de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

Class PMMMutualInformation.PMMMutualInformationParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<Measure>

de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure.MeasureParameterSet

de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation.PMMMutualInformationParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Enclosing class:

PMMMutualInformation

public static class PMMMutualInformation.PMMMutualInformationParameterSet
extends Measure.MeasureParameterSet

Class for the parameters of a PMMMutualInformation structure Measure.

Author:

Jan Grau

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
PMMMutualInformationParameterSet() Creates a new PMMMutualInformation.PMMMutualInformationParameterSet with empty parameter values.
PMMMutualInformationParameterSet(byte order, BTMutualInformation.DataSource clazz, double[] ess) Creates a new PMMMutualInformation.PMMMutualInformationParameterSet with the parameter for the order set to order, the parameter for the BTMutualInformation.DataSource set to clazz and the parameter for the equivalent sample sizes (ess) set to ess.
PMMMutualInformationParameterSet(StringBuffer representation) Creates a new PMMMutualInformation.PMMMutualInformationParameterSet from its XML representation as defined by the Storable interface.

Method Summary

Modifier and Type	Method and Description
BTMutualInformation.DataSource	getClazz() Returns the source of the data to compute the mutual information as defined by this set of parameters.
double[]	getEss() Returns the equivalent sample sizes (ess) defined by this set of parameters.
String	getInstanceComment() Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.
String	getInstanceName() Returns the name of an instance of the class that can be constructed using this ParameterSet.
byte	getOrder() Returns the order defined by this set of parameters.

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

fromXML, getInstance, getInstanceClass, toXML

Methods inherited from class de.jstacs.parameters.ParameterSet

clone, fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent, toGalaxy

Methods inherited from class java.lang.Object

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

Constructor Detail

PMMMutualInformationParameterSet

public PMMMutualInformationParameterSet()
                                 throws ParameterException

Creates a new PMMMutualInformation.PMMMutualInformationParameterSet with empty parameter values.

Throws:

ParameterException - if the parameters could not be created

PMMMutualInformationParameterSet

public PMMMutualInformationParameterSet(byte order,
                                        BTMutualInformation.DataSource clazz,
                                        double[] ess)
                                 throws Exception

Creates a new PMMMutualInformation.PMMMutualInformationParameterSet with the parameter for the order set to order, the parameter for the BTMutualInformation.DataSource set to clazz and the parameter for the equivalent sample sizes (ess) set to ess.

Parameters:

order - the order

clazz - the source of the data to compute the mutual information

ess - the equivalent sample sizes for the foreground class and the background, i.e. the background class or (in case of more than two classes) all non-foreground classes

Throws:

Exception - if the parameters could not be created or set

PMMMutualInformationParameterSet

public PMMMutualInformationParameterSet(StringBuffer representation)
                                 throws NonParsableException

Creates a new PMMMutualInformation.PMMMutualInformationParameterSet from its XML representation as defined by the Storable interface.

Parameters:

representation - the XML code as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

getEss

public double[] getEss()

Returns the equivalent sample sizes (ess) defined by this set of parameters.

Returns:

the ess

getClazz

public BTMutualInformation.DataSource getClazz()

Returns the source of the data to compute the mutual information as defined by this set of parameters.

Returns:

the source of the data

getOrder

public byte getOrder()

Returns the order defined by this set of parameters.

Returns:

the order

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<Measure>

Returns:

the comment of the class

getInstanceName

public String getInstanceName()

Description copied from class: InstanceParameterSet

Returns the name of an instance of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceName in class InstanceParameterSet<Measure>

Returns:

the name of the class