de.jstacs.models.discrete
Class DGMParameterSet

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

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

Direct Known Subclasses:

HomogeneousModelParameterSet, IDGMParameterSet

public abstract class DGMParameterSet
extends SequenceScoringParameterSet

The super ParameterSet for any parameter set of a DiscreteGraphicalModel.

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	DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass, AlphabetContainer alphabet, double ess, String description) The constructor for models that can handle variable lengths.
protected	DGMParameterSet(Class<? extends DiscreteGraphicalModel> 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	DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass, boolean simple, boolean variableLength) An empty constructor.
protected	DGMParameterSet(StringBuffer s) The standard constructor for the interface Storable.

Method Summary

DGMParameterSet	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.
protected void	loadParameters() Loads the parameters for this ParameterSet.
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, 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

DGMParameterSet

protected DGMParameterSet(StringBuffer s)
                   throws NonParsableException

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

Parameters:

s - the XML representation as StringBuffer

Throws:

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

See Also:

Storable, SequenceScoringParameterSet.SequenceScoringParameterSet(StringBuffer)

DGMParameterSet

protected DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass,
                          boolean simple,
                          boolean variableLength)

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

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)

DGMParameterSet

protected DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass,
                          AlphabetContainer alphabet,
                          double ess,
                          String description)
                   throws Exception

The constructor for models that can handle variable lengths. Creates a new DGMParameterSet with a description from the class that can be instantiated using this DGMParameterSet, 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

DGMParameterSet

protected DGMParameterSet(Class<? extends DiscreteGraphicalModel> 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 DGMParameterSet with a description from the class that can be instantiated using this DGMParameterSet, 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

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.

Specified by:

loadParameters in class ParameterSet

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 SequenceScoringParameterSet

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

Returns:

the name of the class

clone

public DGMParameterSet 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

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