de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters

Class HomogeneousTrainSMParameterSet

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.homogeneous.parameters.HomogeneousTrainSMParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

HomMMParameterSet

public abstract class HomogeneousTrainSMParameterSet
extends DGTrainSMParameterSet

This class implements a container for all parameters of any homogeneous model.

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	HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass) This is the constructor that creates an empty HomogeneousTrainSMParameterSet from the class that can be instantiated using this HomogeneousTrainSMParameterSet.
protected	HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass, AlphabetContainer alphabet, double ess, String description, byte order) Creates a new HomogeneousTrainSMParameterSet with AlphabetContainer, ess (equivalent sample size), description and order of the homogeneous Markov model.
protected	HomogeneousTrainSMParameterSet(StringBuffer s) The standard constructor for the interface Storable.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	hasDefaultOrIsSet() Returns true if all parameters in this ParameterSet are either set by the user or have default values.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DGTrainSMParameterSet

clone, getInstanceName, setEss

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

HomogeneousTrainSMParameterSet

protected HomogeneousTrainSMParameterSet(StringBuffer s)
                                  throws NonParsableException

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

Parameters:

s - the XML representation as StringBuffer

Throws:

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

See Also:

Storable, DGTrainSMParameterSet.DGTrainSMParameterSet(StringBuffer)

HomogeneousTrainSMParameterSet

protected HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass)

This is the constructor that creates an empty HomogeneousTrainSMParameterSet from the class that can be instantiated using this HomogeneousTrainSMParameterSet.

Parameters:

instanceClass - the (sub-)class

See Also:

HomogeneousMM, HomogeneousTrainSM, DGTrainSMParameterSet.DGTrainSMParameterSet(Class, boolean, boolean)

HomogeneousTrainSMParameterSet

protected HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass,
                              AlphabetContainer alphabet,
                              double ess,
                              String description,
                              byte order)
                                  throws Exception

Creates a new HomogeneousTrainSMParameterSet with AlphabetContainer, ess (equivalent sample size), description and order of the homogeneous Markov model. This constructor is for models that can handle variable lengths.

Parameters:

instanceClass - the (sub-)class

alphabet - the AlphabetContainer

ess - the ess (equivalent sample size)

description - the description

order - the order of the model

Throws:

Exception - if something went wrong

See Also:

DGTrainSMParameterSet.DGTrainSMParameterSet(Class, AlphabetContainer, double, String)

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 DGTrainSMParameterSet

Returns:

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