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

java.lang.Object
  extended by de.jstacs.parameters.ParameterSet
      extended by de.jstacs.parameters.InstanceParameterSet
          extended by de.jstacs.parameters.SequenceScoringParameterSet
              extended by de.jstacs.models.discrete.DGMParameterSet
                  extended by de.jstacs.models.discrete.inhomogeneous.parameters.IDGMParameterSet
                      extended by 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)