de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Class BasicPluginTransitionElement

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.BasicTransitionElement

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.BasicPluginTransitionElement

All Implemented Interfaces:

Storable, Cloneable

public class BasicPluginTransitionElement
extends BasicTransitionElement

Basic transition element without random initialization of parameters.

Author:

Michael Seifert

Field Summary

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

context, descendants, hyperParameters, logNorm, parameters, states, statistic

Constructor Summary

Constructors

Constructor and Description
BasicPluginTransitionElement(int[] context, int[] states, double[] probs, double[] hyperParameters) Constructor creating a new instance with given context, descendant states, and hyper parameters.
BasicPluginTransitionElement(int[] context, int[] states, double[] probs, double[] hyperParameters, double[] weight) Constructor creating a new instance with given context, descendant states, and hyper parameters.
BasicPluginTransitionElement(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
protected void	appendFurtherInformation(StringBuffer xml) This method appends further information to the XML representation.
protected void	extractFurtherInformation(StringBuffer xml) This method extracts further information from the XML representation.
protected String	getXMLTag() This method returns the xml tag used in BasicHigherOrderTransition.AbstractTransitionElement.toXML().
void	initializeRandomly() This method draws new parameters from the prior.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

addToStatistic, appendGraphvizDescription, appendTransitions, clone, drawParametersFromStatistic, estimateFromStatistic, getArrowOption, getChild, getContext, getDescendant, getGraphvizEdgeWeight, getLabel, getLastContextState, getLogGammaScoreFromStatistic, getLogPriorTerm, getLogScoreFor, getNextContext, getNumberOfChildren, getNumberOfParameters, init, joinStatistics, precompute, resetStatistic, setIndexOfDescendantTransitionElement, setParameters, toString, toString, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicPluginTransitionElement

public BasicPluginTransitionElement(int[] context,
                                    int[] states,
                                    double[] probs,
                                    double[] hyperParameters)

Constructor creating a new instance with given context, descendant states, and hyper parameters.

Parameters:

context - previously visited state indices; last entry corresponds to the last state visited

states - all possible states that can be reached from the context; if null then no transition allowed

probs - initial probabilities

hyperParameters - hyper-parameters for transitions; if null then no prior is used

See Also:

BasicPluginTransitionElement(int[], int[], double[], double[], double[])

BasicPluginTransitionElement

public BasicPluginTransitionElement(int[] context,
                                    int[] states,
                                    double[] probs,
                                    double[] hyperParameters,
                                    double[] weight)

Constructor creating a new instance with given context, descendant states, and hyper parameters.

Parameters:

context - previously visited state indices; last entry corresponds to the last state visited

states - all possible states that can be reached from the context; if null then no transition allowed

probs - initial probabilities

hyperParameters - hyper-parameters for transitions; if null then no prior is used

weight - the weight for plotting the edge in Graphviz, enables to modify the edge length, larger weights imply shorter edges (default: 1)

BasicPluginTransitionElement

public BasicPluginTransitionElement(StringBuffer xml)
                             throws NonParsableException

The standard constructor for the interface Storable. Constructs a BasicPluginTransitionElement out of an XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the BasicPluginTransitionElement could not be reconstructed out of the StringBuffer xml

Method Detail

initializeRandomly

public void initializeRandomly()

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method draws new parameters from the prior.

Overrides:

initializeRandomly in class BasicHigherOrderTransition.AbstractTransitionElement

appendFurtherInformation

protected void appendFurtherInformation(StringBuffer xml)

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method appends further information to the XML representation. It allows subclasses to save further parameters that are not defined in the superclass.

Overrides:

appendFurtherInformation in class BasicTransitionElement

Parameters:

xml - the XML representation

extractFurtherInformation

protected void extractFurtherInformation(StringBuffer xml)
                                  throws NonParsableException

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method extracts further information from the XML representation. It allows subclasses to cast further parameters that are not defined in the superclass.

Overrides:

extractFurtherInformation in class BasicTransitionElement

Parameters:

xml - the XML representation

Throws:

NonParsableException - if the information could not be reconstructed out of the StringBuffer xml

getXMLTag

protected String getXMLTag()

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method returns the xml tag used in BasicHigherOrderTransition.AbstractTransitionElement.toXML().

Overrides:

getXMLTag in class BasicHigherOrderTransition.AbstractTransitionElement

Returns:

the xml tag used in BasicHigherOrderTransition.AbstractTransitionElement.toXML()