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

java.lang.Object
  extended by de.jstacs.parameters.ParameterSet
      extended by de.jstacs.parameters.InstanceParameterSet<Measure>
          extended by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure.MeasureParameterSet
              extended by 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
PMMMutualInformation.PMMMutualInformationParameterSet()
          Creates a new PMMMutualInformation.PMMMutualInformationParameterSet with empty parameter values.
PMMMutualInformation.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.
PMMMutualInformation.PMMMutualInformationParameterSet(StringBuffer representation)
          Creates a new PMMMutualInformation.PMMMutualInformationParameterSet from its XML representation as defined by the Storable interface.
 
Method Summary
 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

PMMMutualInformation.PMMMutualInformationParameterSet

public PMMMutualInformation.PMMMutualInformationParameterSet()
                                                      throws ParameterException
Creates a new PMMMutualInformation.PMMMutualInformationParameterSet with empty parameter values.

Throws:
ParameterException - if the parameters could not be created

PMMMutualInformation.PMMMutualInformationParameterSet

public PMMMutualInformation.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

PMMMutualInformation.PMMMutualInformationParameterSet

public PMMMutualInformation.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