de.jstacs.data
Class AlphabetContainerParameterSet.AlphabetArrayParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.ExpandableParameterSet
          de.jstacs.parameters.ArrayParameterSet
              de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet

All Implemented Interfaces:

RangeIterator, Storable, Cloneable

Enclosing class:

AlphabetContainerParameterSet

public static class AlphabetContainerParameterSet.AlphabetArrayParameterSet
extends ArrayParameterSet

Class for the parameters of an array of Alphabets of defined length.

Author:

Jan Grau

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet

ParameterSet.ParameterList

Field Summary

Fields inherited from class de.jstacs.parameters.ExpandableParameterSet

commentTemplate, nameTemplate, template

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent, ranged

Constructor Summary

AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets, AlphabetContainer.AlphabetContainerType type)
Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of Alphabets and the information if all alphabets are discrete.

AlphabetContainerParameterSet.AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType type)
Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from the information if the array shall contain only the parameters for discrete Alphabets.

AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)
Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from its XML representation.

Method Summary

AlphabetContainerParameterSet.AlphabetArrayParameterSet	clone() Creates a full clone (deep copy) of this ParameterSet.
void	fromXML(StringBuffer representation) Parses the instance fields of a ParameterSet from the XML-representation as returned by ParameterSet.toXML().
String	getInstanceComment() Returns a descriptive comment on this ParameterSet.
String	getInstanceName() Returns a descriptive name for this ParameterSet.
StringBuffer	toXML() This method returns an XML-representation of an instance of the implementing class.

Methods inherited from class de.jstacs.parameters.ArrayParameterSet

getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, loadParameters

Methods inherited from class de.jstacs.parameters.ExpandableParameterSet

addParameterToSet, parameterRemovable, removeParameterFromSet, replaceContentWith, replaceParametersWithRangedInstance

Methods inherited from class de.jstacs.parameters.ParameterSet

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

Methods inherited from class java.lang.Object

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

Constructor Detail

AlphabetContainerParameterSet.AlphabetArrayParameterSet

public AlphabetContainerParameterSet.AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType type)
                                                        throws Exception

Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from the information if the array shall contain only the parameters for discrete Alphabets.

Parameters:

type - the type of the alphabet(s)

Throws:

Exception - is thrown if the parameters could not be created

AlphabetContainerParameterSet.AlphabetArrayParameterSet

public AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)
                                                        throws NonParsableException

Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from its XML representation.

Parameters:

representation - the XML representation

Throws:

NonParsableException - is thrown if representation could not be parsed

AlphabetContainerParameterSet.AlphabetArrayParameterSet

public AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets,
                                                               AlphabetContainer.AlphabetContainerType type)
                                                        throws Exception

Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of Alphabets and the information if all alphabets are discrete.

Parameters:

alphabets - the alphabets

type - the type of the AlphabetContainer

Throws:

Exception - is thrown if the parameters could not be created

Method Detail

clone

public AlphabetContainerParameterSet.AlphabetArrayParameterSet 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 ExpandableParameterSet

Returns:

a deep clone of this ParameterSet

Throws:

CloneNotSupportedException

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML-representation of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class ArrayParameterSet

Returns:

the XML-representation

fromXML

public void fromXML(StringBuffer representation)
             throws NonParsableException

Description copied from class: ParameterSet

Parses the instance fields of a ParameterSet from the XML-representation as returned by ParameterSet.toXML().

Overrides:

fromXML in class ArrayParameterSet

Parameters:

representation - the XML-representation

Throws:

NonParsableException - is thrown if the XML-code could not be parsed

getInstanceName

public String getInstanceName()

Returns a descriptive name for this ParameterSet.

Returns:

the name

getInstanceComment

public String getInstanceComment()

Returns a descriptive comment on this ParameterSet.

Returns:

the comment