de.jstacs.data.alphabets

Class Alphabet.AlphabetParameterSet<T extends Alphabet>

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<T>

de.jstacs.data.alphabets.Alphabet.AlphabetParameterSet<T>

Type Parameters:

T - the type of the Alphabet.AlphabetParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

ContinuousAlphabet.ContinuousAlphabetParameterSet, DiscreteAlphabet.DiscreteAlphabetParameterSet, DNAAlphabet.DNAAlphabetParameterSet, ProteinAlphabet.ProteinAlphabetParameterSet

Enclosing class:

Alphabet

public abstract static class Alphabet.AlphabetParameterSet<T extends Alphabet>
extends InstanceParameterSet<T>

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

Constructor Summary

Constructors

Constructor and Description
Alphabet.AlphabetParameterSet(Class<T> instanceClass) Creates a new Alphabet.AlphabetParameterSet from the class that can be instantiated using this Alphabet.AlphabetParameterSet.
Alphabet.AlphabetParameterSet(StringBuffer representation) The standard constructor for the interface Storable .

Method Summary

Methods

Modifier and Type	Method and Description
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

fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent, toGalaxy

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<T> instanceClass)

Creates a new Alphabet.AlphabetParameterSet from the class that can be instantiated using this Alphabet.AlphabetParameterSet.

Parameters:

instanceClass - the class

See Also:

InstanceParameterSet.InstanceParameterSet(Class)

Alphabet.AlphabetParameterSet

public Alphabet.AlphabetParameterSet(StringBuffer representation)
                              throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

InstanceParameterSet.InstanceParameterSet(StringBuffer), Storable

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/copy 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<T extends Alphabet>

Returns:

the name of the class