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:

GalaxyConvertible, 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

Constructor Summary

Constructors

Constructor and Description
AlphabetContainerParameterSet.AlphabetArrayParameterSet() Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet with type AlphabetContainer.AlphabetContainerType.BOTH.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets, AlphabetContainer.AlphabetContainerType type) Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of Alphabets and the information about the type of the Alphabets.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType type) Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from the information about the type of the Alphabets, e.g.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation) The standard constructor for the interface Storable .

Method Summary

Methods

Modifier and Type	Method and Description
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 AlphabetContainerParameterSet.AlphabetArrayParameterSet.
String	getInstanceName() Returns a descriptive name for this AlphabetContainerParameterSet.AlphabetArrayParameterSet .
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.parameters.ArrayParameterSet

getNumberOfParameters, getParameterAt, hasDefaultOrIsSet

Methods inherited from class de.jstacs.parameters.ExpandableParameterSet

addParameterToSet, fromGalaxy, parameterRemovable, removeParameterFromSet, replaceContentWith, toGalaxy

Methods inherited from class de.jstacs.parameters.ParameterSet

getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent

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 about the type of the Alphabets, e.g. if the array shall contain only the parameters for discrete Alphabet s.

Parameters:

type - the type of the Alphabet(s)

Throws:

Exception - if the AlphabetContainerParameterSet.AlphabetArrayParameterSet could not be created

See Also:

ArrayParameterSet.ArrayParameterSet(ParameterSet, String, String)

AlphabetContainerParameterSet.AlphabetArrayParameterSet

public AlphabetContainerParameterSet.AlphabetArrayParameterSet()
                                                        throws Exception

Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet with type AlphabetContainer.AlphabetContainerType.BOTH.

Throws:

Exception - if the AlphabetContainerParameterSet.AlphabetArrayParameterSet could not be created

AlphabetContainerParameterSet.AlphabetArrayParameterSet

public AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)
                                                        throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

ArrayParameterSet.ArrayParameterSet(StringBuffer), Storable

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 about the type of the Alphabets.

Parameters:

alphabets - the Alphabets

type - the type of the AlphabetContainer

Throws:

Exception - if the AlphabetContainerParameterSet.AlphabetArrayParameterSet 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/copy of this ParameterSet

Throws:

CloneNotSupportedException

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer 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 as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

See Also:

ParameterSet.toXML()

getInstanceName

public String getInstanceName()

Returns a descriptive name for this AlphabetContainerParameterSet.AlphabetArrayParameterSet .

Returns:

the descriptive name

getInstanceComment

public String getInstanceComment()

Returns a descriptive comment on this AlphabetContainerParameterSet.AlphabetArrayParameterSet.

Returns:

the descriptive comment