de.jstacs.data

Class AlphabetContainer.AbstractAlphabetContainerParameterSet<T extends AlphabetContainer>

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<T>

de.jstacs.data.AlphabetContainer.AbstractAlphabetContainerParameterSet<T>

Type Parameters:

T - the type of the AlphabetContainer.AbstractAlphabetContainerParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

AlphabetContainerParameterSet, DNAAlphabetContainer.DNAAlphabetContainerParameterSet

Enclosing class:

AlphabetContainer

public abstract static class AlphabetContainer.AbstractAlphabetContainerParameterSet<T extends AlphabetContainer>
extends InstanceParameterSet<T>

This class is the super class of any InstanceParameterSet for AlphabetContainer.

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

Modifier	Constructor and Description
protected	AlphabetContainer.AbstractAlphabetContainerParameterSet(Class<? extends T> instanceClass) Constructs an AlphabetContainer.AbstractAlphabetContainerParameterSet from the class that can be instantiated using this AlphabetContainer.AbstractAlphabetContainerParameterSet.
protected	AlphabetContainer.AbstractAlphabetContainerParameterSet(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Methods

Modifier and Type	Method and Description
AlphabetContainer.AbstractAlphabetContainerParameterSet<T>	clone() Creates a full clone (deep copy) of this ParameterSet.
abstract int	getPossibleLength() Returns the length of the AlphabetContainer that can be instantiated using this ParameterSet.
abstract boolean	isDiscrete() Indicates if all positions use DiscreteAlphabet.DiscreteAlphabetParameterSet, i.e.
abstract boolean	isSimple() Indicates if all positions use the same Alphabet, i.e.

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

fromXML, getInstance, getInstanceClass, getInstanceComment, getInstanceName, 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

AlphabetContainer.AbstractAlphabetContainerParameterSet

protected AlphabetContainer.AbstractAlphabetContainerParameterSet(Class<? extends T> instanceClass)

Constructs an AlphabetContainer.AbstractAlphabetContainerParameterSet from the class that can be instantiated using this AlphabetContainer.AbstractAlphabetContainerParameterSet.

Parameters:

instanceClass - the class to be instantiated

AlphabetContainer.AbstractAlphabetContainerParameterSet

protected AlphabetContainer.AbstractAlphabetContainerParameterSet(StringBuffer xml)
                                                           throws NonParsableException

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

Parameters:

xml - the XML representation as StringBuffer

Throws:

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

See Also:

InstanceParameterSet.InstanceParameterSet(StringBuffer), Storable

Method Detail

getPossibleLength

public abstract int getPossibleLength()

Returns the length of the AlphabetContainer that can be instantiated using this ParameterSet.

Returns:

the length

See Also:

AlphabetContainer.getPossibleLength()

isDiscrete

public abstract boolean isDiscrete()

Indicates if all positions use DiscreteAlphabet.DiscreteAlphabetParameterSet, i.e. if all Alphabets of the corresponding AlphabetContainer are discrete.

Returns:

true if all positions are discrete, false otherwise

See Also:

AlphabetContainer.isDiscrete()

isSimple

public abstract boolean isSimple()

Indicates if all positions use the same Alphabet, i.e. if the corresponding AlphabetContainer is simple.

Returns:

true if all positions use the same Alphabet, false otherwise

clone

public AlphabetContainer.AbstractAlphabetContainerParameterSet<T> 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