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## Uses of Interface
de.jstacs.models.hmm.states.emissions.Emission

Packages that use Emission
de.jstacs.models.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.models.hmm.models | The package provides different implementations of hidden Markov models based on `AbstractHMM`
de.jstacs.models.hmm.states | The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.models.hmm.states.emissions |
de.jstacs.models.hmm.states.emissions.continuous |
de.jstacs.models.hmm.states.emissions.discrete |

Uses of Emission in de.jstacs.models.hmm

Fields in de.jstacs.models.hmm declared as Emission
`protected Emission[]` | `AbstractHMM.emission` The emissions used in the states.

Methods in de.jstacs.models.hmm with parameters of type Emission
`static AbstractHMM` | `HMMFactory.createErgodicHMM(HMMTrainingParameterSet pars, int order, double ess, double selfTranistionPart, double expectedSequenceLength, Emission... emission)` This method creates an ergodic, i.e. a completely connected, HMM using the given emissions.

Constructors in de.jstacs.models.hmm with parameters of type Emission
`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.models.hmm.models

Constructors in de.jstacs.models.hmm.models with parameters of type Emission
`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.models.hmm.states

Fields in de.jstacs.models.hmm.states declared as Emission
`protected Emission` | `SimpleState.e` The emission that is internally used for scoring subsequences.

Constructors in de.jstacs.models.hmm.states with parameters of type Emission
`SimpleState(Emission e, String name, boolean forward)` This is the constructor of a `SimpleState`.

Uses of Emission in de.jstacs.models.hmm.states.emissions

Subinterfaces of Emission in de.jstacs.models.hmm.states.emissions
`interface` | `DifferentiableEmission` This interface declares all methods needed in an emission during a numerical optimization of HMM.
`interface` | `SamplingEmission`

Classes in de.jstacs.models.hmm.states.emissions that implement Emission
`class` | `MixtureEmission` This class implements a mixture of `Emission`s.
`class` | `SilentEmission` This class implements a silent emission which is used to create silent states.

Constructors in de.jstacs.models.hmm.states.emissions with parameters of type Emission
`MixtureEmission(Emission[] emission, double[] hyperParameters)` The main constructor creating a `MixtureEmission` from a set of emissions.

Uses of Emission in de.jstacs.models.hmm.states.emissions.continuous

Classes in de.jstacs.models.hmm.states.emissions.continuous that implement Emission
`class` | `GaussianEmission` Emission for continuous values following a Gaussian distribution.
`class` | `PluginGaussianEmission` Basic Gaussian emission distribution without random initialization of parameters.

Uses of Emission in de.jstacs.models.hmm.states.emissions.discrete

Classes in de.jstacs.models.hmm.states.emissions.discrete that implement Emission
`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.

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