de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training

Class MaxHMMTrainingParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.HMMTrainingParameterSet

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.MaxHMMTrainingParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

MultiThreadedTrainingParameterSet

public abstract class MaxHMMTrainingParameterSet
extends HMMTrainingParameterSet

This class is the super class for any HMMTrainingParameterSet that is used for a maximizing training algorithm of a hidden Markov model.

Author:

Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet

ParameterSet.ParameterList

Field Summary

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	MaxHMMTrainingParameterSet() This is the empty constructor that can be used to fill the parameters after creation.
protected	MaxHMMTrainingParameterSet(int starts, AbstractTerminationCondition tc) This constructor can be used to create an instance with specified parameters.
protected	MaxHMMTrainingParameterSet(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
AbstractTerminationCondition	getTerminationCondition() This method returns the AbstractTerminationCondition for stopping the training, e.g., if the difference of the scores between two iterations is smaller than a given threshold the training is stopped.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.HMMTrainingParameterSet

getNumberOfStarts

Methods inherited from class de.jstacs.parameters.ParameterSet

clone, fromGalaxy, fromXML, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent, toGalaxy, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

MaxHMMTrainingParameterSet

protected MaxHMMTrainingParameterSet()

This is the empty constructor that can be used to fill the parameters after creation.

MaxHMMTrainingParameterSet

protected MaxHMMTrainingParameterSet(int starts,
                                     AbstractTerminationCondition tc)
                              throws Exception

This constructor can be used to create an instance with specified parameters.

Parameters:

starts - the number of different starts

tc - the termination condition for stopping the algorithm

Throws:

Exception - if this MaxHMMTrainingParameterSet could not be created

MaxHMMTrainingParameterSet

protected MaxHMMTrainingParameterSet(StringBuffer xml)
                              throws NonParsableException

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

Parameters:

xml - the XML representation as StringBuffer

Throws:

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

Method Detail

getTerminationCondition

public AbstractTerminationCondition getTerminationCondition()
                                                     throws ParameterSetParser.NotInstantiableException

This method returns the AbstractTerminationCondition for stopping the training, e.g., if the difference of the scores between two iterations is smaller than a given threshold the training is stopped.

Returns:

the AbstractTerminationCondition for stopping the training

Throws:

ParameterSetParser.NotInstantiableException - if the AbstractTerminationCondition could not be created from its ParameterSet