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

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.FSDAGMParameterSet

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

Direct Known Subclasses:

FSDAGModelForGibbsSamplingParameterSet

public class FSDAGMParameterSet
extends IDGMParameterSet

The class for the parameters of a FSDAGModel (fixed structure directed acyclic graphical model).

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

	FSDAGMParameterSet() This constructor creates an empty FSDAGMParameterSet set for a FSDAGModel.
	FSDAGMParameterSet(AlphabetContainer alphabet, int length, double ess, String description, String graph) This constructor creates an FSDAGMParameterSet instance.
protected	FSDAGMParameterSet(Class<? extends FSDAGModel> clazz) This the constructor creates an empty FSDAGMParameterSet from the class that can be instantiated using this FSDAGMParameterSet.
protected	FSDAGMParameterSet(Class<? extends FSDAGModel> clazz, AlphabetContainer alphabet, int length, double ess, String description, String graph) This constructor creates an FSDAGMParameterSet instance for the specified class.
	FSDAGMParameterSet(StringBuffer s) The standard constructor for the interface Storable.

Method Summary

static String	encode(int[][] graph) This method can be used to encode an adjacency list to a graph description String (e.g. for the different constructors which requires graph description Strings).
String	getInstanceComment() Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.
protected void	loadParameters() Loads the parameters for this ParameterSet.

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

FSDAGMParameterSet

public FSDAGMParameterSet(StringBuffer s)
                   throws NonParsableException

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

Parameters:

s - the XML representation as StringBuffer

Throws:

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

See Also:

Storable, IDGMParameterSet.IDGMParameterSet(StringBuffer)

FSDAGMParameterSet

public FSDAGMParameterSet()

This constructor creates an empty FSDAGMParameterSet set for a FSDAGModel.

See Also:

FSDAGMParameterSet(Class)

FSDAGMParameterSet

public FSDAGMParameterSet(AlphabetContainer alphabet,
                          int length,
                          double ess,
                          String description,
                          String graph)
                   throws Exception

This constructor creates an FSDAGMParameterSet instance. It sets the AlphabetContainer, the length, the ess (equivalent sample size) and the model description as well as a String describing the graph structure.

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)

graph - the graph description String, encodes in XML-like manner the parents of each node "<parents node="i">j,k,l</parents>"

Throws:

Exception - if something went wrong

See Also:

encode(int[][]), FSDAGMParameterSet(Class, AlphabetContainer, int, double, String, String)

FSDAGMParameterSet

protected FSDAGMParameterSet(Class<? extends FSDAGModel> clazz)

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

Parameters:

clazz - the class of the object that will be created with this parameter set

See Also:

FSDAGModel, FSDAGModelForGibbsSampling, IDGMParameterSet.IDGMParameterSet(Class)

FSDAGMParameterSet

protected FSDAGMParameterSet(Class<? extends FSDAGModel> clazz,
                             AlphabetContainer alphabet,
                             int length,
                             double ess,
                             String description,
                             String graph)
                      throws Exception

This constructor creates an FSDAGMParameterSet instance for the specified class. It sets the AlphabetContainer, the length, the ess (equivalent sample size) and the model description as well as a String describing the graph structure.

Parameters:

clazz - the class of the object that will be created with this parameter set

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)

graph - the graph description String, encodes in XML-like manner the parents of each node "<parents node="i">j,k,l</parents>"

Throws:

Exception - if something went wrong

See Also:

encode(int[][]), 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)

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

encode

public static String encode(int[][] graph)

This method can be used to encode an adjacency list to a graph description String (e.g. for the different constructors which requires graph description Strings).

Parameters:

graph - graph[i] contains the parents of node i

Returns:

the graph description String

See Also:

FSDAGMParameterSet(AlphabetContainer, int, double, String, String), FSDAGMParameterSet(Class, AlphabetContainer, int, double, String, String)