de.jstacs.models.discrete.homogeneous.parameters
Class HomogeneousModelParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.InstanceParameterSet
          de.jstacs.parameters.SequenceScoringParameterSet
              de.jstacs.models.discrete.DGMParameterSet
                  de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet

All Implemented Interfaces:

RangeIterator, Storable, Cloneable

Direct Known Subclasses:

HomMMParameterSet

public abstract class HomogeneousModelParameterSet
extends DGMParameterSet

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, ranged

Constructor Summary

protected	HomogeneousModelParameterSet(Class<? extends HomogeneousModel> instanceClass) An empty constructor.
protected	HomogeneousModelParameterSet(Class<? extends HomogeneousModel> instanceClass, AlphabetContainer alphabet, double ess, String description, byte order) The constructor for models, that can handle variable lengths.
protected	HomogeneousModelParameterSet(StringBuffer s) The constructor for the Storable interface.

Method Summary

boolean	hasDefaultOrIsSet() Returns true if all parameters in this ParameterSet are either set by the user or have default values.
protected void	loadParameters() Loads the parameters for this ParameterSet.

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

clone, getInstanceName, setEss

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet

equals, fromXML, getAlphabet, getIndex, getLength, getNumberOfParameters, getParameterAt, replaceParametersWithRangedInstance, reset, toXML

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass, getInstanceComment

Methods inherited from class de.jstacs.parameters.ParameterSet

getErrorMessage, getId, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setParent, simplify, valuesToString

Methods inherited from class java.lang.Object

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

Constructor Detail

HomogeneousModelParameterSet

protected HomogeneousModelParameterSet(StringBuffer s)
                                throws NonParsableException

The constructor for the Storable interface.

Parameters:

s - the StringBuffer

Throws:

NonParsableException - if the StringBuffer is not parsable

HomogeneousModelParameterSet

protected HomogeneousModelParameterSet(Class<? extends HomogeneousModel> instanceClass)

An empty constructor.

Parameters:

instanceClass - the (sub-)class

HomogeneousModelParameterSet

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

The constructor for models, that can handle variable lengths.

Parameters:

instanceClass - the (sub-)class

alphabet - the alphabet

ess - the ESS

description - the description

order - the Markov order of the model

Throws:

Exception - if something went wrong

Method Detail

loadParameters

protected void loadParameters()
                       throws Exception

Description copied from class: ParameterSet

Loads the parameters for this ParameterSet. This is in most cases done by calling ParameterSet.initParameterList() or ParameterSet.initParameterList(int) to initialize ParameterSet.parameters and afterwards filling ParameterSet.parameters with instances of subclasses of Parameter.

Overrides:

loadParameters in class DGMParameterSet

Throws:

Exception - an Exception is thrown if the parameters could not be loaded

See Also:

ParameterSet.parameters, Parameter

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.hasDefaultOrIsSet() should be called prior to checking specific constraints.

Overrides:

hasDefaultOrIsSet in class DGMParameterSet

Returns:

true if all parameters have some allowed value set