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

Class BasicTransitionElement

java.lang.Object

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

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

All Implemented Interfaces:

Storable, Cloneable

Direct Known Subclasses:

BasicPluginTransitionElement, ReferenceBasedTransitionElement, TransitionElement

public class BasicTransitionElement
extends BasicHigherOrderTransition.AbstractTransitionElement

This class implements the probability distribution for a given context, i.e. it contains all possible transition and the corresponding probabilities for a given set of previously visited states. This class just implements the basic functionalities.

Author:

Jan Grau, Jens Keilwagen

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
BasicTransitionElement(int[] context, int[] states, double[] hyperParameters) This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.
BasicTransitionElement(int[] context, int[] states, double[] hyperParameters, double[] weight) This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.
BasicTransitionElement(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.

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, getXMLTag, init, initializeRandomly, 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

BasicTransitionElement

public BasicTransitionElement(int[] context,
                              int[] states,
                              double[] hyperParameters)

This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.

Parameters:

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

states - the transitions to all possible states; if null then no transition allowed

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

See Also:

BasicTransitionElement(int[], int[], double[], double[])

BasicTransitionElement

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

This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.

Parameters:

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

states - the transitions to all possible states; if null then no transition allowed

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

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

BasicTransitionElement

public BasicTransitionElement(StringBuffer xml)
                       throws NonParsableException

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

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the BasicHigherOrderTransition.AbstractTransitionElement could not be reconstructed out of the StringBuffer xml

Method Detail

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.

Specified by:

appendFurtherInformation in class BasicHigherOrderTransition.AbstractTransitionElement

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.

Specified by:

extractFurtherInformation in class BasicHigherOrderTransition.AbstractTransitionElement

Parameters:

xml - the XML representation

Throws:

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