Uses of Interface
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.Emission

Packages that use Emission

Package	Description
de.jstacs.sequenceScores.statisticalModels.trainable.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models	The package provides different implementations of hidden Markov models based on AbstractHMM.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states	The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Uses of Emission in de.jstacs.sequenceScores.statisticalModels.trainable.hmm

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm declared as Emission

Modifier and Type	Field and Description
protected Emission[]	AbstractHMM.emission The emissions used in the states.

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm with parameters of type Emission

Modifier and Type	Method and Description
static AbstractHMM	HMMFactory.createErgodicHMM(HMMTrainingParameterSet pars, int order, double ess, double selfTranistionPart, double expectedSequenceLength, Emission... emission) This method creates an ergodic, i.e.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm with parameters of type Emission

Constructor and Description
AbstractHMM(HMMTrainingParameterSet trainingParameterSet, String[] name, int[] emissionIdx, boolean[] forward, Emission[] emission) This is the main constructor for an HMM.

Uses of Emission in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models that return Emission

Modifier and Type	Method and Description
Emission[]	HigherOrderHMM.getEmissions() Returns a clone of the internal emissions.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models with parameters of type Emission

Constructor and Description
HigherOrderHMM(HMMTrainingParameterSet trainingParameterSet, String[] name, Emission[] emission, BasicHigherOrderTransition.AbstractTransitionElement... te) This is a convenience constructor.
HigherOrderHMM(HMMTrainingParameterSet trainingParameterSet, String[] name, int[] emissionIdx, boolean[] forward, Emission[] emission, BasicHigherOrderTransition.AbstractTransitionElement... te) This is the main constructor.

Uses of Emission in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states declared as Emission

Modifier and Type	Field and Description
protected Emission	SimpleState.e The emission that is internally used for scoring subsequences.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states with parameters of type Emission

Constructor and Description
SimpleState(Emission e, String name, boolean forward) This is the constructor of a SimpleState.

Uses of Emission in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

Subinterfaces of Emission in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

Modifier and Type	Interface and Description
interface	DifferentiableEmission This interface declares all methods needed in an emission during a numerical optimization of HMM.
interface	SamplingEmission

Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions that implement Emission

Modifier and Type	Class and Description
class	MixtureEmission This class implements a mixture of Emissions.
class	SilentEmission This class implements a silent emission which is used to create silent states.
class	UniformEmission This class implements a simple uniform emission.

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions with parameters of type Emission

Modifier and Type	Method and Description
void	UniformEmission.joinStatistics(Emission... emissions)
void	SilentEmission.joinStatistics(Emission... emissions)
void	MixtureEmission.joinStatistics(Emission... emissions)
void	Emission.joinStatistics(Emission... emissions) This method joins the statistics of different instances and sets this joined statistic as statistic of each instance.
void	UniformEmission.setParameters(Emission t)
void	SilentEmission.setParameters(Emission t)
void	MixtureEmission.setParameters(Emission t)
void	Emission.setParameters(Emission t) Set values of parameters of the instance to the value of the parameters of the given instance.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions with parameters of type Emission

Constructor and Description
MixtureEmission(Emission[] emission, double[] hyperParameters) The main constructor creating a MixtureEmission from a set of emissions.

Uses of Emission in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous that implement Emission

Modifier and Type	Class and Description
class	GaussianEmission Emission for continuous values following a Gaussian distribution.
class	MultivariateGaussianEmission Multivariate Gaussian emission density for a Hidden Markov Model.
class	PluginGaussianEmission Basic Gaussian emission distribution without random initialization of parameters.

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous with parameters of type Emission

Modifier and Type	Method and Description
void	MultivariateGaussianEmission.joinStatistics(Emission... emissions)
void	GaussianEmission.joinStatistics(Emission... emissions)
void	MultivariateGaussianEmission.setParameters(Emission t)
void	GaussianEmission.setParameters(Emission t)

Uses of Emission in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete that implement Emission

Modifier and Type	Class and Description
class	AbstractConditionalDiscreteEmission The abstract super class of discrete emissions.
class	DiscreteEmission This class implements a simple discrete emission without any condition.
class	PhyloDiscreteEmission Phylogenetic discrete emission This class uses a phylogenetic tree to describe multidimensional data It implements Felsensteins model for nucleotide substitution (F81)
class	ReferenceSequenceDiscreteEmission This class implements a discrete emission that depends on some ReferenceSequenceAnnotation at a certain reference position.

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete with parameters of type Emission

Modifier and Type	Method and Description
void	AbstractConditionalDiscreteEmission.joinStatistics(Emission... emissions)
void	AbstractConditionalDiscreteEmission.setParameters(Emission t)