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
Method Summary |
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.parameters.ParameterSet |
fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy |
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 modellength
- 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 setalphabet
- the AlphabetContainer
that is used in the modellength
- 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)
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 String
s).
- 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)