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java.lang.Objectde.jstacs.models.AbstractModel
de.jstacs.models.discrete.DiscreteGraphicalModel
public abstract class DiscreteGraphicalModel
This is the main class for all discrete graphical models (DGM)
DGMParameterSet
Field Summary | |
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protected DGMParameterSet |
params
The current parameter set of the model |
protected boolean |
trained
Indicates whether the model is trained or not |
Fields inherited from class de.jstacs.models.AbstractModel |
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alphabets, length |
Constructor Summary | |
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DiscreteGraphicalModel(DGMParameterSet params)
The default constructor. |
|
DiscreteGraphicalModel(StringBuffer representation)
The constructor for a model in xml format. |
Method Summary | |
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protected void |
check(Sequence sequence,
int startpos,
int endpos)
Checks some conditions on a sequence. |
DiscreteGraphicalModel |
clone()
Follows the conventions of Object 's clone-method. |
protected void |
fromXML(StringBuffer representation)
This method should only be used by the constructor that works on StringBuffer. |
DGMParameterSet |
getCurrentParameterSet()
Returns the ParameterSet that has been used to instantiate the current instance of the implementing
class. |
String |
getDescription()
Returns a short description of the model the was given by the user in the parameter set. |
double |
getESS()
This method return the ess that is used in this model. |
protected abstract StringBuffer |
getFurtherModelInfos()
|
protected abstract String |
getXMLTag()
|
boolean |
isTrained()
Returns true if the model has been trained successfully, false otherwise. |
protected void |
set(DGMParameterSet params,
boolean trained)
Sets the parameters as internal parameters and does some essential computations. |
protected abstract void |
setFurtherModelInfos(StringBuffer xml)
This method replaces the internal model infos with those from the StringBuffer. |
String |
toString()
Should give a simple representation (text) of the model as String. |
StringBuffer |
toXML()
This method returns an XML-representation of an instance of the implementing class. |
Methods inherited from class de.jstacs.models.AbstractModel |
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emitSample, getAlphabetContainer, getCharacteristics, getLength, getLogProbFor, getLogProbFor, getLogProbFor, getLogProbFor, getLogProbFor, getMaximalMarkovOrder, getPriorTerm, getProbFor, getProbFor, set, setNewAlphabetContainerInstance, train |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface de.jstacs.models.Model |
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getInstanceName, getLogPriorTerm, getNumericalCharacteristics, getProbFor, train |
Field Detail |
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protected DGMParameterSet params
protected boolean trained
Constructor Detail |
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public DiscreteGraphicalModel(DGMParameterSet params) throws CloneNotSupportedException, IllegalArgumentException, NonParsableException
params
- the parameter set
CloneNotSupportedException
- if the parameter set could not be cloned
IllegalArgumentException
- if the parameter set is not instantiated
NonParsableException
- if the parameter set is not parsablepublic DiscreteGraphicalModel(StringBuffer representation) throws NonParsableException
representation
- the model in xml format
NonParsableException
- if the StringBuffer could not be parsedMethod Detail |
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public DiscreteGraphicalModel clone() throws CloneNotSupportedException
AbstractModel
Object
's clone-method.
clone
in interface Model
clone
in class AbstractModel
AbstractModel
(the member-AlphabetContainer
isn't deeply cloned since it is assumed to be immutable). The type of the returned object is defined by
the class X
directly inherited from AbstractModel
. Hence X
's
clone-method should work as:Object o = (X)super.clone();
2. all additional member variables of o
defined by X
that are not of simple data-types like int, double, ... , have to be deeply
copied 3. return o
CloneNotSupportedException
public final DGMParameterSet getCurrentParameterSet() throws Exception
InstantiableFromParameterSet
ParameterSet
that has been used to instantiate the current instance of the implementing
class. If the current instance was not created using a ParameterSet
, an equivalent
ParameterSet
should be returned, such that an instance created using this
ParameterSet
would be in principle equal to the current instance.
getCurrentParameterSet
in interface InstantiableFromParameterSet
ParameterSet
Exception
- is thrown if the ParameterSet
could not be returnedpublic final String getDescription()
public final double getESS()
protected final void fromXML(StringBuffer representation) throws NonParsableException
AbstractModel
toXML()
.
fromXML
in class AbstractModel
representation
- the representation
NonParsableException
- if the StringBuffer is not parsable or the representation is conflictingAbstractModel.AbstractModel(StringBuffer)
public final boolean isTrained()
Model
isTrained
in interface Model
public String toString()
Model
toString
in interface Model
toString
in class Object
public final StringBuffer toXML()
Storable
toXML
in interface Storable
protected void check(Sequence sequence, int startpos, int endpos) throws NotTrainedException, IllegalArgumentException
sequence
- the sequencestartpos
- the startpositionendpos
- the endposition
NotTrainedException
- if the model is not trained
IllegalArgumentException
- if some constraints are not fulfilledprotected abstract StringBuffer getFurtherModelInfos()
toXML()
protected abstract String getXMLTag()
fromXML(StringBuffer)
,
toXML()
protected abstract void setFurtherModelInfos(StringBuffer xml) throws NonParsableException
xml
- contains the model infos like parameters of the distibution ... in xml format
NonParsableException
- if the StringBuffer could not be parsedfromXML(StringBuffer)
protected void set(DGMParameterSet params, boolean trained) throws CloneNotSupportedException, NonParsableException
params
- the new ParameterSettrained
- the indicator for the model
CloneNotSupportedException
- if the parmeterSet could not be cloned
NonParsableException
- if the parameters of the model could not be parsed
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