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

Class SamplingHMMTrainingParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

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

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

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

public class SamplingHMMTrainingParameterSet
extends HMMTrainingParameterSet

This class contains the parameters for training training an AbstractHMM using a sampling strategy.

Author:

Michael Scharfe, 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
SamplingHMMTrainingParameterSet() This is the empty constructor that can be used to fill the parameters after creation.
SamplingHMMTrainingParameterSet(int starts, int stepsPerIteration, int stationarySteps, AbstractBurnInTestParameterSet burnInTestParameters) This is the main constructor creating an already filled parameter set for training an AbstractHMM using a sampling strategy.
SamplingHMMTrainingParameterSet(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
AbstractBurnInTest	getBurnInTest() This method return the burn in test to be used during sampling.
int	getNumberOfStepsInStationaryPhase() The method returns the number of steps to be done in the stationary phase.
int	getNumberOfStepsPerIteration() This method returns the number of steps to be done in each start before testing for the end of the burn in phase (again).

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

SamplingHMMTrainingParameterSet

public SamplingHMMTrainingParameterSet()

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

SamplingHMMTrainingParameterSet

public SamplingHMMTrainingParameterSet(int starts,
                                       int stepsPerIteration,
                                       int stationarySteps,
                                       AbstractBurnInTestParameterSet burnInTestParameters)
                                throws SimpleParameter.IllegalValueException

This is the main constructor creating an already filled parameter set for training an AbstractHMM using a sampling strategy.

Parameters:

starts - the number of independent starts

stepsPerIteration - the number of steps to be done for each start before testing for the end of the burn in phase

stationarySteps - the number of steps in the stationary phase

burnInTestParameters - the parameter set for the BurnInTest

Throws:

SimpleParameter.IllegalValueException - if some parameter is not permitted

SamplingHMMTrainingParameterSet

public SamplingHMMTrainingParameterSet(StringBuffer xml)
                                throws NonParsableException

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

Parameters:

xml - the XML representation as StringBuffer

Throws:

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

Method Detail

getNumberOfStepsPerIteration

public int getNumberOfStepsPerIteration()

This method returns the number of steps to be done in each start before testing for the end of the burn in phase (again).

Returns:

the number of steps to be done in each start before testing for the end of the burn in phase (again)

getNumberOfStepsInStationaryPhase

public int getNumberOfStepsInStationaryPhase()

The method returns the number of steps to be done in the stationary phase.

Returns:

the number of steps to be done in the stationary phase

getBurnInTest

public AbstractBurnInTest getBurnInTest()
                                 throws ParameterSetParser.NotInstantiableException

This method return the burn in test to be used during sampling.

Returns:

the burn in test to be used

Throws:

ParameterSetParser.NotInstantiableException - if the burn in test could not be created