Uses of Class
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.PositionPrior

Packages that use PositionPrior

Package	Description
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior

Uses of PositionPrior in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif declared as PositionPrior

Modifier and Type	Field and Description
protected PositionPrior	HiddenMotifMixture.posPrior The prior for the positions.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif with parameters of type PositionPrior

Constructor and Description
HiddenMotifMixture(TrainableStatisticalModel[] models, boolean[] optimzeArray, int components, int starts, boolean estimateComponentProbs, double[] componentHyperParams, double[] weights, PositionPrior posPrior, AbstractMixtureTrainSM.Algorithm algorithm, double alpha, TerminationCondition tc, AbstractMixtureTrainSM.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest) Creates a new HiddenMotifMixture.
ZOOPSTrainSM(TrainableStatisticalModel motif, TrainableStatisticalModel bg, boolean trainOnlyMotifModel, int starts, double[] componentHyperParams, double[] weights, PositionPrior posPrior, AbstractMixtureTrainSM.Algorithm algorithm, double alpha, TerminationCondition tc, AbstractMixtureTrainSM.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest) Creates a new ZOOPSTrainSM.
ZOOPSTrainSM(TrainableStatisticalModel motif, TrainableStatisticalModel bg, boolean trainOnlyMotifModel, int starts, double[] componentHyperParams, PositionPrior posPrior, double alpha, TerminationCondition tc, AbstractMixtureTrainSM.Parameterization parametrization) Creates a new ZOOPSTrainSM using EM and estimating the probability for finding a motif.
ZOOPSTrainSM(TrainableStatisticalModel motif, TrainableStatisticalModel bg, boolean trainOnlyMotifModel, int starts, double motifProb, PositionPrior posPrior, double alpha, TerminationCondition tc, AbstractMixtureTrainSM.Parameterization parametrization) Creates a new ZOOPSTrainSM using EM and fixed probability for finding a motif.

Uses of PositionPrior in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior

Subclasses of PositionPrior in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior

Modifier and Type	Class and Description
class	GaussianLikePositionPrior This class implements a gaussian like discrete truncated prior.
class	UniformPositionPrior This prior implements a uniform distribution for the start position.

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior that return PositionPrior

Modifier and Type	Method and Description
PositionPrior	PositionPrior.clone()