de.jstacs.sequenceScores.statisticalModels.trainable.discrete

Class DiscreteGraphicalTrainSM

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM

All Implemented Interfaces:

InstantiableFromParameterSet, SequenceScore, StatisticalModel, TrainableStatisticalModel, Storable, Cloneable

Direct Known Subclasses:

HomogeneousTrainSM, InhomogeneousDGTrainSM

public abstract class DiscreteGraphicalTrainSM
extends AbstractTrainableStatisticalModel
implements InstantiableFromParameterSet

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

Author:

Jens Keilwagen

See Also:

DGTrainSMParameterSet

Field Summary

Fields

Modifier and Type	Field and Description
protected DGTrainSMParameterSet	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.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel

alphabets, length

Constructor Summary

Constructors

Constructor and Description
DiscreteGraphicalTrainSM(DGTrainSMParameterSet params) The default constructor.
DiscreteGraphicalTrainSM(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
protected void	check(Sequence sequence, int startpos, int endpos) Checks some conditions on a Sequence.
DiscreteGraphicalTrainSM	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 a StringBuffer.
DGTrainSMParameterSet	getCurrentParameterSet() Returns the InstanceParameterSet that has been used to instantiate the current instance of the implementing class.
String	getDescription() Returns a short description of the model that was given by the user in the parameter set.
double	getESS() This method returns the ess (equivalent sample size) that is used in this model.
protected abstract StringBuffer	getFurtherModelInfos() Returns further model information as a StringBuffer.
protected abstract String	getXMLTag() Returns the XML tag that is used for this model in fromXML(StringBuffer) and toXML().
boolean	isInitialized() This method can be used to determine whether the instance is initialized.
protected void	set(DGTrainSMParameterSet 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 information with those from a StringBuffer.
String	toString(NumberFormat nf) This method returns a String representation of the instance.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel

emitDataSet, getAlphabetContainer, getCharacteristics, getLength, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getMaximalMarkovOrder, toString, train

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel

train

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.StatisticalModel

getLogPriorTerm, getLogProbFor

Methods inherited from interface de.jstacs.sequenceScores.SequenceScore

getInstanceName, getNumericalCharacteristics

Field Detail

params

protected DGTrainSMParameterSet params

The current parameter set of the model.

trained

protected boolean trained

Indicates whether the model is trained or not.

Constructor Detail

DiscreteGraphicalTrainSM

public DiscreteGraphicalTrainSM(DGTrainSMParameterSet params)
                         throws CloneNotSupportedException,
                                IllegalArgumentException,
                                NonParsableException

The default constructor. Creates a new DiscreteGraphicalTrainSM from a given DGTrainSMParameterSet.

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:

AbstractTrainableStatisticalModel.AbstractTrainableStatisticalModel(de.jstacs.data.AlphabetContainer, int)

DiscreteGraphicalTrainSM

public DiscreteGraphicalTrainSM(StringBuffer representation)
                         throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

Storable, AbstractTrainableStatisticalModel.AbstractTrainableStatisticalModel(StringBuffer)

Method Detail

clone

public DiscreteGraphicalTrainSM clone()
                               throws CloneNotSupportedException

Description copied from class: AbstractTrainableStatisticalModel

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

Specified by:

clone in interface SequenceScore

Specified by:

clone in interface TrainableStatisticalModel

Overrides:

clone in class AbstractTrainableStatisticalModel

Returns:

an object, that is a copy of the current AbstractTrainableStatisticalModel (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 AbstractTrainableStatisticalModel. 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

getCurrentParameterSet

public final DGTrainSMParameterSet getCurrentParameterSet()
                                                   throws Exception

Description copied from interface: InstantiableFromParameterSet

Returns the InstanceParameterSet that has been used to instantiate the current instance of the implementing class. If the current instance was not created using an InstanceParameterSet, an equivalent InstanceParameterSet should be returned, so that an instance created using this InstanceParameterSet would be in principle equal to the current instance.

Specified by:

getCurrentParameterSet in interface InstantiableFromParameterSet

Returns:

the current InstanceParameterSet

Throws:

Exception - if the InstanceParameterSet could not be returned

getDescription

public final String getDescription()

Returns a short description of the model that was given by the user in the parameter set.

Returns:

a short description of the model

getESS

public final double getESS()

This method returns the ess (equivalent sample size) that is used in this model.

Returns:

the ess

fromXML

protected final void fromXML(StringBuffer representation)
                      throws NonParsableException

Description copied from class: AbstractTrainableStatisticalModel

This method should only be used by the constructor that works on a StringBuffer. It is the counter part of Storable.toXML().

Specified by:

fromXML in class AbstractTrainableStatisticalModel

Parameters:

representation - the XML representation of the model

Throws:

NonParsableException - if the StringBuffer is not parsable or the representation is conflicting

See Also:

AbstractTrainableStatisticalModel.AbstractTrainableStatisticalModel(StringBuffer)

isInitialized

public final boolean isInitialized()

Description copied from interface: SequenceScore

This method can be used to determine whether the instance is initialized. If the instance is initialized you should be able to invoke SequenceScore.getLogScoreFor(Sequence).

Specified by:

isInitialized in interface SequenceScore

Returns:

true if the instance is initialized, false otherwise

toString

public String toString(NumberFormat nf)

Description copied from interface: SequenceScore

This method returns a String representation of the instance.

Specified by:

toString in interface SequenceScore

Parameters:

nf - the NumberFormat for the String representation of parameters or probabilities

Returns:

a String representation of the instance

toXML

public final StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Returns:

the XML representation

check

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

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 AbstractTrainableStatisticalModel

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

getFurtherModelInfos

protected abstract StringBuffer getFurtherModelInfos()

Returns further model information as a StringBuffer.

Returns:

further model information like parameters of the distribution etc. in XML format

See Also:

toXML()

getXMLTag

protected abstract String getXMLTag()

Returns the XML tag that is used for this model in fromXML(StringBuffer) and toXML().

Returns:

the XML tag that is used in fromXML(StringBuffer) and toXML()

See Also:

fromXML(StringBuffer), toXML()

setFurtherModelInfos

protected abstract void setFurtherModelInfos(StringBuffer xml)
                                      throws NonParsableException

This method replaces the internal model information with those from a StringBuffer.

Parameters:

xml - contains the model information like parameters of the distribution etc. in XML format

Throws:

NonParsableException - if the StringBuffer could not be parsed

See Also:

fromXML(StringBuffer)

set

protected void set(DGTrainSMParameterSet params,
                   boolean trained)
            throws CloneNotSupportedException,
                   NonParsableException

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

Parameters:

params - 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