de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters

Class BayesianNetworkTrainSMParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<T>

de.jstacs.parameters.SequenceScoringParameterSet<T>

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DGTrainSMParameterSet

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.IDGTrainSMParameterSet

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.BayesianNetworkTrainSMParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

public class BayesianNetworkTrainSMParameterSet
extends IDGTrainSMParameterSet

The ParameterSet for the class BayesianNetworkTrainSM.

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.SequenceScoringParameterSet

alphabet, length

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Constructor Summary

Constructors

Constructor and Description
BayesianNetworkTrainSMParameterSet() The simple constructor for an empty BayesianNetworkTrainSMParameterSet for a BayesianNetworkTrainSM.
BayesianNetworkTrainSMParameterSet(AlphabetContainer alphabet, int length, double ess, String description, StructureLearner.ModelType model, byte order, StructureLearner.LearningType method) This is the constructor of a filled BayesianNetworkTrainSMParameterSet for a BayesianNetworkTrainSM.
BayesianNetworkTrainSMParameterSet(StringBuffer s) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
String	getInstanceComment() Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.
String	getModelInstanceName() This method returns a short description of the model.
void	setModelType(String modelType) This method allows a simple change of the model type.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.IDGTrainSMParameterSet

getModelInstanceName

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DGTrainSMParameterSet

clone, getInstanceName, hasDefaultOrIsSet, setEss

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet

equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, reset, toXML

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass

Methods inherited from class de.jstacs.parameters.ParameterSet

fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy

Methods inherited from class java.lang.Object

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

Constructor Detail

BayesianNetworkTrainSMParameterSet

public BayesianNetworkTrainSMParameterSet(StringBuffer s)
                                   throws NonParsableException

The standard constructor for the interface Storable. Creates a new BayesianNetworkTrainSMParameterSet out of its XML representation.

Parameters:

s - the XML representation as StringBuffer

Throws:

NonParsableException - if the BayesianNetworkTrainSMParameterSet could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)

See Also:

Storable, IDGTrainSMParameterSet.IDGTrainSMParameterSet(StringBuffer)

BayesianNetworkTrainSMParameterSet

public BayesianNetworkTrainSMParameterSet()

The simple constructor for an empty BayesianNetworkTrainSMParameterSet for a BayesianNetworkTrainSM.

See Also:

IDGTrainSMParameterSet.IDGTrainSMParameterSet(Class)

BayesianNetworkTrainSMParameterSet

public BayesianNetworkTrainSMParameterSet(AlphabetContainer alphabet,
                                          int length,
                                          double ess,
                                          String description,
                                          StructureLearner.ModelType model,
                                          byte order,
                                          StructureLearner.LearningType method)
                                   throws Exception

This is the constructor of a filled BayesianNetworkTrainSMParameterSet for a BayesianNetworkTrainSM.

Parameters:

alphabet - the AlphabetContainer that is used in the model

length - the length of the model (has to be positive)

ess - the ess (equivalent sample size) of the model (has to be positive)

description - a short description of the model (for a better handling of the object by the user)

model - the type of model: IMM, PMM or BN

order - the order of the model

method - the method how to learn the structure (only relevant for PMM, BN): ML_OR_MAP or BMA

Throws:

Exception - if something went wrong

See Also:

StructureLearner.ModelType, StructureLearner.ModelType.IMM, StructureLearner.ModelType.PMM, StructureLearner.ModelType.BN, StructureLearner.LearningType, StructureLearner.LearningType.ML_OR_MAP, StructureLearner.LearningType.BMA, IDGTrainSMParameterSet.IDGTrainSMParameterSet(Class, AlphabetContainer, int, double, String)

Method Detail

setModelType

public void setModelType(String modelType)
                  throws SimpleParameter.IllegalValueException

This method allows a simple change of the model type.

Parameters:

modelType - the type of the model, one of "iMM", "pMM" or "BN"

Throws:

SimpleParameter.IllegalValueException - if the modelType is illegal

getInstanceComment

public String getInstanceComment()

Description copied from class: InstanceParameterSet

Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceComment in class InstanceParameterSet

Returns:

the comment of the class

getModelInstanceName

public String getModelInstanceName()

This method returns a short description of the model.

Returns:

a short description of the model