IntaRNA::OutputConstraint Class Reference

#include <OutputConstraint.h>

Public Types
enum	ReportOverlap { OVERLAP_NONE = 0 , OVERLAP_SEQ1 = 1 , OVERLAP_SEQ2 = 2 , OVERLAP_BOTH = 3 }

Public Member Functions
	OutputConstraint (const size_t reportMax=1, const ReportOverlap reportOverlap=OVERLAP_BOTH, const E_type maxE=0.0, const E_type deltaE=E_INF, const bool bestSeedOnly=false, const bool noLP=false, const bool noGUend=false, const bool needZall=false, const bool needBPs=true, const E_type maxED=Accessibility::ED_UPPER_BOUND)
virtual	~OutputConstraint ()
	destruction

Public Attributes
const size_t	reportMax
	the maximal number of (sub)optimal interactions to be reported to the output handler
const ReportOverlap	reportOverlap
	defines whether and where overlapping interaction sites are allowed for reporting
const E_type	maxE
	upper bound (exclusive) for the energy of a reported interaction (E(interaction) < maxE)
const E_type	deltaE
	the maximal energy difference to the mfe of a reported interaction
const bool	bestSeedOnly
	whether or not only the best or all putative seeds are to be reported
const bool	noLP
	whether or not lonely (non-stacked) inter-molecular base pairs are to be considered
const bool	noGUend
	whether or not inter-molecular UG base pairs are allowed at interaction ends
const bool	needZall
	whether or not Zall has to be computed for output generation
const bool	needBPs
	whether or not interaction base pairs have to be traced for output generation
const E_type	maxED
	maximal ED penalty of each interacting subsequence to be considered for output

Detailed Description

Data structure that contains all constraints to be applied to (suboptimal) output generation.

Author

Martin Mann

Member Enumeration Documentation

ReportOverlap

enum IntaRNA::OutputConstraint::ReportOverlap

different possibilities to en-/disable overlapping of interaction sites if suboptimal solutions are enumerated

Enumerator
OVERLAP_NONE
OVERLAP_SEQ1
OVERLAP_SEQ2
OVERLAP_BOTH

Constructor & Destructor Documentation

OutputConstraint()

IntaRNA::OutputConstraint::OutputConstraint	(	const size_t	reportMax = 1,
		const ReportOverlap	reportOverlap = OVERLAP_BOTH,
		const E_type	maxE = 0.0,
		const E_type	deltaE = E_INF,
		const bool	bestSeedOnly = false,
		const bool	noLP = false,
		const bool	noGUend = false,
		const bool	needZall = false,
		const bool	needBPs = true,
		const E_type	maxED = Accessibility::ED_UPPER_BOUND
	)

Construction of an output constraint

Parameters

reportMax	the maximal number of (sub)optimal interactions to be reported to the output handler
reportOverlap	defines whether and where overlapping interaction sites are allowed for reporting
maxE	upper bound (exclusive) for the energy of a reported interaction (E(interaction) < maxE)
deltaE	maximal energy difference of a reported interaction to mfe
bestSeedOnly	whether or not only the best seed is to be reported
noLP	whether or not lonely (non-stacked) inter-molecular bps are allowed
noGUend	whether or not inter-molecular UG base pairs are allowed at interaction ends
needZall	whether or not Zall has to be computed for output generation
needBPs	whether or not interaction base pairs have to be traced for output generation

~OutputConstraint()

virtual IntaRNA::OutputConstraint::~OutputConstraint ( )

virtual

destruction

Member Data Documentation

bestSeedOnly

const bool IntaRNA::OutputConstraint::bestSeedOnly

whether or not only the best or all putative seeds are to be reported

deltaE

const E_type IntaRNA::OutputConstraint::deltaE

the maximal energy difference to the mfe of a reported interaction

maxE

const E_type IntaRNA::OutputConstraint::maxE

upper bound (exclusive) for the energy of a reported interaction (E(interaction) < maxE)

maxED

const E_type IntaRNA::OutputConstraint::maxED

maximal ED penalty of each interacting subsequence to be considered for output

needBPs

const bool IntaRNA::OutputConstraint::needBPs

whether or not interaction base pairs have to be traced for output generation

needZall

const bool IntaRNA::OutputConstraint::needZall

whether or not Zall has to be computed for output generation

noGUend

const bool IntaRNA::OutputConstraint::noGUend

whether or not inter-molecular UG base pairs are allowed at interaction ends

noLP

const bool IntaRNA::OutputConstraint::noLP

whether or not lonely (non-stacked) inter-molecular base pairs are to be considered

reportMax

const size_t IntaRNA::OutputConstraint::reportMax

the maximal number of (sub)optimal interactions to be reported to the output handler

reportOverlap

const ReportOverlap IntaRNA::OutputConstraint::reportOverlap

defines whether and where overlapping interaction sites are allowed for reporting

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

• src/IntaRNA/OutputConstraint.h