de.jstacs.sequenceScores.statisticalModels.trainable.discrete

Class DGTrainSMParameterSet<T extends DiscreteGraphicalTrainSM>

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<T>

de.jstacs.parameters.SequenceScoringParameterSet<T>

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DGTrainSMParameterSet<T>

Type Parameters:

T - the type of the DGTrainSMParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

HomogeneousTrainSMParameterSet, IDGTrainSMParameterSet

public abstract class DGTrainSMParameterSet<T extends DiscreteGraphicalTrainSM>
extends SequenceScoringParameterSet<T>

The super ParameterSet for any parameter set of a DiscreteGraphicalTrainSM.

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

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	DGTrainSMParameterSet(Class<T> instanceClass, AlphabetContainer alphabet, double ess, String description) The constructor for models that can handle variable lengths.
protected	DGTrainSMParameterSet(Class<T> instanceClass, AlphabetContainer alphabet, int length, double ess, String description) The constructor for models that can handle only sequences of fixed length given by length.
protected	DGTrainSMParameterSet(Class<T> instanceClass, boolean simple, boolean variableLength) An empty constructor.
protected	DGTrainSMParameterSet(StringBuffer s) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
DGTrainSMParameterSet	clone() Creates a full clone (deep copy) of this ParameterSet.
String	getInstanceName() Returns the name of an instance of the class that can be constructed using this ParameterSet.
boolean	hasDefaultOrIsSet() Returns true if all parameters in this ParameterSet are either set by the user or have default values.
void	setEss(double ess) This method can be used to set the ess (equivalent sample size) of this parameter set.

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet

equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, reset, toXML

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass, getInstanceComment

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

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DGTrainSMParameterSet

protected DGTrainSMParameterSet(StringBuffer s)
                         throws NonParsableException

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

Parameters:

s - 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, SequenceScoringParameterSet.SequenceScoringParameterSet(StringBuffer)

DGTrainSMParameterSet

protected DGTrainSMParameterSet(Class<T> instanceClass,
                                boolean simple,
                                boolean variableLength)

An empty constructor. Creates a new DGTrainSMParameterSet from the class that can be instantiated using this DGTrainSMParameterSet.

Parameters:

instanceClass - the (sub-)class

simple - indicates whether the alphabet should be simple or not

variableLength - indicates whether the model can handle sequences of variable length

See Also:

SequenceScoringParameterSet.SequenceScoringParameterSet(Class, AlphabetContainer.AlphabetContainerType, boolean, boolean)

DGTrainSMParameterSet

protected DGTrainSMParameterSet(Class<T> instanceClass,
                                AlphabetContainer alphabet,
                                double ess,
                                String description)
                         throws Exception

The constructor for models that can handle variable lengths. Creates a new DGTrainSMParameterSet with a description from the class that can be instantiated using this DGTrainSMParameterSet, a given AlphabetContainer and a given equivalent sample size (ess).

Parameters:

instanceClass - the (sub-)class

alphabet - the alphabet

ess - the ess (equivalent sample size)

description - the description

Throws:

Exception - if something went wrong

DGTrainSMParameterSet

protected DGTrainSMParameterSet(Class<T> instanceClass,
                                AlphabetContainer alphabet,
                                int length,
                                double ess,
                                String description)
                         throws Exception

The constructor for models that can handle only sequences of fixed length given by length. Creates a new DGTrainSMParameterSet with a description from the class that can be instantiated using this DGTrainSMParameterSet, a given AlphabetContainer and a given equivalent sample size (ess).

Parameters:

instanceClass - the (sub-)class

alphabet - the alphabet

length - the length of the modeled sequences

ess - the ess (equivalent sample size)

description - the description

Throws:

Exception - if something went wrong

Method Detail

hasDefaultOrIsSet

public boolean hasDefaultOrIsSet()

Description copied from class: ParameterSet

Returns true if all parameters in this ParameterSet are either set by the user or have default values. If any additional constraints are required on your parameters you should either specify some ParameterValidator on these parameters or implement these constraints by overriding this method in your implementation of ParameterSet. It is recommended to specify a useful remark which constraint failed in the member-variable errorMessage, which will be displayed to the user. In the overriding method super.ParameterSet.hasDefaultOrIsSet() should be called prior to checking specific constraints.

Overrides:

hasDefaultOrIsSet in class SequenceScoringParameterSet<T extends DiscreteGraphicalTrainSM>

Returns:

true if all parameters have some allowed value set, false otherwise

getInstanceName

public String getInstanceName()

Description copied from class: InstanceParameterSet

Returns the name of an instance of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceName in class InstanceParameterSet<T extends DiscreteGraphicalTrainSM>

Returns:

the name of the class

clone

public DGTrainSMParameterSet clone()
                            throws CloneNotSupportedException

Description copied from class: ParameterSet

Creates a full clone (deep copy) of this ParameterSet. As a convenience-method the user can use fillWithStandardFieldsForClone(ParameterSet) on a newly created instance of a subclass of ParameterSet to obtain a clone/copy of all standard member variables (those already defined in ParameterSet) in the passed ParameterSet. Using this method, the cloning process becomes merely three-step:

• Create a new instance of your subclass of ParameterSet, most likely with an empty constructor or the one taking just the instance class.
• Call this.fillWithStandardFieldsForClone on this instance.
• Return the instance.

This method fulfills the conventions of Object's method Object.clone().

Overrides:

clone in class SequenceScoringParameterSet<T extends DiscreteGraphicalTrainSM>

Returns:

a deep clone/copy of this ParameterSet

Throws:

CloneNotSupportedException

setEss

public void setEss(double ess)
            throws SimpleParameter.IllegalValueException

This method can be used to set the ess (equivalent sample size) of this parameter set.

Parameters:

ess - the ess (equivalent sample size)

Throws:

SimpleParameter.IllegalValueException - if the ess is negative