IntaRNA::OutputHandlerSeedCandidates Class Reference

#include <OutputHandlerSeedCandidates.h>

Inheritance diagram for IntaRNA::OutputHandlerSeedCandidates:

Collaboration diagram for IntaRNA::OutputHandlerSeedCandidates:

Public Member Functions
	OutputHandlerSeedCandidates (const OutputConstraint &constraint)
void	add (const Interaction &interaction) override
void	addSeed (const Interaction::BasePair &seed, const Interaction &interaction)
void	report (OutputHandler &destination) const
void	clear ()
Public Member Functions inherited from IntaRNA::OutputHandler
	OutputHandler (const OutputConstraint &outConstraint)
virtual	~OutputHandler ()
virtual size_t	reported () const
virtual void	incrementZ (const Z_type subZ)
virtual Z_type	getZ () const
const OutputConstraint &	getOutputConstraint () const
virtual void	setExactPartition (bool exact)
bool	usesExactPartition () const
bool	hasNonzeroZ () const

Additional Inherited Members
Static Public Member Functions inherited from IntaRNA::OutputHandler
static std::string	reverse (const std::string &str)
Protected Attributes inherited from IntaRNA::OutputHandler
bool	exactPartition = false
	scoped to a supported sequence-pair ensemble, legacy outputs default false
const OutputConstraint	outConstraint
	the output constraints to be applied
size_t	reportedInteractions
	number of reported interactions
Z_type	Z
	overall partition function for the sequences provided in Z_energy

Detailed Description

Collect each seed's best distinct sites across prediction calls/windows. Seed keys and interactions use original sequence coordinates. Final selection deduplicates sites, retaining their lowest eligible energy and its structure, then applies energy, overlap and count restrictions without refilling quotas. Partition statistics are accumulated independently through OutputHandler.

Constructor & Destructor Documentation

OutputHandlerSeedCandidates()

IntaRNA::OutputHandlerSeedCandidates::OutputHandlerSeedCandidates ( const OutputConstraint &  constraint )

explicit

Parameters

constraint

final restrictions, including a positive per-seed quota

Member Function Documentation

add()

void IntaRNA::OutputHandlerSeedCandidates::add ( const Interaction &  interaction )

overridevirtual

Ordinary ranked reports have no seed identity and are ignored.

Parameters

interaction

ordinary report from the statistics-only prediction

Implements IntaRNA::OutputHandler.

addSeed()

void IntaRNA::OutputHandlerSeedCandidates::addSeed	(	const Interaction::BasePair &	seed,
		const Interaction &	interaction
	)

Retain a candidate before any global output pruning.

Parameters

seed	generating seed start in original coordinates
interaction	candidate, including its qualifying conformation/energy

clear()

void IntaRNA::OutputHandlerSeedCandidates::clear

(

)

Reset quotas for an independent region combination; retain statistics.

report()

void IntaRNA::OutputHandlerSeedCandidates::report

(

OutputHandler &

destination

)

const

Publish the selected union, leaving partition forwarding to the caller.

Parameters

destination

output receiving at most reportMax distinct sites

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

• src/IntaRNA/OutputHandlerSeedCandidates.h