MessagePasserFactory< Label > Class Template Reference

#include <OpenMS/ANALYSIS/ID/MessagePasserFactory.h>

Public Member Functions
TableDependency< Label >	createProteinFactor (Label id, int nrMissingPeps=0)
TableDependency< Label >	createProteinFactor (Label id, double prior, int nrMissingPeps=0)
TableDependency< Label >	createPeptideEvidenceFactor (Label id, double prob)
TableDependency< Label >	createSumEvidenceFactor (size_t nrParents, Label nId, Label pepId)
TableDependency< Label >	createSumFactor (size_t nrParents, Label nId)
AdditiveDependency< Label >	createPeptideProbabilisticAdderFactor (const std::set< Label > &parentProteinIDs, Label nId)
AdditiveDependency< Label >	createPeptideProbabilisticAdderFactor (const std::vector< Label > &parentProteinIDs, Label nId)
PseudoAdditiveDependency< Label >	createBFPeptideProbabilisticAdderFactor (const std::set< Label > &parentProteinIDs, Label nId, const std::vector< TableDependency< Label > > &deps)
	MessagePasserFactory (double alpha, double beta, double gamma, double p)
void	fillVectorsOfMessagePassers (const std::vector< Label > &protIDs, const std::vector< std::vector< Label >> &parentsOfPeps, const std::vector< double > &pepEvidences, InferenceGraphBuilder< Label > &igb)
	Works on a vector of protein indices (potentially not consecutive) More...

Private Member Functions
double	notConditionalGivenSum (unsigned long summ)

Private Attributes
const int	minInputsPAF = 3
double	alpha
double	beta
double	gamma
double	p
Label	offset

Constructor & Destructor Documentation

MessagePasserFactory()

MessagePasserFactory	(	double	alpha,
		double	beta,
		double	gamma,
		double	p
	)

Member Function Documentation

createBFPeptideProbabilisticAdderFactor()

PseudoAdditiveDependency< L > createBFPeptideProbabilisticAdderFactor	(	const std::set< Label > &	parentProteinIDs,
		Label	nId,
		const std::vector< TableDependency< Label > > &	deps
	)

createPeptideEvidenceFactor()

TableDependency< L > createPeptideEvidenceFactor	(	Label	id,
		double	prob
	)

createPeptideProbabilisticAdderFactor() [1/2]

AdditiveDependency<Label> createPeptideProbabilisticAdderFactor	(	const std::set< Label > &	parentProteinIDs,
		Label	nId
	)

createPeptideProbabilisticAdderFactor() [2/2]

AdditiveDependency<Label> createPeptideProbabilisticAdderFactor	(	const std::vector< Label > &	parentProteinIDs,
		Label	nId
	)

createProteinFactor() [1/2]

TableDependency<Label> createProteinFactor	(	Label	id,
		int	nrMissingPeps = 0
	)

createProteinFactor() [2/2]

TableDependency<Label> createProteinFactor	(	Label	id,
		double	prior,
		int	nrMissingPeps = 0
	)

createSumEvidenceFactor()

TableDependency< L > createSumEvidenceFactor	(	size_t	nrParents,
		Label	nId,
		Label	pepId
	)

createSumFactor()

TableDependency< L > createSumFactor	(	size_t	nrParents,
		Label	nId
	)

fillVectorsOfMessagePassers()

void fillVectorsOfMessagePassers	(	const std::vector< Label > &	protIDs,
		const std::vector< std::vector< Label >> &	parentsOfPeps,
		const std::vector< double > &	pepEvidences,
		InferenceGraphBuilder< Label > &	igb
	)

Works on a vector of protein indices (potentially not consecutive)

References seqan::find().

notConditionalGivenSum()

double notConditionalGivenSum ( unsigned long  summ )

inlineprivate

References MessagePasserFactory< Label >::alpha, and MessagePasserFactory< Label >::beta.

Member Data Documentation

alpha

double alpha

private

Referenced by MessagePasserFactory< Label >::notConditionalGivenSum().

beta

double beta

private

Referenced by MessagePasserFactory< Label >::notConditionalGivenSum().

gamma

double gamma

private

minInputsPAF

const int minInputsPAF = 3

private

offset

Label offset

private

p

double p

private