de.jstacs.models.discrete.inhomogeneous.parameters
Class BayesianNetworkModelParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.InstanceParameterSet
          de.jstacs.parameters.SequenceScoringParameterSet
              de.jstacs.models.discrete.DGMParameterSet
                  de.jstacs.models.discrete.inhomogeneous.parameters.IDGMParameterSet
                      de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

public class BayesianNetworkModelParameterSet
extends IDGMParameterSet

The ParameterSet for the class BayesianNetworkModel.

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, ranged

Constructor Summary

BayesianNetworkModelParameterSet()
The simple constructor for an empty BayesianNetworkModelParameterSet for a BayesianNetworkModel.

BayesianNetworkModelParameterSet(AlphabetContainer alphabet, int length, double ess, String description, StructureLearner.ModelType model, byte order, StructureLearner.LearningType method)
This is the constructor of a filled BayesianNetworkModelParameterSet for a BayesianNetworkModel.

BayesianNetworkModelParameterSet(StringBuffer s)
The standard constructor for the interface Storable.

Method Summary

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.
protected void	loadParameters() Loads the parameters for this ParameterSet.
void	setModelType(String modelType) This method allows a simple change of the model type.

Methods inherited from class de.jstacs.models.discrete.inhomogeneous.parameters.IDGMParameterSet

getModelInstanceName

Methods inherited from class de.jstacs.models.discrete.DGMParameterSet

clone, getInstanceName, hasDefaultOrIsSet, setEss

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet

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

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass

Methods inherited from class de.jstacs.parameters.ParameterSet

fromGalaxy, getErrorMessage, getId, getIndex, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setParent, simplify, toGalaxy, valuesToString

Methods inherited from class java.lang.Object

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

Constructor Detail

BayesianNetworkModelParameterSet

public BayesianNetworkModelParameterSet(StringBuffer s)
                                 throws NonParsableException

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

Parameters:

s - the XML representation as StringBuffer

Throws:

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

See Also:

Storable, IDGMParameterSet.IDGMParameterSet(StringBuffer)

BayesianNetworkModelParameterSet

public BayesianNetworkModelParameterSet()

The simple constructor for an empty BayesianNetworkModelParameterSet for a BayesianNetworkModel.

See Also:

IDGMParameterSet.IDGMParameterSet(Class)

BayesianNetworkModelParameterSet

public BayesianNetworkModelParameterSet(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 BayesianNetworkModelParameterSet for a BayesianNetworkModel.

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, IDGMParameterSet.IDGMParameterSet(Class, AlphabetContainer, int, double, String)

Method Detail

loadParameters

protected void loadParameters()
                       throws Exception

Description copied from class: ParameterSet

Loads the parameters for this ParameterSet. This is in most cases done by calling ParameterSet.initParameterList() or ParameterSet.initParameterList(int) to initialize ParameterSet.parameters and afterwards filling ParameterSet.parameters with instances of subclasses of Parameter.

Overrides:

loadParameters in class DGMParameterSet

Throws:

Exception - if the parameters could not be loaded

See Also:

Parameter, ParameterSet.parameters, ParameterSet.initParameterList(), ParameterSet.initParameterList(int)

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