de.jstacs.data.alphabets

Class DNAAlphabetContainer.DNAAlphabetContainerParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<T>

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

de.jstacs.data.alphabets.DNAAlphabetContainer.DNAAlphabetContainerParameterSet

All Implemented Interfaces:

GalaxyConvertible, Singleton, Storable, Cloneable

Enclosing class:

DNAAlphabetContainer

public static final class DNAAlphabetContainer.DNAAlphabetContainerParameterSet
extends AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer>
implements Singleton

This class implements a singleton for the ParameterSet of a DNAAlphabetContainer.

Author:

Jens Keilwagen

Nested Class Summary

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

ParameterSet.ParameterList

Nested classes/interfaces inherited from interface de.jstacs.Singleton

Singleton.SingletonHandler

Field Summary

Fields

Modifier and Type	Field and Description
static DNAAlphabetContainer.DNAAlphabetContainerParameterSet	SINGLETON The only instance of this class.

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Method Summary

Methods

Modifier and Type	Method and Description
DNAAlphabetContainer.DNAAlphabetContainerParameterSet	clone() Creates a full clone (deep copy) of this ParameterSet.
String	getInstanceComment() Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.
String	getInstanceName() Returns the name of an instance of the class that can be constructed using this ParameterSet.
int	getPossibleLength() Returns the length of the AlphabetContainer that can be instantiated using this ParameterSet.
boolean	isDiscrete() Indicates if all positions use DiscreteAlphabet.DiscreteAlphabetParameterSet, i.e.
boolean	isSimple() Indicates if all positions use the same Alphabet, i.e.

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

fromXML, getInstance, getInstanceClass, 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

Field Detail

SINGLETON

public static final DNAAlphabetContainer.DNAAlphabetContainerParameterSet SINGLETON

The only instance of this class.

See Also:

Singleton

Method Detail

clone

public DNAAlphabetContainer.DNAAlphabetContainerParameterSet clone()

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 AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer>

Returns:

a deep clone/copy of this ParameterSet

getInstanceComment

public String getInstanceComment()

Description copied from class: InstanceParameterSet

Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceComment in class InstanceParameterSet<DNAAlphabetContainer>

Returns:

the comment of the class

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<DNAAlphabetContainer>

Returns:

the name of the class

getPossibleLength

public int getPossibleLength()

Description copied from class: AlphabetContainer.AbstractAlphabetContainerParameterSet

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

Specified by:

getPossibleLength in class AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer>

Returns:

the length

See Also:

AlphabetContainer.getPossibleLength()

isDiscrete

public boolean isDiscrete()

Description copied from class: AlphabetContainer.AbstractAlphabetContainerParameterSet

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

Specified by:

isDiscrete in class AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer>

Returns:

true if all positions are discrete, false otherwise

See Also:

AlphabetContainer.isDiscrete()

isSimple

public boolean isSimple()

Description copied from class: AlphabetContainer.AbstractAlphabetContainerParameterSet

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

Specified by:

isSimple in class AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer>

Returns:

true if all positions use the same Alphabet, false otherwise