IntaRNA::ReverseAccessibility Class Reference

#include <ReverseAccessibility.h>

Inheritance diagram for IntaRNA::ReverseAccessibility:

Collaboration diagram for IntaRNA::ReverseAccessibility:

Public Member Functions
	ReverseAccessibility (Accessibility &origAcc)
virtual	~ReverseAccessibility ()
virtual E_type	getED (const size_t from, const size_t to) const
virtual const RnaSequence &	getSequence () const
virtual const AccessibilityConstraint &	getAccConstraint () const
virtual const Accessibility &	getAccessibilityOrigin () const
size_t	getReversedIndex (const size_t i) const
IndexRange	getReversedIndexRange (const IndexRange &r) const
Public Member Functions inherited from IntaRNA::Accessibility
	Accessibility (const RnaSequence &sequence, const size_t maxLength, const AccessibilityConstraint *const accConstr)
virtual	~Accessibility ()
virtual size_t	getMaxLength () const
void	writeRNAplfold_Pu_text (std::ostream &out, const Z_type RT) const
void	writeRNAplfold_ED_text (std::ostream &out) const
virtual void	writeBinary (std::ostream &out) const
IndexRangeList	decomposeByMaxED (const size_t maxRangeLength, const size_t winSize, const size_t minRangeLength) const
void	decomposeByMaxED (IndexRangeList &ranges, const E_type maxED, const size_t minRangeLength) const

Static Protected Member Functions
static std::string	getReversedString (const RnaSequence &seq)
static std::string	getReversedString (const std::string &str)

Protected Attributes
Accessibility &	origAcc
	Access to the accessibility object to reverse.
RnaSequence	seqReversed
	reversed sequence object
AccessibilityConstraint	accConstrReversed
	reversed accessibility constraint object
Protected Attributes inherited from IntaRNA::Accessibility
const RnaSequence &	seq
	the RNA sequence the accessibilities correspond to
const size_t	maxLength
	the maximal length of an unpaired regions to be considered
AccessibilityConstraint	accConstraint
	accessibility constraint

Additional Inherited Members
Static Public Attributes inherited from IntaRNA::Accessibility
static const E_type	ED_UPPER_BOUND
	upper bound for all ED return values
Protected Member Functions inherited from IntaRNA::Accessibility
void	writeBinary (std::ostream &out, const UpperBandedMatrix< E_type > *matrix) const
virtual void	checkIndices (const size_t from, const size_t to) const
void	writeRNAplfold_text (std::ostream &out, const Z_type RT, const bool writeProbs) const

Detailed Description

Defines an accessibility meta object with reversed index access to sequence and accessibility.

Constructor & Destructor Documentation

ReverseAccessibility()

IntaRNA::ReverseAccessibility::ReverseAccessibility ( Accessibility &  origAcc )

inline

Construction based on a given accessibility object to represent reversed

Parameters

origAcc

Access to the accessibility object to reverse

~ReverseAccessibility()

IntaRNA::ReverseAccessibility::~ReverseAccessibility ( )

inlinevirtual

destruction

Member Function Documentation

getAccConstraint()

const AccessibilityConstraint & IntaRNA::ReverseAccessibility::getAccConstraint ( ) const

inlinevirtual

Access to the globally enforced accessibility constraint. Here '.' denotes unconstrained positions and 'x' positions that have to be unstructured. Regions covering constrained positions will result in ED_UPPER_BOUND accessibility values.

Returns

the global accessibility constraint applied

Reimplemented from IntaRNA::Accessibility.

getAccessibilityOrigin()

const Accessibility & IntaRNA::ReverseAccessibility::getAccessibilityOrigin ( ) const

inlinevirtual

Access to the original not-reversed accessibility object.

Returns

the original (index reversed) accessibility object.

getED()

E_type IntaRNA::ReverseAccessibility::getED ( const size_t  from, const size_t  to  ) const

inlinevirtual

Access to the accessibility energy value (according to reversed indices).

Parameters

from	the start index of the regions (from <= to)
to	the end index of the regions (to <= seq.length())

Returns

0 if (j-1+1) <= maxLength or ED_UPPER_BOUND otherwise

Implements IntaRNA::Accessibility.

getReversedIndex()

size_t IntaRNA::ReverseAccessibility::getReversedIndex ( const size_t  i ) const

inline

Provides the reverse index of a given sequence position.

Parameters

i	the index of interest

Returns

the reverse index, i.e. (seq.size()-i-1)

getReversedIndexRange()

IndexRange IntaRNA::ReverseAccessibility::getReversedIndexRange ( const IndexRange &  r ) const

inline

Provides the reverse index range of a given sequence position.

Parameters

r	the index range of interest

Returns

the reversed index range, i.e. for index i : (seq.size()-i-1)

getReversedString() [1/2]

static std::string IntaRNA::ReverseAccessibility::getReversedString ( const RnaSequence &  seq )

staticprotected

Computes a reversed string representation of a sequence

Parameters

seq	the sequence to reverse

Returns

the reversed string representation

getReversedString() [2/2]

static std::string IntaRNA::ReverseAccessibility::getReversedString ( const std::string &  str )

staticprotected

Computes a reversed string representation of a given string

Parameters

str	the string to reverse

Returns

the reversed string

getSequence()

const RnaSequence & IntaRNA::ReverseAccessibility::getSequence ( ) const

inlinevirtual

Access to the RnaSequence this accessibility values are accounting for.

Returns

the underlying sequence for this accessibility object.

Reimplemented from IntaRNA::Accessibility.

Member Data Documentation

accConstrReversed

AccessibilityConstraint IntaRNA::ReverseAccessibility::accConstrReversed

protected

reversed accessibility constraint object

origAcc

Accessibility& IntaRNA::ReverseAccessibility::origAcc

protected

Access to the accessibility object to reverse.

seqReversed

RnaSequence IntaRNA::ReverseAccessibility::seqReversed

protected

reversed sequence object

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

• src/IntaRNA/ReverseAccessibility.h