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Packages that use Emission | |
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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 |
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Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm declared as Emission | |
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protected Emission[] |
AbstractHMM.emission
The emissions used in the states. |
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm with parameters of type Emission | |
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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.sequenceScores.statisticalModels.trainable.hmm with parameters of type Emission | |
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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 |
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models with parameters of type Emission | |
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HigherOrderHMM(HMMTrainingParameterSet trainingParameterSet,
String[] name,
Emission[] emission,
BasicHigherOrderTransition.AbstractTransitionElement... te)
This is a convenience constructor. |
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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 |
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Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states declared as Emission | |
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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 | |
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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 |
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Subinterfaces of Emission in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions | |
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interface |
DifferentiableEmission
This interface declares all methods needed in an emission during a numerical optimization of HMM. |
interface |
SamplingEmission
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Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions that implement Emission | |
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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. |
class |
UniformEmission
This class implements a simple uniform emission. |
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions with parameters of type Emission | |
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void |
UniformEmission.joinStatistics(Emission... emissions)
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void |
SilentEmission.joinStatistics(Emission... emissions)
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void |
MixtureEmission.joinStatistics(Emission... emissions)
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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)
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void |
SilentEmission.setParameters(Emission t)
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void |
MixtureEmission.setParameters(Emission t)
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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 | |
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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 |
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Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous that implement Emission | |
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class |
GaussianEmission
Emission for continuous values following a Gaussian distribution. |
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 | |
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void |
GaussianEmission.joinStatistics(Emission... emissions)
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void |
GaussianEmission.setParameters(Emission t)
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Uses of Emission in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete |
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Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete that implement Emission | |
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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 | |
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void |
AbstractConditionalDiscreteEmission.joinStatistics(Emission... emissions)
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void |
AbstractConditionalDiscreteEmission.setParameters(Emission t)
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