filename or an empty string if no SHAPE data available

getShapeMethod()

const std::string & IntaRNA::AccessibilityConstraint::getShapeMethod ( ) const

inline

Get method how to convert SHAPE reactivity data to pseudo energies.

Returns

the encoding or an empty string if no SHAPE data available

getVrnaDotBracket()

char IntaRNA::AccessibilityConstraint::getVrnaDotBracket ( const size_t  i ) const

inline

Provides the VRNA dot-bracket notation of the constraint for position i

Parameters

i	the position of interest

Returns

the VRNA conform constraint encoding for position i

isAccessible()

bool IntaRNA::AccessibilityConstraint::isAccessible ( const size_t  i ) const

inline

Checks whether or not a position is available for interaction

Parameters

i	the position of interest

Returns

true if the position i is available interaction; false otherwise

isEmpty()

bool IntaRNA::AccessibilityConstraint::isEmpty ( ) const

inline

Checks whether or not any accessibility constraints (base pairs, blocked, accessible, etc.) are given

Returns

true if no structural constraints are present; false otherwise

isMarkedAccessible()

bool IntaRNA::AccessibilityConstraint::isMarkedAccessible ( const size_t  i ) const

inline

Checks whether or not a sequence position is marked as accessible or not

Parameters

i	the position of interest

Returns

true if position i is marked accessible

isMarkedBlocked()

bool IntaRNA::AccessibilityConstraint::isMarkedBlocked ( const size_t  i ) const

inline

Checks whether or not a sequence position is marked as blocked or not

Parameters

i	the position of interest

Returns

true if position i is marked blocked

isMarkedPaired()

bool IntaRNA::AccessibilityConstraint::isMarkedPaired ( const size_t  i ) const

inline

Checks whether or not a sequence position is marked as intramolecularly paired or not

Parameters

i	the position of interest

Returns

true if position i is marked accessible

isUnconstrained()

bool IntaRNA::AccessibilityConstraint::isUnconstrained ( const size_t  i ) const

inline

Checks whether or not a sequence position is not constrained

Parameters

i	the position of interest

Returns

true if position i is not constrained

operator=()

AccessibilityConstraint & IntaRNA::AccessibilityConstraint::operator= ( const AccessibilityConstraint &  c )

inline

Assignment of constraints for the same rna sequence.

Parameters

c	the interaction to make this a copy of

screenDotBracket()

static void IntaRNA::AccessibilityConstraint::screenDotBracket ( const std::string &  dotBracket, const char  marker, IndexRangeList &  storage  )

staticprotected

screens the given dot-bracket string for consecutive regions of marker characters and pushes the according regions to the storage

Parameters

dotBracket	the dot-bracket encoding to screen
marker	the marker character to screen for
storage	the container to push the identified regions to

Friends And Related Symbol Documentation

operator<<

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

friend

Prints the accessibility constraint in range-based encoding to stream

Parameters

out	the ostream to write to
c	the AccessibilityConstraint object to add

Returns

the altered stream out

Member Data Documentation

accessible

IndexRangeList IntaRNA::AccessibilityConstraint::accessible

protected

sorted list of ranges that are marked as accessible

blocked

IndexRangeList IntaRNA::AccessibilityConstraint::blocked

protected

sorted list of ranges that are marked as blocked

dotBracket_accessible

const char IntaRNA::AccessibilityConstraint::dotBracket_accessible

static

the marker for accessible positions in dot-bracket notation

dotBracket_blocked

const char IntaRNA::AccessibilityConstraint::dotBracket_blocked

static

the marker for blocked positions in dot-bracket notation

dotBracket_constraints

const std::string IntaRNA::AccessibilityConstraint::dotBracket_constraints

static

collection of all allowed encoding of constraints

dotBracket_paired

const char IntaRNA::AccessibilityConstraint::dotBracket_paired

static

the marker for paired positions in dot-bracket notation

dotBracket_unconstrained

const char IntaRNA::AccessibilityConstraint::dotBracket_unconstrained

static

the marker for unconstrained positions in dot-bracket notation

dotBracketAlphabet

const std::string IntaRNA::AccessibilityConstraint::dotBracketAlphabet

static

the alphabet to encode accessibility constraints in dot-bracket notation

length

size_t IntaRNA::AccessibilityConstraint::length

protected

the overall sequence length this constraint is about

maxBpSpan

size_t IntaRNA::AccessibilityConstraint::maxBpSpan

protected

the maximal base pair span to be used for accessibility computation

paired

IndexRangeList IntaRNA::AccessibilityConstraint::paired

protected

sorted list of ranges that are marked as paired (intramolecular)

regex

const boost::regex IntaRNA::AccessibilityConstraint::regex

static

the regular expression that marks a non-empty valid constraint encoding

regexShapeConversion

const boost::regex IntaRNA::AccessibilityConstraint::regexShapeConversion

static

the regular expression to be matched by shapeConversion encodings

regexShapeMethod

const boost::regex IntaRNA::AccessibilityConstraint::regexShapeMethod

static

the regular expression to be matched by shapeMethod encodings

regionIndexList

const std::string IntaRNA::AccessibilityConstraint::regionIndexList

static

regular expression that encodes a single region encoding as index list

shapeConversion

std::string IntaRNA::AccessibilityConstraint::shapeConversion

protected

method for conversion of SHAPE reactivity data to paired probabilities

shapeFile

std::string IntaRNA::AccessibilityConstraint::shapeFile

protected

filename of SHAPE reactivity data or empty if no SHAPE data to be used

shapeMethod

std::string IntaRNA::AccessibilityConstraint::shapeMethod

protected

method for converting SHAPE reactivity data to pseudo energies

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

• src/IntaRNA/AccessibilityConstraint.h