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

Class NumericalHMMTrainingParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

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

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

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

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

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

public class NumericalHMMTrainingParameterSet
extends MultiThreadedTrainingParameterSet

This class implements an ParameterSet for numerical training of an AbstractHMM.

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

Constructor and Description
NumericalHMMTrainingParameterSet() This is the empty constructor that can be used to fill the parameters after creation.
NumericalHMMTrainingParameterSet(int starts, AbstractTerminationCondition tc, int threads, byte algorithm, double lineEps, double startDist) This constructor can be used to create an instance with specified parameters.
NumericalHMMTrainingParameterSet(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Methods

Modifier and Type	Method and Description
byte	getAlgorithm() This method returns a byte encoding for the algorithm that should be used for optimization.
double	getLineEps() This method returns the threshold that should be used for stopping the line search during the optimization.
double	getStartDistance() This method returns the start distance that should be used in the line search during the optimization.

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

getNumberOfThreads

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

getTerminationCondition

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

NumericalHMMTrainingParameterSet

public NumericalHMMTrainingParameterSet()

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

NumericalHMMTrainingParameterSet

public NumericalHMMTrainingParameterSet(int starts,
                                AbstractTerminationCondition tc,
                                int threads,
                                byte algorithm,
                                double lineEps,
                                double startDist)
                                 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

threads - the number of threads that should be used during optimization

algorithm - the algorithm that shall be used

lineEps - the threshold for stopping the line search

startDist - the start distance for the line search

Throws:

Exception - if this NumericalHMMTrainingParameterSet could not be created

NumericalHMMTrainingParameterSet

public NumericalHMMTrainingParameterSet(StringBuffer xml)
                                 throws NonParsableException

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

Parameters:

xml - the XML representation as StringBuffer

Throws:

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

Method Detail

getAlgorithm

public byte getAlgorithm()

This method returns a byte encoding for the algorithm that should be used for optimization.

Returns:

a byte encoding for the algorithm that should be used for optimization

getLineEps

public double getLineEps()

This method returns the threshold that should be used for stopping the line search during the optimization.

Returns:

the threshold that should be used for stopping the line search during the optimization.

getStartDistance

public double getStartDistance()

This method returns the start distance that should be used in the line search during the optimization.

Returns:

the start distance that should be used in the line search during the optimization.