de.jstacs.data
Class Alphabet.AlphabetParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.InstanceParameterSet
          de.jstacs.data.Alphabet.AlphabetParameterSet

All Implemented Interfaces:

RangeIterator, Storable, Cloneable

Direct Known Subclasses:

ContinuousAlphabet.ContinuousAlphabetParameterSet, DiscreteAlphabet.DiscreteAlphabetParameterSet, DNAAlphabet.DNAAlphabetParameterSet

Enclosing class:

Alphabet

public abstract static class Alphabet.AlphabetParameterSet
extends InstanceParameterSet

The super class for the InstanceParameterSet of any Alphabet.

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.ParameterSet

errorMessage, parameters, parent, ranged

Constructor Summary

Alphabet.AlphabetParameterSet(Class<? extends Alphabet> instanceClass)
Creates a new Alphabet.AlphabetParameterSet.

Alphabet.AlphabetParameterSet(StringBuffer representation)
Creates a new Alphabet.AlphabetParameterSet from its XML representation.

Method Summary

Alphabet.AlphabetParameterSet	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.

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

fromXML, getInstance, getInstanceClass, getInstanceComment, toXML

Methods inherited from class de.jstacs.parameters.ParameterSet

getErrorMessage, getId, getNumberOfParameters, getNumberOfValues, getParameterAt, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isRanged, loadParameters, makeRanged, next, parametersLoaded, propagateId, recieveId, replaceParametersWithRangedInstance, reset, resetToFirst, setParent, simplify, valuesToString

Methods inherited from class java.lang.Object

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

Constructor Detail

Alphabet.AlphabetParameterSet

public Alphabet.AlphabetParameterSet(Class<? extends Alphabet> instanceClass)

Creates a new Alphabet.AlphabetParameterSet.

Parameters:

instanceClass - the class

Alphabet.AlphabetParameterSet

public Alphabet.AlphabetParameterSet(StringBuffer representation)
                              throws NonParsableException

Creates a new Alphabet.AlphabetParameterSet from its XML representation.

Parameters:

representation - the XML representation

Throws:

NonParsableException - is thrown if representation could not be parsed

Method Detail

clone

public Alphabet.AlphabetParameterSet 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 ParameterSet

Returns:

a deep clone of this ParameterSet

Throws:

CloneNotSupportedException

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