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:

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

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, getAlphabetContainer, 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

fromGalaxy, getErrorMessage, getId, getIndex, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setParent, simplify, toGalaxy, 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 standard constructor for the interface Storable. Creates a new HomogeneousModelParameterSet out of its XML representation.

Parameters:

s - the XML representation as StringBuffer

Throws:

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

See Also:

Storable, DGMParameterSet.DGMParameterSet(StringBuffer)

HomogeneousModelParameterSet

protected HomogeneousModelParameterSet(Class<? extends HomogeneousModel> instanceClass)

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

Parameters:

instanceClass - the (sub-)class

See Also:

HomogeneousMM, HomogeneousModel, DGMParameterSet.DGMParameterSet(Class, boolean, boolean)

HomogeneousModelParameterSet

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

Creates a new HomogeneousModelParameterSet 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:

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

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 - if the parameters could not be loaded

See Also:

Parameter, ParameterSet.parameters, ParameterSet.initParameterList(), ParameterSet.initParameterList(int)

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 DGMParameterSet

Returns:

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