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

Class IDGTrainSMParameterSet

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

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

BayesianNetworkTrainSMParameterSet, FSDAGTrainSMParameterSet, MEManagerParameterSet

public abstract class IDGTrainSMParameterSet
extends DGTrainSMParameterSet

This is the abstract container of parameters that is a root container for all inhomogeneous discrete graphical model parameter containers.

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

Modifier	Constructor and Description
protected	IDGTrainSMParameterSet(Class<? extends InhomogeneousDGTrainSM> instanceClass) This constructor creates an empty IDGTrainSMParameterSet instance from the class that can be instantiated using this IDGTrainSMParameterSet.
protected	IDGTrainSMParameterSet(Class<? extends InhomogeneousDGTrainSM> instanceClass, AlphabetContainer alphabet, int length, double ess, String description) This constructor creates an IDGTrainSMParameterSet instance for the specified class.
protected	IDGTrainSMParameterSet(StringBuffer s) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
static String	getModelInstanceName(StructureLearner.ModelType model, byte order, StructureLearner.LearningType method, double ess) This method returns a short textual representation of the model instance.

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, getInstanceComment

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

IDGTrainSMParameterSet

protected IDGTrainSMParameterSet(StringBuffer s)
                          throws NonParsableException

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

Parameters:

s - the XML representation as StringBuffer

Throws:

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

See Also:

Storable, DGTrainSMParameterSet.DGTrainSMParameterSet(StringBuffer)

IDGTrainSMParameterSet

protected IDGTrainSMParameterSet(Class<? extends InhomogeneousDGTrainSM> instanceClass)

This constructor creates an empty IDGTrainSMParameterSet instance from the class that can be instantiated using this IDGTrainSMParameterSet.

Parameters:

instanceClass - the instance class

See Also:

DGTrainSMParameterSet.DGTrainSMParameterSet(Class, boolean, boolean)

IDGTrainSMParameterSet

protected IDGTrainSMParameterSet(Class<? extends InhomogeneousDGTrainSM> instanceClass,
                                 AlphabetContainer alphabet,
                                 int length,
                                 double ess,
                                 String description)
                          throws Exception

This constructor creates an IDGTrainSMParameterSet instance for the specified class. It sets the AlphabetContainer, the length, the ess (equivalent sample size) and the model description.

Parameters:

instanceClass - the instance class

alphabet - the AlphabetContainer for the model

length - the length of the model

ess - the ess of the model

description - the model description

Throws:

Exception - if something went wrong

Method Detail

getModelInstanceName

public static String getModelInstanceName(StructureLearner.ModelType model,
                                          byte order,
                                          StructureLearner.LearningType method,
                                          double ess)

This method returns a short textual representation of the model instance.

Parameters:

model - the type of the model

order - the order of the model

method - the learning method

ess - the used ess (equivalent sample size)

Returns:

a short textual representation of the model instance

See Also:

StructureLearner.ModelType, StructureLearner.LearningType