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

Class FSDAGTrainSMParameterSet

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

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

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

FSDAGModelForGibbsSamplingParameterSet

public class FSDAGTrainSMParameterSet
extends IDGTrainSMParameterSet

The class for the parameters of a FSDAGTrainSM (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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
static String	encode(int[][] graph) This method can be used to encode an adjacency list to a graph description String (e.g.
String	getInstanceComment() Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.IDGTrainSMParameterSet

getModelInstanceName

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

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

FSDAGTrainSMParameterSet

public FSDAGTrainSMParameterSet(StringBuffer s)
                         throws NonParsableException

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

Parameters:

s - the XML representation as StringBuffer

Throws:

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

See Also:

Storable, IDGTrainSMParameterSet.IDGTrainSMParameterSet(StringBuffer)

FSDAGTrainSMParameterSet

public FSDAGTrainSMParameterSet()

This constructor creates an empty FSDAGTrainSMParameterSet set for a FSDAGTrainSM.

See Also:

FSDAGTrainSMParameterSet(Class)

FSDAGTrainSMParameterSet

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

This constructor creates an FSDAGTrainSMParameterSet 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[][]), FSDAGTrainSMParameterSet(Class, AlphabetContainer, int, double, String, String)

FSDAGTrainSMParameterSet

protected FSDAGTrainSMParameterSet(Class<? extends FSDAGTrainSM> clazz)

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

Parameters:

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

See Also:

FSDAGTrainSM, FSDAGModelForGibbsSampling, IDGTrainSMParameterSet.IDGTrainSMParameterSet(Class)

FSDAGTrainSMParameterSet

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

This constructor creates an FSDAGTrainSMParameterSet 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[][]), IDGTrainSMParameterSet.IDGTrainSMParameterSet(Class, AlphabetContainer, int, double, String)

Method Detail

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:

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