Uses of Interface
psidev.psi.mi.jami.model.Entity

Packages that use Entity

Package	Description
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.enricher
psidev.psi.mi.jami.enricher.impl
psidev.psi.mi.jami.enricher.impl.full
psidev.psi.mi.jami.enricher.impl.minimal
psidev.psi.mi.jami.enricher.listener
psidev.psi.mi.jami.enricher.listener.impl
psidev.psi.mi.jami.enricher.listener.impl.log
psidev.psi.mi.jami.enricher.listener.impl.writer
psidev.psi.mi.jami.enricher.util
psidev.psi.mi.jami.json.elements
psidev.psi.mi.jami.json.nary
psidev.psi.mi.jami.listener
psidev.psi.mi.jami.listener.impl
psidev.psi.mi.jami.model
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.tab.extension
psidev.psi.mi.jami.utils.clone
psidev.psi.mi.jami.utils.comparator.participant
psidev.psi.mi.jami.xml
psidev.psi.mi.jami.xml.cache
psidev.psi.mi.jami.xml.io.writer.compact
psidev.psi.mi.jami.xml.model.extension
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300
psidev.psi.mi.jami.xml.model.reference
psidev.psi.mi.jami.xml.model.reference.xml253
psidev.psi.mi.jami.xml.model.reference.xml254
psidev.psi.mi.jami.xml.model.reference.xml300

Uses of Entity in psidev.psi.mi.jami.crosslink.extension

Classes in psidev.psi.mi.jami.crosslink.extension that implement Entity

Modifier and Type	Class	Description
class	CsvExperimentalParticipantCandidate	Crosslink CSV extension of ExperimentalParticipantCandidate.
class	CsvExperimentalParticipantPool	Crosslink CSV extension of ParticipantEvidencePool.
class	CsvParticipantEvidence	Crosslink CSV extension of ParticipantEvidence.

Uses of Entity in psidev.psi.mi.jami.enricher

Classes in psidev.psi.mi.jami.enricher with type parameters of type Entity

Modifier and Type	Interface	Description
interface	EntityEnricher<P extends Entity,F extends Feature>	Sub enrichers: Protein, CvTerm, Feature, Bioactive3Entity

Uses of Entity in psidev.psi.mi.jami.enricher.impl

Methods in psidev.psi.mi.jami.enricher.impl that return types with arguments of type Entity

Modifier and Type	Method	Description
EntityEnricher<Entity,Feature>	CompositeEntityEnricher.getEntityBaseEnricher()	Getter for the field entityBaseEnricher.

Methods in psidev.psi.mi.jami.enricher.impl with parameters of type Entity

Modifier and Type	Method	Description
void	CompositeEntityEnricher.enrich(Entity object)	enrich.
void	CompositeEntityEnricher.enrich(Entity object, Entity objectSource)	enrich.

Method parameters in psidev.psi.mi.jami.enricher.impl with type arguments of type Entity

Modifier and Type	Method	Description
void	CompositeEntityEnricher.enrich(Collection<Entity> objects)	enrich.

Constructor parameters in psidev.psi.mi.jami.enricher.impl with type arguments of type Entity

Constructor	Description
CompositeEntityEnricher(EntityEnricher<Entity,Feature> entityBaseEnricher)	Constructor for CompositeEntityEnricher.

Uses of Entity in psidev.psi.mi.jami.enricher.impl.full

Classes in psidev.psi.mi.jami.enricher.impl.full with type parameters of type Entity

Modifier and Type	Class	Description
class	FullEntityEnricher<P extends Entity,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.
class	FullEntityUpdater<P extends Entity,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.

Uses of Entity in psidev.psi.mi.jami.enricher.impl.minimal

Classes in psidev.psi.mi.jami.enricher.impl.minimal with type parameters of type Entity

Modifier and Type	Class	Description
class	MinimalEntityEnricher<P extends Entity,F extends Feature>	The entity enricher is an enricher which can enrich either single participant or a collection.
class	MinimalEntityUpdater<P extends Entity,F extends Feature>	The participant enricher is an enricher which can enrich either single participant or a collection.

Uses of Entity in psidev.psi.mi.jami.enricher.listener

Classes in psidev.psi.mi.jami.enricher.listener with type parameters of type Entity

Modifier and Type	Interface	Description
interface	EntityEnricherListener<P extends Entity>	Entity enricher listener

Uses of Entity in psidev.psi.mi.jami.enricher.listener.impl

Classes in psidev.psi.mi.jami.enricher.listener.impl with type parameters of type Entity

Modifier and Type	Class	Description
class	EntityEnricherListenerManager<P extends Entity>	A manager for listeners which holds a list of listeners.

Methods in psidev.psi.mi.jami.enricher.listener.impl with parameters of type Entity

Modifier and Type	Method	Description
void	EntityEnricherListenerManager.onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate

Uses of Entity in psidev.psi.mi.jami.enricher.listener.impl.log

Classes in psidev.psi.mi.jami.enricher.listener.impl.log with type parameters of type Entity

Modifier and Type	Class	Description
class	EntityEnricherLogger<P extends Entity>	A logging listener.

Uses of Entity in psidev.psi.mi.jami.enricher.listener.impl.writer

Classes in psidev.psi.mi.jami.enricher.listener.impl.writer with type parameters of type Entity

Modifier and Type	Class	Description
class	EntityEnricherStatisticsWriter<P extends Entity>	A statistics logger which records changes made by the enricher.

Methods in psidev.psi.mi.jami.enricher.listener.impl.writer with parameters of type Entity

Modifier and Type	Method	Description
void	EntityEnricherStatisticsWriter.onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate

Uses of Entity in psidev.psi.mi.jami.enricher.util

Methods in psidev.psi.mi.jami.enricher.util with parameters of type Entity

Modifier and Type	Method	Description
static void	EnricherUtils.mergeCausalRelationships(Entity termToEnrich, Collection<CausalRelationship> toEnrichRelationships, Collection<CausalRelationship> fetchedRelationships, boolean remove, EntityChangeListener entityListener)	mergeCausalRelationships.
static <F extends Feature> void	EnricherUtils.mergeFeatures(Entity termToEnrich, Collection<F> toEnrichFeatures, Collection<F> fetchedFeatures, boolean remove, EntityChangeListener entityListener, FeatureEnricher<F> featureEnricher)	mergeFeatures.

Uses of Entity in psidev.psi.mi.jami.json.elements

Methods in psidev.psi.mi.jami.json.elements that return types with arguments of type Entity

Modifier and Type	Method	Description
protected Map<Entity,Integer>	SimpleJsonInteractionWriter.getProcessedParticipants()	Getter for the field processedParticipants.
protected Map<Entity,Integer>	SimpleJsonParticipantWriter.getProcessedParticipants()	Getter for the field processedParticipants.

Uses of Entity in psidev.psi.mi.jami.json.nary

Methods in psidev.psi.mi.jami.json.nary that return types with arguments of type Entity

Modifier and Type	Method	Description
protected Map<Entity,Integer>	AbstractMIJsonWriter.getProcessedParticipants()	Getter for the field processedParticipants.

Uses of Entity in psidev.psi.mi.jami.listener

Classes in psidev.psi.mi.jami.listener with type parameters of type Entity

Modifier and Type	Interface	Description
interface	EntityChangeListener<F extends Entity>	Listener for changes in an entity

Methods in psidev.psi.mi.jami.listener with parameters of type Entity

Modifier and Type	Method	Description
void	EntityInteractorChangeListener.onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate

Uses of Entity in psidev.psi.mi.jami.listener.impl

Classes in psidev.psi.mi.jami.listener.impl with type parameters of type Entity

Modifier and Type	Class	Description
class	EntityChangeLogger<T extends Entity>	This listener will just interactor change events

Methods in psidev.psi.mi.jami.listener.impl with parameters of type Entity

Modifier and Type	Method	Description
void	EntityChangeLogger.onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate
void	ParticipantChangeLogger.onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate

Uses of Entity in psidev.psi.mi.jami.model

Classes in psidev.psi.mi.jami.model with type parameters of type Entity

Modifier and Type	Interface	Description
interface	Feature<P extends Entity,F extends Feature>	Property of a participant that may interfere with the binding of a molecule.

Subinterfaces of Entity in psidev.psi.mi.jami.model

Modifier and Type	Interface	Description
interface	ExperimentalEntity	An experimental entity with experimental features
interface	ExperimentalParticipantCandidate	Interface for experimental participant candidates
interface	ExperimentalParticipantPool	A pool of experimental participants
interface	ModelledEntity	An modelled entity with modelled features
interface	ModelledParticipant	Participant of a modelled interaction.
interface	ModelledParticipantCandidate	Interface for modelled participant candidates
interface	ModelledParticipantPool	A pool of modelled participant candidates
interface	NamedParticipant<I extends Interaction,F extends Feature>	A named entity is an entity having a short name and a fullname in addition to aliases.
interface	Participant<I extends Interaction,F extends Feature>	Participant identified in an interaction
interface	ParticipantCandidate<P extends ParticipantPool,F extends Feature>	A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationships
interface	ParticipantEvidence	Participant of an interaction which is supported by experimental evidences
interface	ParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	A pool of participants that can be grouped together as a single participant as they are interchangeable

Methods in psidev.psi.mi.jami.model that return Entity

Modifier and Type	Method	Description
Entity	Range.getParticipant()	The participating molecule that this range refers to.
Entity	CausalRelationship.getTarget()	The participant/entity target of this causalRelationship.

Methods in psidev.psi.mi.jami.model with parameters of type Entity

Modifier and Type	Method	Description
void	Range.setParticipant(Entity participant)	Sets the participating molecule that the range refers to

Uses of Entity in psidev.psi.mi.jami.model.impl

Classes in psidev.psi.mi.jami.model.impl with type parameters of type Entity

Modifier and Type	Class	Description
class	AbstractFeature<P extends Entity,F extends Feature>	Abstract class for Feature

Classes in psidev.psi.mi.jami.model.impl that implement Entity

Modifier and Type	Class	Description
class	AbstractEntity<F extends Feature>	Abstract class for Entity
class	AbstractParticipant<I extends Interaction,F extends Feature>	Abstract class for Participant
class	AbstractParticipantCandidate<P extends ParticipantPool,F extends Feature>	Abstract class for participant candidate
class	AbstractParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	Abstract class for Participant pool
class	DefaultExperimentalParticipantCandidate	Default implementation of experimental participant candidate
class	DefaultExperimentalParticipantPool	Default implementation of ExperimentalParticipantPool
class	DefaultModelledParticipant	Default implementation for ModelledParticipant Notes: The equals and hashcode methods have NOT been overridden because the ModelledParticipant object is a complex object.
class	DefaultModelledParticipantCandidate	Default implementation of modelled participant candidate
class	DefaultModelledParticipantPool	Default implementation of ParticipantPool
class	DefaultNamedModelledParticipant	Default implementation of Named modelled participant
class	DefaultNamedParticipant	Default implementation of named participant.
class	DefaultNamedParticipantEvidence	Default implementation of named participant evidence
class	DefaultParticipant	Default implementation for participant Notes: The equals and hashcode methods have NOT been overridden because the participant object is a complex object.
class	DefaultParticipantCandidate	Default implementation of participant candidate
class	DefaultParticipantEvidence	Default implementation for ParticipantEvidence Notes: The equals and hashcode methods have NOT been overridden because the ParticipantEvidence object is a complex object.
class	DefaultParticipantPool	Default implementation of ParticipantPool

Methods in psidev.psi.mi.jami.model.impl that return Entity

Modifier and Type	Method	Description
Entity	DefaultRange.getParticipant()	Getter for the field participant.
Entity	DefaultCausalRelationship.getTarget()	Getter for the field target.

Methods in psidev.psi.mi.jami.model.impl with parameters of type Entity

Modifier and Type	Method	Description
void	AbstractParticipantPool.onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate
void	DefaultRange.setParticipant(Entity participant)	Sets the participating molecule that the range refers to

Uses of Entity in psidev.psi.mi.jami.tab.extension

Classes in psidev.psi.mi.jami.tab.extension with type parameters of type Entity

Modifier and Type	Interface	Description
interface	MitabFeature<P extends Entity,F extends Feature>	Basic interface for Mitab features

Classes in psidev.psi.mi.jami.tab.extension that implement Entity

Modifier and Type	Class	Description
class	MitabModelledParticipant	Mitab extension for ModelledParticipant It contains a FileSourceLocator
class	MitabParticipant	Mitab extension for Participant.
class	MitabParticipantEvidence	Mitab extension of ParticipantEvidence.

Uses of Entity in psidev.psi.mi.jami.utils.clone

Methods in psidev.psi.mi.jami.utils.clone with parameters of type Entity

Modifier and Type	Method	Description
static void	ParticipantCloner.copyAndOverrideBasicEntityProperties(Entity source, Entity target, boolean createNewFeature)	copyAndOverrideBasicEntityProperties

Uses of Entity in psidev.psi.mi.jami.utils.comparator.participant

Classes in psidev.psi.mi.jami.utils.comparator.participant with type parameters of type Entity

Modifier and Type	Class	Description
class	ParticipantCollectionComparator<T extends Entity>	Comparator for collection of participants
class	ParticipantInteractorComparator<T extends Entity>	Participant comparator only based on the interactor.

Methods in psidev.psi.mi.jami.utils.comparator.participant that return types with arguments of type Entity

Modifier and Type	Method	Description
CollectionComparator<Entity>	ParticipantPoolComparator.getParticipantCollectionComparator()	getParticipantCollectionComparator

Methods in psidev.psi.mi.jami.utils.comparator.participant with parameters of type Entity

Modifier and Type	Method	Description
static boolean	DefaultEntityBaseComparator.areEquals(Entity participant1, Entity participant2, boolean ignoreInteractors)	Use DefaultParticipantBaseComparator to know if two participants are equals.
static boolean	DefaultEntityComparator.areEquals(Entity participant1, Entity participant2)	Use DefaultExactEntityComparator to know if two participants are equals.
static boolean	DefaultExactEntityBaseComparator.areEquals(Entity participant1, Entity participant2, boolean ignoreInteractors)	Use DefaultExactParticipantBaseComparator to know if two participants are equals.
static boolean	DefaultExactEntityComparator.areEquals(Entity participant1, Entity participant2)	Use DefaultExactEntityComparator to know if two participants are equals.
static boolean	DefaultExactParticipantInteractorComparator.areEquals(Entity participant1, Entity participant2)	Use DefaultExactParticipantInteractorComparator to know if two participants are equals.
static boolean	DefaultParticipantInteractorComparator.areEquals(Entity participant1, Entity participant2)	Use DefaultParticipantInteractorComparator to know if two participants are equals.
static boolean	UnambiguousEntityBaseComparator.areEquals(Entity participant1, Entity participant2)	Use UnambiguousParticipantBaseComparator to know if two participants are equals.
static boolean	UnambiguousEntityComparator.areEquals(Entity participant1, Entity participant2)	Use UnambiguousExactEntityComparator to know if two participants are equals.
static boolean	UnambiguousExactEntityBaseComparator.areEquals(Entity participant1, Entity participant2)	Use UnambiguousExactParticipantBaseComparator to know if two participants are equals.
static boolean	UnambiguousExactEntityComparator.areEquals(Entity participant1, Entity participant2)	Use UnambiguousExactEntityComparator to know if two participants are equals.
static boolean	UnambiguousExactParticipantInteractorComparator.areEquals(Entity participant1, Entity participant2)	Use UnambiguousExactParticipantInteractorComparator to know if two participants are equals.
static boolean	UnambiguousParticipantInteractorComparator.areEquals(Entity participant1, Entity participant2)	Use UnambiguousParticipantInteractorComparator to know if two participants are equals.
int	EntityBaseComparator.compare(Entity participant1, Entity participant2)	It will first compare the interactors using InteractorComparator.
int	EntityComparator.compare(Entity participant1, Entity participant2)	Modelled participants come first and then experimental participants.
int	UnambiguousEntityBaseComparator.compare(Entity participant1, Entity participant2)	It will first compare the interactors using UnambiguousInteractorComparator.
int	UnambiguousEntityComparator.compare(Entity participant1, Entity participant2)	Modelled participants come first and then experimental participants.
int	UnambiguousExactEntityBaseComparator.compare(Entity participant1, Entity participant2)	It will first compare the interactors using UnambiguousExactInteractorComparator.
int	UnambiguousExactEntityComparator.compare(Entity participant1, Entity participant2)
int	UnambiguousExactParticipantInteractorComparator.compare(Entity participant1, Entity participant2)	It will compare the interactors using InteractorComparator.
int	UnambiguousParticipantInteractorComparator.compare(Entity participant1, Entity participant2)	It will compare the interactors using UnambiguousInteractorComparator.
static int	UnambiguousEntityBaseComparator.hashCode(Entity participant)
static int	UnambiguousExactEntityBaseComparator.hashCode(Entity participant)

Constructor parameters in psidev.psi.mi.jami.utils.comparator.participant with type arguments of type Entity

Constructor	Description
ParticipantPoolComparator(ParticipantBaseComparator participantBaseComparator, CollectionComparator<Entity> entityCollectionComparator)	Constructor for ParticipantPoolComparator.

Uses of Entity in psidev.psi.mi.jami.xml

Methods in psidev.psi.mi.jami.xml with parameters of type Entity

Modifier and Type	Method	Description
void	XmlEntryContext.registerParticipant(int id, Entity o)	registerParticipant.

Uses of Entity in psidev.psi.mi.jami.xml.cache

Methods in psidev.psi.mi.jami.xml.cache that return Entity

Modifier and Type	Method	Description
Entity	InMemoryPsiXmlCache.getParticipant(int id)	getParticipant.
Entity	PsiXmlFileIndexCache.getParticipant(int id)	getParticipant.
Entity	PsiXmlIdCache.getParticipant(int id)	getParticipant.

Methods in psidev.psi.mi.jami.xml.cache with parameters of type Entity

Modifier and Type	Method	Description
int	InMemoryIdentityObjectCache.extractIdForParticipant(Entity o)	This method will extract the id for this object if it is already registered, assign an id and register the object if not already registered
int	InMemoryLightIdentityObjectCache.extractIdForParticipant(Entity o)	This method will extract the id for this object if it is already registered, assign an id and register the object if not already registered
int	PsiXmlObjectCache.extractIdForParticipant(Entity o)	This method will extract the id for this object if it is already registered, assign an id and register the object if not already registered
ModelledEntity	InMemoryPsiXmlCache.registerModelledParticipantLoadedFrom(Entity f)	registerModelledParticipantLoadedFrom.
ModelledEntity	PsiXmlFileIndexCache.registerModelledParticipantLoadedFrom(Entity f)	registerModelledParticipantLoadedFrom.
ModelledEntity	PsiXmlIdCache.registerModelledParticipantLoadedFrom(Entity f)	registerModelledParticipantLoadedFrom.
void	InMemoryPsiXmlCache.registerParticipant(int id, Entity object)	Register a participant with an id
void	PsiXmlFileIndexCache.registerParticipant(int id, Entity object)	Register a participant with an id
void	PsiXmlIdCache.registerParticipant(int id, Entity object)	Register a participant with an id

Uses of Entity in psidev.psi.mi.jami.xml.io.writer.compact

Methods in psidev.psi.mi.jami.xml.io.writer.compact with parameters of type Entity

Modifier and Type	Method	Description
protected void	AbstractCompactXmlWriter.registerParticipantInteractor(Entity participant)	registerParticipantInteractor.

Uses of Entity in psidev.psi.mi.jami.xml.model.extension

Classes in psidev.psi.mi.jami.xml.model.extension with type parameters of type Entity

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlFeature<P extends Entity,F extends Feature>	Interface for psi25 xml features

Subinterfaces of Entity in psidev.psi.mi.jami.xml.model.extension

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlEntity<F extends Feature>	Extended participant for PSI-XML 2,5 standards
interface	ExtendedPsiXmlParticipant<I extends Interaction,F extends Feature>	Extended participant for PSI-XML 2,5 standards
interface	ExtendedPsiXmlParticipantEvidence	Extended participant evidence for PSI-XML 2,5 standards

Methods in psidev.psi.mi.jami.xml.model.extension that return Entity

Modifier and Type	Method	Description
Entity	AbstractInferredInteractionParticipant.getParticipant()	Getter for the field participant.

Methods in psidev.psi.mi.jami.xml.model.extension with parameters of type Entity

Modifier and Type	Method	Description
void	AbstractInferredInteractionParticipant.setJAXBParticipantRef(Entity participant)	Sets the value of the participantRef property.
void	AbstractInferredInteractionParticipant.setParticipant(Entity participant)	Setter for the field participant.

Uses of Entity in psidev.psi.mi.jami.xml.model.extension.xml253

Classes in psidev.psi.mi.jami.xml.model.extension.xml253 with type parameters of type Entity

Modifier and Type	Class	Description
class	AbstractXmlFeature<P extends Entity,F extends Feature>	Abstract class for Xml features

Classes in psidev.psi.mi.jami.xml.model.extension.xml253 that implement Entity

Modifier and Type	Class	Description
class	AbstractXmlEntity<F extends Feature>	Abstract class for XmlEntity
class	AbstractXmlParticipant<I extends Interaction,F extends Feature>	Abstract class for XmlParticipant
class	AbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	Abstract class for XML Participant pool
class	XmlExperimentalParticipantCandidate	Xml implementation of ParticipantEvidence
class	XmlExperimentalParticipantCandidateWrapper	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.
class	XmlExperimentalParticipantPool	Xml implementation of participant pool
class	XmlExperimentalParticipantPoolWrapper	Wrapper for Xml participants pools Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
class	XmlModelledParticipant	XML implementation of ModelledParticipant
class	XmlModelledParticipantCandidate	XML implementation of ModelledParticipantCandidate
class	XmlModelledParticipantPool	Xml implementation of participant pool
class	XmlParticipant	Xml implementation of a simple participant
class	XmlParticipantCandidateWrapper	Wrapper for XmlParticipantCandidate so it implements ModelledParticipantCanidate
class	XmlParticipantEvidence	Xml implementation of ParticipantEvidence
class	XmlParticipantEvidenceWrapper	Wrapper for Xml participants Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
class	XmlParticipantPoolWrapper	Wrapper for XmlParticipant
class	XmlParticipantWrapper	Wrapper for XmlParticipant

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 that return Entity

Modifier and Type	Method	Description
Entity	XmlRange.getParticipant()	Getter for the field participant.

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Entity

Modifier and Type	Method	Description
void	AbstractXmlParticipantPool.onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate
void	XmlRange.setParticipant(Entity participant)	Sets the participating molecule that the range refers to

Uses of Entity in psidev.psi.mi.jami.xml.model.extension.xml254

Classes in psidev.psi.mi.jami.xml.model.extension.xml254 with type parameters of type Entity

Modifier and Type	Class	Description
class	AbstractXmlFeature<P extends Entity,F extends Feature>	Abstract class for Xml features

Classes in psidev.psi.mi.jami.xml.model.extension.xml254 that implement Entity

Modifier and Type	Class	Description
class	AbstractXmlEntity<F extends Feature>	Abstract class for XmlEntity
class	AbstractXmlParticipant<I extends Interaction,F extends Feature>	Abstract class for XmlParticipant
class	AbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	Abstract class for XML Participant pool
class	XmlExperimentalParticipantCandidate	Xml implementation of ParticipantEvidence
class	XmlExperimentalParticipantCandidateWrapper	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.
class	XmlExperimentalParticipantPool	Xml implementation of participant pool
class	XmlExperimentalParticipantPoolWrapper	Wrapper for Xml participants pools Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
class	XmlModelledParticipant	XML implementation of ModelledParticipant
class	XmlModelledParticipantCandidate	XML implementation of ModelledParticipantCandidate
class	XmlModelledParticipantPool	Xml implementation of participant pool
class	XmlParticipant	Xml implementation of a simple participant
class	XmlParticipantCandidateWrapper	Wrapper for XmlParticipantCandidate so it implements ModelledParticipantCanidate
class	XmlParticipantEvidence	Xml implementation of ParticipantEvidence
class	XmlParticipantEvidenceWrapper	Wrapper for Xml participants Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
class	XmlParticipantPoolWrapper	Wrapper for XmlParticipant
class	XmlParticipantWrapper	Wrapper for XmlParticipant

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 that return Entity

Modifier and Type	Method	Description
Entity	XmlRange.getParticipant()	Getter for the field participant.

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Entity

Modifier and Type	Method	Description
void	AbstractXmlParticipantPool.onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate
void	XmlRange.setParticipant(Entity participant)	Sets the participating molecule that the range refers to

Uses of Entity in psidev.psi.mi.jami.xml.model.extension.xml300

Classes in psidev.psi.mi.jami.xml.model.extension.xml300 with type parameters of type Entity

Modifier and Type	Class	Description
class	AbstractXmlFeature<P extends Entity,F extends Feature>	Abstract class for Xml features

Classes in psidev.psi.mi.jami.xml.model.extension.xml300 that implement Entity

Modifier and Type	Class	Description
class	AbstractXmlEntity<F extends Feature>	Abstract class for XmlEntity
class	AbstractXmlParticipant<I extends Interaction,F extends Feature>	Abstract class for XmlParticipant
class	AbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>	Abstract class for XML Participant pool
class	XmlExperimentalParticipantCandidate	Xml implementation of ParticipantEvidence
class	XmlExperimentalParticipantCandidateWrapper	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.
class	XmlExperimentalParticipantPool	Xml implementation of participant pool
class	XmlExperimentalParticipantPoolWrapper	Wrapper for Xml participants pools Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
class	XmlModelledParticipant	XML implementation of ModelledParticipant
class	XmlModelledParticipantCandidate	XML implementation of ModelledParticipantCandidate
class	XmlModelledParticipantPool	Xml implementation of participant pool
class	XmlParticipant	Xml implementation of a simple participant
class	XmlParticipantCandidateWrapper	Wrapper for XmlParticipantCandidate so it implements ModelledParticipantCanidate
class	XmlParticipantEvidence	Xml implementation of ParticipantEvidence
class	XmlParticipantEvidenceWrapper	Wrapper for Xml participants Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
class	XmlParticipantPoolWrapper	Wrapper for XmlParticipant
class	XmlParticipantWrapper	Wrapper for XmlParticipant

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 that return Entity

Modifier and Type	Method	Description
Entity	XmlRange.getParticipant()	Getter for the field participant.
Entity	ExtendedPsiXmlCausalRelationship.getSource()	getSource.
Entity	XmlCausalRelationship.getSource()	getSource.
Entity	XmlCausalRelationship.getTarget()	Getter for the field target.

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Entity

Modifier and Type	Method	Description
void	AbstractXmlParticipantPool.onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate
void	XmlRange.setParticipant(Entity participant)	Sets the participating molecule that the range refers to

Uses of Entity in psidev.psi.mi.jami.xml.model.reference

Classes in psidev.psi.mi.jami.xml.model.reference with type parameters of type Entity

Modifier and Type	Class	Description
class	AbstractFeatureRef<E extends Entity,F extends Feature>	Abstract feature reference

Uses of Entity in psidev.psi.mi.jami.xml.model.reference.xml253

Classes in psidev.psi.mi.jami.xml.model.reference.xml253 that implement Entity

Modifier and Type	Class	Description
class	AbstractEntityRef<T extends Feature>	Abstract entity reference
class	AbstractParticipantRef<I extends Interaction,T extends Feature>	Abstract participant reference

Uses of Entity in psidev.psi.mi.jami.xml.model.reference.xml254

Classes in psidev.psi.mi.jami.xml.model.reference.xml254 that implement Entity

Modifier and Type	Class	Description
class	AbstractEntityRef<T extends Feature>	Abstract entity reference
class	AbstractParticipantRef<I extends Interaction,T extends Feature>	Abstract participant reference

Uses of Entity in psidev.psi.mi.jami.xml.model.reference.xml300

Classes in psidev.psi.mi.jami.xml.model.reference.xml300 that implement Entity

Modifier and Type	Class	Description
class	AbstractEntityRef<T extends Feature>	Abstract entity reference
class	AbstractParticipantRef<I extends Interaction,T extends Feature>	Abstract participant reference