de.jstacs.models.discrete.inhomogeneous
Class InhomogeneousDGM

java.lang.Object
  de.jstacs.models.AbstractModel
      de.jstacs.models.discrete.DiscreteGraphicalModel
          de.jstacs.models.discrete.inhomogeneous.InhomogeneousDGM

All Implemented Interfaces:

InstantiableFromParameterSet, Model, Storable, Cloneable

Direct Known Subclasses:

DAGModel

public abstract class InhomogeneousDGM
extends DiscreteGraphicalModel

This class is the main class for all inhomogeneous discrete graphical models (InhomogeneousDGM).

Author:

Jens Keilwagen

See Also:

IDGMParameterSet

Field Summary

protected static OutputStream	DEFAULT_STREAM The default OutputStream.
protected SafeOutputStream	sostream This stream is used for comments, computation steps/results or any other kind of output during the training, ... etc.

Fields inherited from class de.jstacs.models.discrete.DiscreteGraphicalModel

params, trained

Fields inherited from class de.jstacs.models.AbstractModel

alphabets, length

Constructor Summary

InhomogeneousDGM(IDGMParameterSet params)
Creates a new InhomogeneousDGM from a given IDGMParameterSet.

InhomogeneousDGM(StringBuffer representation)
The standard constructor for the interface Storable.

Method Summary

protected void	check(Sequence sequence, int startpos, int endpos) Checks some conditions on a Sequence.
InhomogeneousDGM	clone() Follows the conventions of Object's clone()-method.
abstract String	getStructure() Returns a String representation of the underlying graph.
protected void	set(DGMParameterSet parameter, boolean trained) Sets the parameters as internal parameters and does some essential computations.
void	setOutputStream(OutputStream stream) Sets the OutputStream for the model.

Methods inherited from class de.jstacs.models.discrete.DiscreteGraphicalModel

fromXML, getCurrentParameterSet, getDescription, getESS, getFurtherModelInfos, getXMLTag, isTrained, setFurtherModelInfos, toString, toXML

Methods inherited from class de.jstacs.models.AbstractModel

emitSample, getAlphabetContainer, getCharacteristics, getLength, getLogProbFor, getLogProbFor, getLogProbFor, getLogProbFor, getLogProbFor, getMaximalMarkovOrder, getPriorTerm, getProbFor, getProbFor, set, setNewAlphabetContainerInstance, train

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface de.jstacs.models.Model

getInstanceName, getLogPriorTerm, getNumericalCharacteristics, getProbFor, train

Field Detail

sostream

protected SafeOutputStream sostream

This stream is used for comments, computation steps/results or any other kind of output during the training, ... etc.

DEFAULT_STREAM

protected static final OutputStream DEFAULT_STREAM

The default OutputStream.

Constructor Detail

InhomogeneousDGM

public InhomogeneousDGM(IDGMParameterSet params)
                 throws CloneNotSupportedException,
                        IllegalArgumentException,
                        NonParsableException

Creates a new InhomogeneousDGM from a given IDGMParameterSet.

Parameters:

params - the given parameter set

Throws:

CloneNotSupportedException - if the parameter set could not be cloned

IllegalArgumentException - if the parameter set is not instantiated

NonParsableException - if the parameter set is not parsable

See Also:

DiscreteGraphicalModel.DiscreteGraphicalModel(DGMParameterSet)

InhomogeneousDGM

public InhomogeneousDGM(StringBuffer representation)
                 throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

Storable, DiscreteGraphicalModel.DiscreteGraphicalModel(StringBuffer)

Method Detail

clone

public InhomogeneousDGM clone()
                       throws CloneNotSupportedException

Description copied from class: AbstractModel

Follows the conventions of Object's clone()-method.

Specified by:

clone in interface Model

Overrides:

clone in class DiscreteGraphicalModel

Returns:

an object, that is a copy of the current 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:
1. 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

Throws:

CloneNotSupportedException - if something went wrong while cloning

getStructure

public abstract String getStructure()
                             throws NotTrainedException

Returns a String representation of the underlying graph.

Returns:

a String representation of the underlying graph

Throws:

NotTrainedException - if the structure is not set, this can only be the case if the model is not trained

setOutputStream

public void setOutputStream(OutputStream stream)

Sets the OutputStream for the model. This stream will sometimes be used to write some information about the training/progress/computation... etc. to the screen, a file ... etc.

Parameters:

stream - the OutputStream

See Also:

SafeOutputStream

check

protected void check(Sequence sequence,
                     int startpos,
                     int endpos)
              throws NotTrainedException,
                     IllegalArgumentException

Description copied from class: DiscreteGraphicalModel

Checks some conditions on a Sequence. These are in general conditions on the AlphabetContainer of a (sub) Sequence between startpos und endpos.

Overrides:

check in class DiscreteGraphicalModel

Parameters:

sequence - the Sequence

startpos - the startposition

endpos - the endposition

Throws:

NotTrainedException - if the model is not trained

IllegalArgumentException - if some constraints are not fulfilled

set

protected void set(DGMParameterSet parameter,
                   boolean trained)
            throws CloneNotSupportedException,
                   NonParsableException

Description copied from class: DiscreteGraphicalModel

Sets the parameters as internal parameters and does some essential computations. Used in fromParameterSet-methods.

Overrides:

set in class DiscreteGraphicalModel

Parameters:

parameter - the new ParameterSet

trained - indicates if the model is trained or not

Throws:

CloneNotSupportedException - if the parameter set could not be cloned

NonParsableException - if the parameters of the model could not be parsed