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

Packages that use ModelledEntity

Package	Description
psidev.psi.mi.jami.enricher.impl
psidev.psi.mi.jami.model
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.tab.extension
psidev.psi.mi.jami.utils.comparator.participant
psidev.psi.mi.jami.xml
psidev.psi.mi.jami.xml.cache
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300

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

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

Modifier and Type	Method	Description
EntityEnricher<ModelledEntity,ModelledFeature>	CompositeEntityEnricher.getModelledEntityEnricher()	Getter for the field modelledEntityEnricher.

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

Modifier and Type	Method	Description
void	CompositeEntityEnricher.setModelledEntityEnricher(EntityEnricher<ModelledEntity,ModelledFeature> modelledEntityEnricher)	Setter for the field modelledEntityEnricher.

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

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

Modifier and Type	Interface	Description
interface	ModelledParticipant	Participant of a modelled interaction.
interface	ModelledParticipantCandidate	Interface for modelled participant candidates
interface	ModelledParticipantPool	A pool of modelled participant candidates

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

Modifier and Type	Method	Description
ModelledEntity	Allostery.getAllostericMolecule()	A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site.
ModelledEntity	MoleculeEffector.getMolecule()	Refers to the participant (any participating entity such as simple participant, participant pool or participant candidate) that elicits an allosteric response in an allosteric molecule upon binding to that molecule.

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

Modifier and Type	Method	Description
void	Allostery.setAllostericMolecule(ModelledEntity participant)	Sets the allosteric molecule.

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

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

Modifier and Type	Class	Description
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

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

Modifier and Type	Method	Description
ModelledEntity	DefaultAllostery.getAllostericMolecule()	Getter for the field allostericMolecule.
ModelledEntity	DefaultMoleculeEffector.getMolecule()	getMolecule

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

Modifier and Type	Method	Description
void	DefaultAllostery.setAllostericMolecule(ModelledEntity participant)	Sets the allosteric molecule.

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

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

Modifier and Type	Class	Description
class	MitabModelledParticipant	Mitab extension for ModelledParticipant It contains a FileSourceLocator

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

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

Modifier and Type	Interface	Description
interface	CustomizableModelledParticipantComparator<E extends ModelledEntity>	A ModelledParticipantComparator that can be customized so we can ignore interactors when comparing modelled participants

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

Modifier and Type	Method	Description
Comparator<ModelledEntity>	ModelledParticipantPoolComparator.getModelledEntityComparator()	Getter for the field modelledEntityComparator.

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

Modifier and Type	Method	Description
static boolean	DefaultExactModelledEntityComparator.areEquals(ModelledEntity bioParticipant1, ModelledEntity bioParticipant2, boolean checkComplexesAsInteractors)	Use DefaultExactModelledEntityComparator to know if two biological entities are equals.
static boolean	DefaultExactModelledParticipantInteractorComparator.areEquals(ModelledEntity participant1, ModelledEntity participant2)	Use DefaultExactModelledParticipantInteractorComparator to know if two biological participants are equals.
static boolean	DefaultModelledEntityComparator.areEquals(ModelledEntity bioParticipant1, ModelledEntity bioParticipant2, boolean checkComplexesAsInteractors)	Use DefaultModelledEntityComparator to know if two biological entities are equals.
static boolean	DefaultModelledParticipantInteractorComparator.areEquals(ModelledEntity participant1, ModelledEntity participant2)	Use DefaultModelledParticipantInteractorComparator to know if two biological participants are equals.
static boolean	UnambiguousExactModelledEntityComparator.areEquals(ModelledEntity component1, ModelledEntity component2)	Use UnambiguousExactModelledParticipantComparator to know if two biological participant are equals.
static boolean	UnambiguousExactModelledParticipantInteractorComparator.areEquals(ModelledEntity component1, ModelledEntity component2)	Use UnambiguousExactModelledParticipantInteractorComparator to know if two biological participants are equals.
static boolean	UnambiguousModelledEntityComparator.areEquals(ModelledEntity component1, ModelledEntity component2)	Use UnambiguousModelledParticipantComparator to know if two biological participant are equals.
static boolean	UnambiguousModelledParticipantInteractorComparator.areEquals(ModelledEntity component1, ModelledEntity component2)	Use UnambiguousModelledParticipantInteractorComparator to know if two biological participants are equals.
int	ModelledEntityComparator.compare(ModelledEntity bioParticipant1, ModelledEntity bioParticipant2)	It will compare the basic properties of a biological participant using ParticipantInteractorComparator.
int	UnambiguousExactModelledEntityComparator.compare(ModelledEntity component1, ModelledEntity component2)	It will compare the basic properties of a component using UnambiguousExactParticipantBaseComparator.
int	UnambiguousExactModelledParticipantInteractorComparator.compare(ModelledEntity component1, ModelledEntity component2)	It will compare the basic properties of an interactor using UnambiguousInteractorComparator.
int	UnambiguousModelledEntityComparator.compare(ModelledEntity component1, ModelledEntity component2)	It will compare the basic properties of a biological participant using ParticipantInteractorComparator.
int	UnambiguousModelledParticipantInteractorComparator.compare(ModelledEntity component1, ModelledEntity component2)	It will compare the basic properties of an interactor using UnambiguousInteractorComparator.

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

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

Modifier and Type	Method	Description
void	XmlEntryContext.registerComplexParticipant(int id, ModelledEntity o)	registerComplexParticipant.

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

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

Modifier and Type	Method	Description
ModelledEntity	InMemoryPsiXmlCache.getComplexParticipant(int id)	getComplexParticipant.
ModelledEntity	PsiXmlFileIndexCache.getComplexParticipant(int id)	getComplexParticipant.
ModelledEntity	PsiXmlIdCache.getComplexParticipant(int id)	getComplexParticipant.
ModelledEntity	InMemoryPsiXmlCache.registerModelledParticipantLoadedFrom(Entity f)	registerModelledParticipantLoadedFrom.
ModelledEntity	PsiXmlFileIndexCache.registerModelledParticipantLoadedFrom(Entity f)	registerModelledParticipantLoadedFrom.
ModelledEntity	PsiXmlIdCache.registerModelledParticipantLoadedFrom(Entity f)	registerModelledParticipantLoadedFrom.

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

Modifier and Type	Method	Description
void	InMemoryPsiXmlCache.registerComplexParticipant(int id, ModelledEntity object)	Register a participant involved in a complex with an id
void	PsiXmlFileIndexCache.registerComplexParticipant(int id, ModelledEntity object)	Register a participant involved in a complex with an id
void	PsiXmlIdCache.registerComplexParticipant(int id, ModelledEntity object)	Register a participant involved in a complex with an id

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

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

Modifier and Type	Class	Description
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	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	XmlParticipantCandidateWrapper	Wrapper for XmlParticipantCandidate so it implements ModelledParticipantCanidate
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 ModelledEntity

Modifier and Type	Method	Description
ModelledEntity	XmlAllostery.getAllostericMolecule()	Getter for the field allostericMolecule.
ModelledEntity	XmlMoleculeEffector.getMolecule()	getMolecule.
ModelledEntity	XmlFeatureEvidenceWrapper.getParticipant()	The participant to which the feature is attached.
ModelledEntity	XmlFeatureWrapper.getParticipant()	The participant to which the feature is attached.

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

Modifier and Type	Method	Description
void	XmlAllostery.setAllostericMolecule(ModelledEntity participant)	Sets the allosteric molecule.
void	XmlFeatureEvidenceWrapper.setParticipant(ModelledEntity participant)	Sets the participant.
void	XmlFeatureWrapper.setParticipant(ModelledEntity participant)	Sets the participant.
void	XmlFeatureEvidenceWrapper.setParticipantAndAddFeature(ModelledEntity participant)	Sets the participant and add this feature to its list of features.
void	XmlFeatureWrapper.setParticipantAndAddFeature(ModelledEntity participant)	Sets the participant and add this feature to its list of features.

Constructors in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type ModelledEntity

Constructor	Description
XmlFeatureEvidenceWrapper(ExtendedPsiXmlFeatureEvidence part, ModelledEntity wrapper)	Constructor for XmlFeatureEvidenceWrapper.
XmlFeatureWrapper(ExtendedPsiXmlFeature part, ModelledEntity parent)	Constructor for XmlFeatureWrapper.

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

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

Modifier and Type	Class	Description
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	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	XmlParticipantCandidateWrapper	Wrapper for XmlParticipantCandidate so it implements ModelledParticipantCanidate
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 ModelledEntity

Modifier and Type	Method	Description
ModelledEntity	XmlAllostery.getAllostericMolecule()	Getter for the field allostericMolecule.
ModelledEntity	XmlMoleculeEffector.getMolecule()	getMolecule.
ModelledEntity	XmlFeatureEvidenceWrapper.getParticipant()	The participant to which the feature is attached.
ModelledEntity	XmlFeatureWrapper.getParticipant()	The participant to which the feature is attached.

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

Modifier and Type	Method	Description
void	XmlAllostery.setAllostericMolecule(ModelledEntity participant)	Sets the allosteric molecule.
void	XmlFeatureEvidenceWrapper.setParticipant(ModelledEntity participant)	Sets the participant.
void	XmlFeatureWrapper.setParticipant(ModelledEntity participant)	Sets the participant.
void	XmlFeatureEvidenceWrapper.setParticipantAndAddFeature(ModelledEntity participant)	Sets the participant and add this feature to its list of features.
void	XmlFeatureWrapper.setParticipantAndAddFeature(ModelledEntity participant)	Sets the participant and add this feature to its list of features.

Constructors in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type ModelledEntity

Constructor	Description
XmlFeatureEvidenceWrapper(ExtendedPsiXmlFeatureEvidence part, ModelledEntity wrapper)	Constructor for XmlFeatureEvidenceWrapper.
XmlFeatureWrapper(ExtendedPsiXmlFeature part, ModelledEntity parent)	Constructor for XmlFeatureWrapper.

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

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

Modifier and Type	Class	Description
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	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	XmlParticipantCandidateWrapper	Wrapper for XmlParticipantCandidate so it implements ModelledParticipantCanidate
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 ModelledEntity

Modifier and Type	Method	Description
ModelledEntity	XmlAllostery.getAllostericMolecule()	Getter for the field allostericMolecule.
ModelledEntity	XmlMoleculeEffector.getMolecule()	getMolecule.
ModelledEntity	XmlFeatureEvidenceWrapper.getParticipant()	The participant to which the feature is attached.
ModelledEntity	XmlFeatureWrapper.getParticipant()	The participant to which the feature is attached.

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

Modifier and Type	Method	Description
void	XmlAllostery.setAllostericMolecule(ModelledEntity participant)	Sets the allosteric molecule.
void	XmlFeatureEvidenceWrapper.setParticipant(ModelledEntity participant)	Sets the participant.
void	XmlFeatureWrapper.setParticipant(ModelledEntity participant)	Sets the participant.
void	XmlFeatureEvidenceWrapper.setParticipantAndAddFeature(ModelledEntity participant)	Sets the participant and add this feature to its list of features.
void	XmlFeatureWrapper.setParticipantAndAddFeature(ModelledEntity participant)	Sets the participant and add this feature to its list of features.

Constructors in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type ModelledEntity

Constructor	Description
XmlFeatureEvidenceWrapper(ExtendedPsiXmlFeatureEvidence part, ModelledEntity wrapper)	Constructor for XmlFeatureEvidenceWrapper.
XmlFeatureWrapper(ExtendedPsiXmlFeature part, ModelledEntity parent)	Constructor for XmlFeatureWrapper.