Package psidev.psi.mi.jami.xml.model.extension.xml253

Class AbstractXmlEntity<F extends Feature>

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlEntity<F>

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Entity<F>, ExtendedPsiXmlEntity<F>

Direct Known Subclasses:

AbstractXmlParticipant, XmlExperimentalParticipantCandidate, XmlModelledParticipantCandidate

public abstract class AbstractXmlEntity<F extends Feature>
extends Object
implements ExtendedPsiXmlEntity<F>, FileSourceContext, com.sun.xml.bind.Locatable

Abstract class for XmlEntity

Since:

07/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbstractXmlEntity.JAXBFeatureWrapper<F extends Feature>

Constructor Summary

Constructors

Constructor	Description
AbstractXmlEntity()	Constructor for AbstractXmlEntity.
AbstractXmlEntity(Interactor interactor)	Constructor for AbstractXmlEntity.
AbstractXmlEntity(Interactor interactor, Stoichiometry stoichiometry)	Constructor for AbstractXmlEntity.

Method Summary

Modifier and Type	Method	Description
boolean	addAllFeatures(Collection<? extends F> features)	This method will add all features and set the entity of the new features to this current entity
boolean	addFeature(F feature)	addFeature.
Collection<CausalRelationship>	getCausalRelationships()	Getter for the field causalRelationships.
EntityInteractorChangeListener	getChangeListener()	Getter for the field changeListener.
Collection<F>	getFeatures()	getFeatures.
int	getId()	Gets the value of the id property.
Interactor	getInteractor()	Getter for the field interactor.
protected FileSourceLocator	getParticipantLocator()	getParticipantLocator.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
Stoichiometry	getStoichiometry()	Getter for the field stoichiometry.
protected void	initialiseFeatureWrapper()	initialiseFeatureWrapper.
protected void	initialiseUnspecifiedInteractor()	initialiseUnspecifiedInteractor.
protected void	processAddedFeature(F feature)	processAddedFeature.
boolean	removeAllFeatures(Collection<? extends F> features)	This method will remove all the features and set the entity of the removed features to null.
boolean	removeFeature(F feature)	removeFeature.
void	setChangeListener(EntityInteractorChangeListener listener)	Sets the entity change listener
protected void	setFeatureWrapper(AbstractXmlEntity.JAXBFeatureWrapper<F> jaxbFeatureWrapper)	setFeatureWrapper.
void	setId(int value)	setId.
void	setInteractor(Interactor interactor)	Sets the interactor
void	setJAXBInteractor(DefaultXmlInteractor interactor)	setJAXBInteractor.
void	setJAXBInteractorRef(Integer value)	Sets the value of the interactorRef property.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
void	setStoichiometry(Integer stoichiometry)	Sets the mean stoichiometry for this participant.
void	setStoichiometry(Stoichiometry stoichiometry)	Setter for the field stoichiometry.
Locator	sourceLocation()
String	toString()	toString

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractXmlEntity

public AbstractXmlEntity()

Constructor for AbstractXmlEntity.

AbstractXmlEntity

public AbstractXmlEntity(Interactor interactor)

Constructor for AbstractXmlEntity.

Parameters:

interactor - a Interactor object.

AbstractXmlEntity

public AbstractXmlEntity(Interactor interactor,
                         Stoichiometry stoichiometry)

Constructor for AbstractXmlEntity.

Parameters:

interactor - a Interactor object.

stoichiometry - a Stoichiometry object.

Method Detail

getInteractor

public Interactor getInteractor()

Getter for the field interactor.

Specified by:

getInteractor in interface Entity<F extends Feature>

Returns:

a Interactor object.

setInteractor

public void setInteractor(Interactor interactor)

Sets the interactor

Specified by:

setInteractor in interface Entity<F extends Feature>

Parameters:

interactor - : interactor

getCausalRelationships

public Collection<CausalRelationship> getCausalRelationships()

Getter for the field causalRelationships.

Specified by:

getCausalRelationships in interface Entity<F extends Feature>

Returns:

a Collection object.

getStoichiometry

public Stoichiometry getStoichiometry()

Getter for the field stoichiometry.

Specified by:

getStoichiometry in interface Entity<F extends Feature>

Returns:

a Stoichiometry object.

setStoichiometry

public void setStoichiometry(Integer stoichiometry)

Sets the mean stoichiometry for this participant.

Specified by:

setStoichiometry in interface Entity<F extends Feature>

Parameters:

stoichiometry - : mean stoichiometry value

setStoichiometry

public void setStoichiometry(Stoichiometry stoichiometry)

Setter for the field stoichiometry.

Specified by:

setStoichiometry in interface Entity<F extends Feature>

Parameters:

stoichiometry - a Stoichiometry object.

getChangeListener

public EntityInteractorChangeListener getChangeListener()

Getter for the field changeListener.

Specified by:

getChangeListener in interface Entity<F extends Feature>

Returns:

a EntityInteractorChangeListener object.

setChangeListener

public void setChangeListener(EntityInteractorChangeListener listener)

Sets the entity change listener

Specified by:

setChangeListener in interface Entity<F extends Feature>

Parameters:

listener - : the entity change listener

getFeatures

public Collection<F> getFeatures()

getFeatures.

Specified by:

getFeatures in interface Entity<F extends Feature>

Returns:

a Collection object.

addFeature

public boolean addFeature(F feature)

addFeature.

Specified by:

addFeature in interface Entity<F extends Feature>

Parameters:

feature - a F object.

Returns:

a boolean.

removeFeature

public boolean removeFeature(F feature)

removeFeature.

Specified by:

removeFeature in interface Entity<F extends Feature>

Parameters:

feature - a F object.

Returns:

a boolean.

addAllFeatures

public boolean addAllFeatures(Collection<? extends F> features)

This method will add all features and set the entity of the new features to this current entity

Specified by:

addAllFeatures in interface Entity<F extends Feature>

Parameters:

features - : features to add

Returns:

true if features are added to the list of features

removeAllFeatures

public boolean removeAllFeatures(Collection<? extends F> features)

This method will remove all the features and set the entity of the removed features to null.

Specified by:

removeAllFeatures in interface Entity<F extends Feature>

Parameters:

features - : features to remove

Returns:

true if features are removed from the list of features

setJAXBInteractor

public void setJAXBInteractor(DefaultXmlInteractor interactor)

setJAXBInteractor.

Parameters:

interactor - a DefaultXmlInteractor object.

setJAXBInteractorRef

public void setJAXBInteractorRef(Integer value)

Sets the value of the interactorRef property.

Parameters:

value - allowed object is Integer

getId

public int getId()

Gets the value of the id property.

Specified by:

getId in interface ExtendedPsiXmlEntity<F extends Feature>

Returns:

a int.

setId

public void setId(int value)

setId.

Sets the value of the id property.

Specified by:

setId in interface ExtendedPsiXmlEntity<F extends Feature>

Parameters:

value - a int.

sourceLocation

public Locator sourceLocation()

Specified by:

sourceLocation in interface com.sun.xml.bind.Locatable

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator sourceLocator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

sourceLocator - : the file locator

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class Object

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties

setFeatureWrapper

protected void setFeatureWrapper(AbstractXmlEntity.JAXBFeatureWrapper<F> jaxbFeatureWrapper)

setFeatureWrapper.

Parameters:

jaxbFeatureWrapper - a AbstractXmlEntity.JAXBFeatureWrapper object.

processAddedFeature

protected void processAddedFeature(F feature)

processAddedFeature.

Parameters:

feature - a F object.

initialiseUnspecifiedInteractor

protected void initialiseUnspecifiedInteractor()

initialiseUnspecifiedInteractor.

initialiseFeatureWrapper

protected void initialiseFeatureWrapper()

initialiseFeatureWrapper.

getParticipantLocator

protected FileSourceLocator getParticipantLocator()

getParticipantLocator.

Returns:

a FileSourceLocator object.