de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

Class PluginGaussianEmission

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.PluginGaussianEmission

All Implemented Interfaces:

DifferentiableEmission, Emission, Storable, Cloneable

public class PluginGaussianEmission
extends GaussianEmission

Basic Gaussian emission distribution without random initialization of parameters.

Author:

Michael Seifert

Field Summary

Fields

Modifier and Type	Field and Description
protected double	meanValue Initial mean value.
protected double	standardDeviation Initial standard deviation.

Constructor Summary

Constructors

Constructor and Description
PluginGaussianEmission(double mean, double sd, double ess, double priorMu, double priorAlpha, double priorBeta) Creates a Gaussian emission density with mean mean and standard deviation sd.
PluginGaussianEmission(StringBuffer xml) Creates a PluginGaussianEmission from its XML representation.

Method Summary

Modifier and Type	Method and Description
protected void	fromXML(StringBuffer xml) This method is internally used by the constructor GaussianEmission.GaussianEmission(StringBuffer).
void	initializeFunctionRandomly() This method initializes the emission randomly.
String	toString()
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission

addGradientOfLogPriorTerm, addToStatistic, clone, estimateFromStatistic, fillCurrentParameter, fillSamplingGroups, getAlphabetContainer, getLogPriorTerm, getLogProbAndPartialDerivationFor, getLogProbFor, getNodeLabel, getNodeShape, getNumberOfParameters, getSizeOfEventSpace, joinStatistics, precompute, resetStatistic, setParameter, setParameterOffset, setParameters, toString

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

meanValue

protected double meanValue

Initial mean value.

standardDeviation

protected double standardDeviation

Initial standard deviation.

Constructor Detail

PluginGaussianEmission

public PluginGaussianEmission(double mean,
                              double sd,
                              double ess,
                              double priorMu,
                              double priorAlpha,
                              double priorBeta)

Creates a Gaussian emission density with mean mean and standard deviation sd.

Parameters:

mean - mean value

sd - standard deviation (initially handled as precision)

ess - scale factor of a priori mean (epsilon)

priorMu - a priori mean (nhi)

priorAlpha - shape parameter (r)

priorBeta - scale parameter (alpha)

PluginGaussianEmission

public PluginGaussianEmission(StringBuffer xml)
                       throws NonParsableException

Creates a PluginGaussianEmission from its XML representation.

Parameters:

xml - the XML representation.

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

initializeFunctionRandomly

public void initializeFunctionRandomly()

Description copied from interface: Emission

This method initializes the emission randomly.

Specified by:

initializeFunctionRandomly in interface Emission

Overrides:

initializeFunctionRandomly in class GaussianEmission

toString

public String toString()

Overrides:

toString in class Object

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class GaussianEmission

Returns:

the XML representation

fromXML

protected void fromXML(StringBuffer xml)
                throws NonParsableException

Description copied from class: GaussianEmission

This method is internally used by the constructor GaussianEmission.GaussianEmission(StringBuffer).

Overrides:

fromXML in class GaussianEmission

Parameters:

xml - the StringBuffer containing the xml representation of an instance

Throws:

NonParsableException - if the StringBuffer is not parsable

See Also:

GaussianEmission.GaussianEmission(StringBuffer)