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

Class XmlExperimentalParticipantCandidateWrapper

java.lang.Object

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

All Implemented Interfaces:

FileSourceContext, Entity<ModelledFeature>, ModelledEntity, ModelledParticipantCandidate, ParticipantCandidate<ModelledParticipantPool,ModelledFeature>, ExtendedPsiXmlEntity<ModelledFeature>

public class XmlExperimentalParticipantCandidateWrapper
extends Object
implements ModelledParticipantCandidate, ExtendedPsiXmlEntity<ModelledFeature>, FileSourceContext

Wrapper for Xml participants candidates Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.

Since:

11/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
XmlExperimentalParticipantCandidateWrapper(ExperimentalParticipantCandidate part, ModelledParticipantPool wrapper)	Constructor for XmlExperimentalParticipantCandidateWrapper.

Method Summary

Modifier and Type	Method	Description
boolean	addAllFeatures(Collection<? extends ModelledFeature> features)	This method will add all features and set the entity of the new features to this current entity
boolean	addFeature(ModelledFeature feature)	This method will add the feature and set the entity of the new feature to this current entity
Collection<CausalRelationship>	getCausalRelationships()	The causal relationships of this entity on other entities usually part of an interaction.
EntityInteractorChangeListener	getChangeListener()	The entity change listener if set, null otherwise.
Collection<ModelledFeature>	getFeatures()	Properties for this entity.
int	getId()	getId.
Interactor	getInteractor()	The molecule/complex of molecules which interacts.
ModelledParticipantPool	getParentPool()	The participant pool parent with which the candidate is involved.
FileSourceLocator	getSourceLocator()	The locator of a position in a file.
Stoichiometry	getStoichiometry()	The stoichiometry for this participant.
ExperimentalParticipantCandidate	getWrappedParticipant()	getWrappedParticipant.
protected void	initialiseFeatures()	initialiseFeatures.
boolean	removeAllFeatures(Collection<? extends ModelledFeature> features)	This method will remove all the features and set the entity of the removed features to null.
boolean	removeFeature(ModelledFeature feature)	This method will remove the feature and set the entity of the removed feature to null.
void	setChangeListener(EntityInteractorChangeListener listener)	Sets the entity change listener
void	setId(int id)	setId.
void	setInteractor(Interactor interactor)	Sets the interactor
void	setParentPool(ModelledParticipantPool pool)	Sets the participant pool parent.
void	setSourceLocator(FileSourceLocator locator)	Sets the source locator
void	setStoichiometry(Integer stoichiometry)	Sets the mean stoichiometry for this participant.
void	setStoichiometry(Stoichiometry stoichiometry)	Sets the stoichiometry for this participant.
String	toString()	toString

Methods inherited from class java.lang.Object

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

Constructor Detail

XmlExperimentalParticipantCandidateWrapper

public XmlExperimentalParticipantCandidateWrapper(ExperimentalParticipantCandidate part,
                                                  ModelledParticipantPool wrapper)

Constructor for XmlExperimentalParticipantCandidateWrapper.

Parameters:

part - a ExperimentalParticipantCandidate object.

wrapper - a ModelledParticipantPool object.

Method Detail

getInteractor

public Interactor getInteractor()

The molecule/complex of molecules which interacts. It cannot be null.

Specified by:

getInteractor in interface Entity<ModelledFeature>

Returns:

the interactor

setInteractor

public void setInteractor(Interactor interactor)

Sets the interactor

Specified by:

setInteractor in interface Entity<ModelledFeature>

Parameters:

interactor - : interactor

getCausalRelationships

public Collection<CausalRelationship> getCausalRelationships()

The causal relationships of this entity on other entities usually part of an interaction. The set of causal relationship cannot be null. If the entity does not have any causal relationship, the method should return an empty Collection. Ex: increasing, decreasing, disrupting, etc.

Specified by:

getCausalRelationships in interface Entity<ModelledFeature>

Returns:

the collection of causal relationships attached to this entity

getStoichiometry

public Stoichiometry getStoichiometry()

The stoichiometry for this participant. If the stoichiometry for this participant is unknown, the method should return null.

Specified by:

getStoichiometry in interface Entity<ModelledFeature>

Returns:

the stoichiometry

setStoichiometry

public void setStoichiometry(Integer stoichiometry)

Sets the mean stoichiometry for this participant.

Specified by:

setStoichiometry in interface Entity<ModelledFeature>

Parameters:

stoichiometry - : mean stoichiometry value

setStoichiometry

public void setStoichiometry(Stoichiometry stoichiometry)

Sets the stoichiometry for this participant.

Specified by:

setStoichiometry in interface Entity<ModelledFeature>

Parameters:

stoichiometry - : the stoichiometry

getFeatures

public Collection<ModelledFeature> getFeatures()

Properties for this entity. The collection cannot be null. If the entity does not have any features, the method should return an empty collection.

Specified by:

getFeatures in interface Entity<ModelledFeature>

Returns:

the features

setChangeListener

public void setChangeListener(EntityInteractorChangeListener listener)

Sets the entity change listener

Specified by:

setChangeListener in interface Entity<ModelledFeature>

Parameters:

listener - : the entity change listener

addFeature

public boolean addFeature(ModelledFeature feature)

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

Specified by:

addFeature in interface Entity<ModelledFeature>

Parameters:

feature - : feature to add

Returns:

true if feature is added to the list of features

removeFeature

public boolean removeFeature(ModelledFeature feature)

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

Specified by:

removeFeature in interface Entity<ModelledFeature>

Parameters:

feature - : feature to remove

Returns:

true if feature is removed from the list of features

addAllFeatures

public boolean addAllFeatures(Collection<? extends ModelledFeature> 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<ModelledFeature>

Parameters:

features - : features to add

Returns:

true if features are added to the list of features

removeAllFeatures

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

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

Specified by:

removeAllFeatures in interface Entity<ModelledFeature>

Parameters:

features - : features to remove

Returns:

true if features are removed from the list of features

getChangeListener

public EntityInteractorChangeListener getChangeListener()

The entity change listener if set, null otherwise. The entity change listener listen to changes in entity (interactor changes)

Specified by:

getChangeListener in interface Entity<ModelledFeature>

Returns:

the participant change listener

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

getParentPool

public ModelledParticipantPool getParentPool()

The participant pool parent with which the candidate is involved. It can be null if the participant candidate is not part of any participant pool. It can happen if the participant candidate has been removed from a participant pool and is now invalid.

Specified by:

getParentPool in interface ParticipantCandidate<ModelledParticipantPool,ModelledFeature>

Returns:

the participant pool parent

setParentPool

public void setParentPool(ModelledParticipantPool pool)

Sets the participant pool parent.

Specified by:

setParentPool in interface ParticipantCandidate<ModelledParticipantPool,ModelledFeature>

Parameters:

pool - : participant pool

getWrappedParticipant

public ExperimentalParticipantCandidate getWrappedParticipant()

getWrappedParticipant.

Returns:

a ExperimentalParticipantCandidate object.

initialiseFeatures

protected void initialiseFeatures()

initialiseFeatures.

getSourceLocator

public FileSourceLocator getSourceLocator()

The locator of a position in a file. It can be null

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

the file locator

setSourceLocator

public void setSourceLocator(FileSourceLocator locator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

locator - : the file locator

getId

public int getId()

getId.

Specified by:

getId in interface ExtendedPsiXmlEntity<ModelledFeature>

Returns:

a int.

setId

public void setId(int id)

setId.

Specified by:

setId in interface ExtendedPsiXmlEntity<ModelledFeature>

Parameters:

id - a int.