#include <AccessibilityFromStream.h>

Inheritance diagram for IntaRNA::AccessibilityFromStream:

Collaboration diagram for IntaRNA::AccessibilityFromStream:

[legend]

Public Types
enum	InStreamType { Pu_RNAplfold_Text , ED_RNAplfold_Text , IntaRNA_Binary }

Public Member Functions
	AccessibilityFromStream (const RnaSequence &sequence, const size_t maxLength, const AccessibilityConstraint *const accConstraint, std::istream &inStream, const InStreamType inStreamType, const Z_type RT)

virtual	~AccessibilityFromStream ()

virtual E_type	getED (const size_t from, const size_t to) const

virtual size_t	getMaxLength () const

void	writeBinary (std::ostream &out) const override

Public Member Functions inherited from IntaRNA::Accessibility
	Accessibility (const RnaSequence &sequence, const size_t maxLength, const AccessibilityConstraint *const accConstr)

virtual	~Accessibility ()

virtual const RnaSequence &	getSequence () const

virtual const AccessibilityConstraint &	getAccConstraint () const

void	writeRNAplfold_Pu_text (std::ostream &out, const Z_type RT) const

void	writeRNAplfold_ED_text (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

Protected Types
typedef UpperBandedMatrix< E_type >	EdMatrix
	type for the ED value matrix (upper triangular matrix banded by maxLength)

Protected Member Functions
void	parseBinary (std::istream &inStream)

void	parsePu_RNAplfold_text (std::istream &inStream, const Z_type RT)

void	parseED_RNAplfold_text (std::istream &inStream)

void	parseRNAplfold_text (std::istream &inStream, const Z_type RT, const bool parseProbs)

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

Protected Attributes
EdMatrix	edValues
	the ED values for the given sequence

size_t	availMaxLength
	maximal available window size

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

Detailed Description

Reads accessibility information from a data stream, e.g. from file or STDIN

Member Typedef Documentation

◆ EdMatrix

typedef UpperBandedMatrix<E_type> IntaRNA::AccessibilityFromStream::EdMatrix

protected

type for the ED value matrix (upper triangular matrix banded by maxLength)

Member Enumeration Documentation

◆ InStreamType

enum IntaRNA::AccessibilityFromStream::InStreamType

Enumerator
Pu_RNAplfold_Text	Pu values in RNAplfold text format.
ED_RNAplfold_Text	ED values in RNAplfold text Pu format.
IntaRNA_Binary	native Boost binary ED archive, already decompressed

Constructor & Destructor Documentation

◆ AccessibilityFromStream()

IntaRNA::AccessibilityFromStream::AccessibilityFromStream	(	const RnaSequence &	sequence,
		const size_t	maxLength,
		const AccessibilityConstraint *const	accConstraint,
		std::istream &	inStream,
		const InStreamType	inStreamType,
		const Z_type	RT
	)

construction

Parameters

sequence	the sequence the accessibility data is about
maxLength	the maximal length of accessible regions (>0) to be considered. 0 defaults to the full sequence's length, otherwise is is internally set to min(maxLength,seq.length).
accConstraint	if not NULL, accessibility constraint that enforces some regions to be unstructured both in sequence and interaction
inStream	the input stream to read the accessibility data from
inStreamType	inStream data type to be expected
RT	the RT constant to be used to transform the probabilities to ED values

◆ ~AccessibilityFromStream()

virtual IntaRNA::AccessibilityFromStream::~AccessibilityFromStream ( )

virtual

destruction

Member Function Documentation

◆ getED()

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

inlinevirtual

Returns the accessibility energy value for the given range in the sequence, i.e. the energy difference (ED) to make the region accessible.

Parameters

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

Returns: the ED value if (j-1+1) <= maxLength or ED_UPPER_BOUND otherwise

Exceptions

std::runtime_error in case it does not hold 0 <= from <= to < seq.length

Implements IntaRNA::Accessibility.

◆ getMaxLength()

size_t IntaRNA::AccessibilityFromStream::getMaxLength ( ) const

inlinevirtual

Access to the maximal length of accessible regions (>0) to be considered.

Here, it returns the minimum of the originally targeted interaction range and the from the data parsed maximal window size.

Returns: the maximal length of accessible regions considered

Reimplemented from IntaRNA::Accessibility.

◆ parseBinary()

void IntaRNA::AccessibilityFromStream::parseBinary ( std::istream & inStream )

protected

Load and validate a decompressed IntaRNA binary accessibility archive.

◆ parseED_RNAplfold_text()

void IntaRNA::AccessibilityFromStream::parseED_RNAplfold_text ( std::istream & inStream )

inlineprotected

Parses ED values from a VRNA unpaired probability file styled stream

Parameters

inStream the stream to read the ED values from

◆ parsePu_RNAplfold_text()

void IntaRNA::AccessibilityFromStream::parsePu_RNAplfold_text	(	std::istream &	inStream,
		const Z_type	RT
	)

inlineprotected

Parses a VRNA unpaired probability file and fills the ED data

Parameters

inStream	the stream to read the probabilities from
RT	the RT constant to be used to transform the probabilities to ED values

◆ parseRNAplfold_text()

void IntaRNA::AccessibilityFromStream::parseRNAplfold_text	(	std::istream &	inStream,
		const Z_type	RT,
		const bool	parseProbs
	)

protected

Parses ED values from a VRNA unpaired probability file styled stream

Parameters

inStream	the stream to read the ED values from
RT	the RT constant to be used to transform the probabilities to ED values
parseProbs	whether or not to expect unpaired probabilities (true) or ED values within the file

◆ writeBinary()

void IntaRNA::AccessibilityFromStream::writeBinary ( std::ostream & out ) const

inlineoverridevirtual

Write the stored ED matrix directly, without copying rows or calling getED() for unconstrained data. Constraints retain the generic getED() path. Subclasses changing getED() semantics must also override this method.

Parameters

out	binary output stream; compression is supplied by the stream

Reimplemented from IntaRNA::Accessibility.

Member Data Documentation

◆ availMaxLength

size_t IntaRNA::AccessibilityFromStream::availMaxLength

protected

maximal available window size

◆ edValues

EdMatrix IntaRNA::AccessibilityFromStream::edValues

protected

the ED values for the given sequence

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

src/IntaRNA/AccessibilityFromStream.h

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ EdMatrix

Member Enumeration Documentation

◆ InStreamType

Constructor & Destructor Documentation

◆ AccessibilityFromStream()

◆ ~AccessibilityFromStream()

Member Function Documentation

◆ getED()

◆ getMaxLength()

◆ parseBinary()

◆ parseED_RNAplfold_text()

◆ parsePu_RNAplfold_text()

◆ parseRNAplfold_text()

◆ writeBinary()

Member Data Documentation

◆ availMaxLength

◆ edValues