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

Packages that use ModelledParticipant

Package	Description
psidev.psi.mi.jami.binary.expansion
psidev.psi.mi.jami.binary.impl
psidev.psi.mi.jami.enricher.impl
psidev.psi.mi.jami.factory
psidev.psi.mi.jami.html
psidev.psi.mi.jami.model
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.tab.extension
psidev.psi.mi.jami.tab.io.iterator
psidev.psi.mi.jami.tab.io.writer
psidev.psi.mi.jami.tab.io.writer.feeder
psidev.psi.mi.jami.tab.io.writer.feeder.extended
psidev.psi.mi.jami.tab.utils
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.clone
psidev.psi.mi.jami.utils.comparator.interaction
psidev.psi.mi.jami.utils.comparator.participant
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml30
psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30
psidev.psi.mi.jami.xml.model.extension.binary
psidev.psi.mi.jami.xml.model.extension.binary.xml30
psidev.psi.mi.jami.xml.model.extension.factory.xml25
psidev.psi.mi.jami.xml.model.extension.factory.xml30
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.xml253
psidev.psi.mi.jami.xml.model.reference.xml254
psidev.psi.mi.jami.xml.model.reference.xml300

Uses of ModelledParticipant in psidev.psi.mi.jami.binary.expansion

Methods in psidev.psi.mi.jami.binary.expansion that return ModelledParticipant

Modifier and Type	Method	Description
protected ModelledParticipant	ModelledInteractionSpokeExpansion.collectBestBaitForSpokeExpansion(ModelledInteraction interaction)	collectBestBaitForSpokeExpansion
protected ModelledParticipant	ModelledInteractionBipartiteExpansion.createParticipantForComplexEntity(Complex complexEntity)	createParticipantForComplexEntity
protected ModelledParticipant[]	ModelledInteractionMatrixExpansion.createParticipantsArray(ModelledInteraction interaction)	createParticipantsArray

Uses of ModelledParticipant in psidev.psi.mi.jami.binary.impl

Constructors in psidev.psi.mi.jami.binary.impl with parameters of type ModelledParticipant

Constructor	Description
DefaultModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for DefaultModelledBinaryInteraction.
DefaultModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for DefaultModelledBinaryInteraction.
DefaultModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion, CvTerm causalRegulatoryMechanism)	Constructor for DefaultModelledBinaryInteraction.
DefaultModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for DefaultModelledBinaryInteraction.
DefaultModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for DefaultModelledBinaryInteraction.
DefaultModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for DefaultModelledBinaryInteraction.
DefaultModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for DefaultModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for DefaultNamedModelledBinaryInteraction.
DefaultNamedModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for DefaultNamedModelledBinaryInteraction.

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

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

Modifier and Type	Method	Description
void	CompositeModelledParticipantEnricher.enrich(ModelledParticipant object)	enrich.
void	CompositeModelledParticipantEnricher.enrich(ModelledParticipant object, ModelledParticipant objectSource)	enrich.

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

Modifier and Type	Method	Description
void	CompositeModelledParticipantEnricher.enrich(Collection<ModelledParticipant> objects)	enrich.

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

Constructor	Description
CompositeModelledParticipantEnricher(ParticipantEnricher<ModelledParticipant,ModelledFeature> entityBaseEnricher)	Constructor for CompositeModelledParticipantEnricher.

Uses of ModelledParticipant in psidev.psi.mi.jami.factory

Methods in psidev.psi.mi.jami.factory with parameters of type ModelledParticipant

Modifier and Type	Method	Description
ModelledBinaryInteraction	BinaryInteractionFactory.createModelledBinaryInteractionFrom(ModelledInteraction interaction, ModelledParticipant p1, ModelledParticipant p2, CvTerm expansionMethod)	Create a new ModelledBinaryInteraction object from a ModelledInteraction parent and two modelled participants
ModelledBinaryInteraction	DefaultBinaryInteractionFactory.createModelledBinaryInteractionFrom(ModelledInteraction interaction, ModelledParticipant p1, ModelledParticipant p2, CvTerm expansionMethod)	Create a new ModelledBinaryInteraction object from a ModelledInteraction parent and two modelled participants

Uses of ModelledParticipant in psidev.psi.mi.jami.html

Methods in psidev.psi.mi.jami.html that return types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
protected AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature>	AbstractMIHtmlWriter.getComplexWriter()	Getter for the field complexWriter.

Methods in psidev.psi.mi.jami.html with parameters of type ModelledParticipant

Modifier and Type	Method	Description
protected void	MIModelledHtmlWriter.writeConfidences(ModelledParticipant participant)	writeConfidences
protected void	MIModelledHtmlWriter.writeExperimentalPreparations(ModelledParticipant participant)	writeExperimentalPreparations
protected void	MIModelledHtmlWriter.writeExperimentalRole(ModelledParticipant participant)	writeExperimentalRole
protected void	MIModelledHtmlWriter.writeExpressedInOrganism(ModelledParticipant participant)	writeExpressedInOrganism
protected void	MIModelledHtmlWriter.writeParameters(ModelledParticipant participant)	writeParameters
protected void	MIModelledHtmlWriter.writeParticipantIdentificationMethods(ModelledParticipant participant)	writeParticipantIdentificationMethods

Constructor parameters in psidev.psi.mi.jami.html with type arguments of type ModelledParticipant

Constructor	Description
AbstractMIHtmlWriter(File file, AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)	Constructor for AbstractMIHtmlWriter.
AbstractMIHtmlWriter(OutputStream output, AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)	Constructor for AbstractMIHtmlWriter.
AbstractMIHtmlWriter(Writer writer, AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)	Constructor for AbstractMIHtmlWriter.
AbstractMIHtmlWriter(AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)	Constructor for AbstractMIHtmlWriter.

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

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

Modifier and Type	Interface	Description
interface	ModelledParticipantPool	A pool of modelled participant candidates

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

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

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	DefaultModelledParticipantPool	Default implementation of ParticipantPool
class	DefaultNamedModelledParticipant	Default implementation of Named modelled participant

Methods in psidev.psi.mi.jami.model.impl that return types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
Collection<ModelledParticipant>	DefaultComplex.getParticipants()	getParticipants

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

Modifier and Type	Method	Description
boolean	DefaultComplex.addParticipant(ModelledParticipant part)	addParticipant
boolean	DefaultComplex.removeParticipant(ModelledParticipant part)	removeParticipant

Method parameters in psidev.psi.mi.jami.model.impl with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
boolean	DefaultComplex.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
protected void	DefaultComplex.initialiseComponentsWith(Collection<ModelledParticipant> components)	initialiseComponentsWith
boolean	DefaultComplex.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.

Constructors in psidev.psi.mi.jami.model.impl with parameters of type ModelledParticipant

Constructor	Description
DefaultAllostery(CvTerm outcome, CvTerm response, ModelledParticipant allostericMolecule, T allostericEffector)	Constructor for DefaultAllostery.
DefaultAllostery(CvTerm outcome, ModelledParticipant allostericMolecule, T allostericEffector)	Constructor for DefaultAllostery.
DefaultModelledFeature(ModelledParticipant participant)	Constructor for DefaultModelledFeature.
DefaultModelledFeature(ModelledParticipant participant, String shortName, String fullName)	Constructor for DefaultModelledFeature.
DefaultModelledFeature(ModelledParticipant participant, String shortName, String fullName, CvTerm type)	Constructor for DefaultModelledFeature.
DefaultModelledFeature(ModelledParticipant participant, CvTerm type)	Constructor for DefaultModelledFeature.
DefaultMoleculeEffector(ModelledParticipant participant)	Constructor for DefaultMoleculeEffector.

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

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

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

Constructors in psidev.psi.mi.jami.tab.extension with parameters of type ModelledParticipant

Constructor	Description
MitabModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for MitabModelledBinaryInteraction.
MitabModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for MitabModelledBinaryInteraction.
MitabModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for MitabModelledBinaryInteraction.
MitabModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for MitabModelledBinaryInteraction.
MitabModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for MitabModelledBinaryInteraction.
MitabModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for MitabModelledBinaryInteraction.
MitabModelledFeature(ModelledParticipant participant)	Constructor for MitabModelledFeature.
MitabModelledFeature(ModelledParticipant participant, String shortName, String fullName)	Constructor for MitabModelledFeature.
MitabModelledFeature(ModelledParticipant participant, String shortName, String fullName, CvTerm type)	Constructor for MitabModelledFeature.
MitabModelledFeature(ModelledParticipant participant, CvTerm type)	Constructor for MitabModelledFeature.

Uses of ModelledParticipant in psidev.psi.mi.jami.tab.io.iterator

Constructor parameters in psidev.psi.mi.jami.tab.io.iterator with type arguments of type ModelledParticipant

Constructor	Description
MitabModelledBinaryIterator(MitabLineParser<ModelledBinaryInteraction,ModelledParticipant,ModelledFeature> lineParser)	Constructor for MitabModelledBinaryIterator.
MitabModelledInteractionIterator(MitabLineParser<ModelledInteraction,ModelledParticipant,ModelledFeature> lineParser)	Constructor for MitabModelledInteractionIterator.

Uses of ModelledParticipant in psidev.psi.mi.jami.tab.io.writer

Method parameters in psidev.psi.mi.jami.tab.io.writer with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
protected void	Mitab25BinaryWriter.setModelledBinaryWriter(AbstractMitab25BinaryWriter<ModelledBinaryInteraction,ModelledParticipant> modelledBinaryWriter)	Setter for the field modelledBinaryWriter.
protected void	Mitab26BinaryWriter.setModelledBinaryWriter(AbstractMitab26BinaryWriter<ModelledBinaryInteraction,ModelledParticipant> modelledBinaryWriter)	Setter for the field modelledBinaryWriter.
protected void	Mitab27BinaryWriter.setModelledBinaryWriter(AbstractMitab27BinaryWriter<ModelledBinaryInteraction,ModelledParticipant> modelledBinaryWriter)	Setter for the field modelledBinaryWriter.
protected void	Mitab28BinaryWriter.setModelledBinaryWriter(AbstractMitab28BinaryWriter<ModelledBinaryInteraction,ModelledParticipant> modelledBinaryWriter)	Setter for the field modelledBinaryWriter.

Uses of ModelledParticipant in psidev.psi.mi.jami.tab.io.writer.feeder

Methods in psidev.psi.mi.jami.tab.io.writer.feeder with parameters of type ModelledParticipant

Modifier and Type	Method	Description
void	MitabModelledInteractionFeeder.writeAlias(ModelledParticipant participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.
void	MitabModelledInteractionFeeder.writeExperimentalRole(ModelledParticipant participant)	writeExperimentalRole.
void	MitabModelledInteractionFeeder.writeParticipantIdentificationMethod(ModelledParticipant participant)	writeParticipantIdentificationMethod.

Uses of ModelledParticipant in psidev.psi.mi.jami.tab.io.writer.feeder.extended

Methods in psidev.psi.mi.jami.tab.io.writer.feeder.extended with parameters of type ModelledParticipant

Modifier and Type	Method	Description
void	ExtendedMitabModelledInteractionFeeder.writeAlias(ModelledParticipant participant, Alias alias)	This methods write the dbsource, alias name and alias type of an alias.

Uses of ModelledParticipant in psidev.psi.mi.jami.tab.utils

Methods in psidev.psi.mi.jami.tab.utils with parameters of type ModelledParticipant

Modifier and Type	Method	Description
static String	MitabUtils.findDbSourceForAlias(ModelledParticipant participant, Alias alias)	The source of the Alias is uniprotkb if the alias type is gene name, gene name synonym, isoform synonym, locus name or orf name.

Uses of ModelledParticipant in psidev.psi.mi.jami.utils

Methods in psidev.psi.mi.jami.utils that return ModelledParticipant

Modifier and Type	Method	Description
static ModelledParticipant	ParticipantUtils.createBasicModelledParticipant()	createBasicModelledParticipant

Methods in psidev.psi.mi.jami.utils that return types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
static Collection<ModelledParticipant>	ComplexUtils.expandComplexIntoParticipants(ModelledParticipant parentParticipant)	Expands the given complex participant.

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

Modifier and Type	Method	Description
static Collection<ModelledParticipant>	ComplexUtils.expandComplexIntoParticipants(ModelledParticipant parentParticipant)	Expands the given complex participant.
static void	ComplexUtils.maintainProteinComparableParticipantMap(Map<String,ModelledComparableParticipant> map, ModelledParticipant... modelledParticipants)

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

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

Modifier and Type	Method	Description
static void	ParticipantCloner.copyAndOverrideModelledParticipantProperties(ModelledParticipant source, ModelledParticipant target, boolean createNewFeature)	This method will copy properties of modelled participant source in modelled participant target and will override all the other properties of Target modelled participant.

Uses of ModelledParticipant in psidev.psi.mi.jami.utils.comparator.interaction

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

Modifier and Type	Method	Description
CollectionComparator<ModelledParticipant>	ModelledInteractionComparator.getParticipantCollectionComparator()	Getter for the field participantCollectionComparator.

Constructor parameters in psidev.psi.mi.jami.utils.comparator.interaction with type arguments of type ModelledParticipant

Constructor	Description
ModelledInteractionComparator(CollectionComparator<ModelledParticipant> participantComparator, Comparator<Interaction> interactionComparator)	Constructor for ModelledInteractionComparator.

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

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

Modifier and Type	Method	Description
static boolean	DefaultExactModelledParticipantComparator.areEquals(ModelledParticipant bioParticipant1, ModelledParticipant bioParticipant2, boolean checkComplexesAsInteractors)	It will compare the basic properties of a biological participant using DefaultExactParticipantBaseComparator.
static boolean	DefaultModelledParticipantComparator.areEquals(ModelledParticipant bioParticipant1, ModelledParticipant bioParticipant2, boolean checkComplexesAsInteractors)	It will compare the basic properties of a biological participant using DefaultParticipantBaseComparator.
static boolean	UnambiguousExactModelledParticipantComparator.areEquals(ModelledParticipant component1, ModelledParticipant component2)	Use UnambiguousExactModelledParticipantComparator to know if two biological participant are equals.
static boolean	UnambiguousModelledParticipantComparator.areEquals(ModelledParticipant component1, ModelledParticipant component2)	Use UnambiguousModelledParticipantComparator to know if two biological participants are equals.
int	ModelledParticipantComparator.compare(ModelledParticipant bioParticipant1, ModelledParticipant bioParticipant2)	It will compare the basic properties of a biological participant using ParticipantBaseComparator.
int	UnambiguousExactModelledParticipantComparator.compare(ModelledParticipant component1, ModelledParticipant component2)	It will compare the basic properties of a component using UnambiguousExactParticipantBaseComparator.
int	UnambiguousModelledParticipantComparator.compare(ModelledParticipant component1, ModelledParticipant component2)	It will compare the basic properties of a biological participant using UnambiguousParticipantBaseComparator.

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

Constructor	Description
ModelledParticipantCollectionComparator(CustomizableModelledParticipantComparator<ModelledParticipant> biologicalParticipantComparator)	Creates a new component CollectionComparator.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with parameters of type ModelledParticipant

Modifier and Type	Method	Description
protected void	AbstractXmlModelledParticipantWriter.writeConfidences(ModelledParticipant object)	writeConfidences.
protected void	AbstractXmlModelledParticipantWriter.writeExperimentalInteractor(ModelledParticipant object)	writeExperimentalInteractor.
protected void	AbstractXmlModelledParticipantWriter.writeExperimentalPreparations(ModelledParticipant object)	writeExperimentalPreparations.
protected void	AbstractXmlModelledParticipantWriter.writeExperimentalRoles(ModelledParticipant object)	writeExperimentalRoles.
protected void	AbstractXmlModelledParticipantWriter.writeHostOrganisms(ModelledParticipant object)	writeHostOrganisms.
protected void	AbstractXmlModelledParticipantWriter.writeParameters(ModelledParticipant object)	writeParameters.
protected void	AbstractXmlModelledParticipantWriter.writeParticipantIdentificationMethods(ModelledParticipant object, CvTerm method)	writeParticipantIdentificationMethods.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
protected void	AbstractXmlModelledParticipantWriter.writeOtherAttributes(ModelledParticipant object, boolean writeAttributeList)	writeOtherAttributes.
protected void	AbstractXmlModelledParticipantWriter.writeStoichiometry(ModelledParticipant object)	writeStoichiometry.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
protected void	AbstractXmlModelledParticipantWriter.writeConfidences(ModelledParticipant object)	writeConfidences.
protected void	AbstractXmlModelledParticipantWriter.writeExperimentalInteractor(ModelledParticipant object)	writeExperimentalInteractor.
protected void	AbstractXmlModelledParticipantWriter.writeExperimentalPreparations(ModelledParticipant object)	writeExperimentalPreparations.
protected void	AbstractXmlModelledParticipantWriter.writeExperimentalRoles(ModelledParticipant object)	writeExperimentalRoles.
protected void	AbstractXmlModelledParticipantWriter.writeHostOrganisms(ModelledParticipant object)	writeHostOrganisms.
protected void	AbstractXmlModelledParticipantWriter.writeOtherAttributes(ModelledParticipant object, boolean writeAttributeList)	writeOtherAttributes.
protected void	AbstractXmlModelledParticipantWriter.writeParameters(ModelledParticipant object)	writeParameters.
protected void	AbstractXmlModelledParticipantWriter.writeParticipantIdentificationMethods(ModelledParticipant object, CvTerm method)	writeParticipantIdentificationMethods.
protected void	AbstractXmlModelledParticipantWriter.writeStoichiometry(ModelledParticipant object)	writeStoichiometry.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml25

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml25 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
protected void	XmlNamedModelledParticipantWriter.writeNames(ModelledParticipant object)	writeNames.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml30

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml30 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
protected void	XmlNamedModelledParticipantWriter.writeNames(ModelledParticipant object)	writeNames.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml25

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml25 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
protected void	XmlNamedModelledParticipantWriter.writeNames(ModelledParticipant object)	writeNames.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
protected void	XmlNamedModelledParticipantWriter.writeNames(ModelledParticipant object)	writeNames.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.model.extension.binary

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

Modifier and Type	Method	Description
ModelledParticipant	XmlModelledBinaryInteractionWrapper.getParticipantA()	getParticipantA.
ModelledParticipant	XmlModelledBinaryInteractionWrapper.getParticipantB()	getParticipantB.

Methods in psidev.psi.mi.jami.xml.model.extension.binary that return types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
Collection<ModelledParticipant>	XmlModelledBinaryInteractionWrapper.getParticipants()	The collection of participants involved in this interaction.

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

Modifier and Type	Method	Description
boolean	XmlModelledBinaryInteractionWrapper.addParticipant(ModelledParticipant part)	This method will add the participant and set the interaction of the new participant to this current interaction
boolean	XmlModelledBinaryInteractionWrapper.removeParticipant(ModelledParticipant part)	This method will remove the participant and set the interaction of the new participant to null
void	XmlModelledBinaryInteractionWrapper.setParticipantA(ModelledParticipant participantA)	setParticipantA.
void	XmlModelledBinaryInteractionWrapper.setParticipantB(ModelledParticipant participantB)	setParticipantB.

Method parameters in psidev.psi.mi.jami.xml.model.extension.binary with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
boolean	XmlModelledBinaryInteractionWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlModelledBinaryInteractionWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.

Constructors in psidev.psi.mi.jami.xml.model.extension.binary with parameters of type ModelledParticipant

Constructor	Description
XmlModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.model.extension.binary.xml30

Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 that return ModelledParticipant

Modifier and Type	Method	Description
ModelledParticipant	XmlModelledBinaryInteractionWrapper.getParticipantA()	getParticipantA.
ModelledParticipant	XmlModelledBinaryInteractionWrapper.getParticipantB()	getParticipantB.

Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 that return types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
Collection<ModelledParticipant>	XmlModelledBinaryInteractionWrapper.getParticipants()	The collection of participants involved in this interaction.

Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
boolean	XmlModelledBinaryInteractionWrapper.addParticipant(ModelledParticipant part)	This method will add the participant and set the interaction of the new participant to this current interaction
boolean	XmlModelledBinaryInteractionWrapper.removeParticipant(ModelledParticipant part)	This method will remove the participant and set the interaction of the new participant to null
void	XmlModelledBinaryInteractionWrapper.setParticipantA(ModelledParticipant participantA)	setParticipantA.
void	XmlModelledBinaryInteractionWrapper.setParticipantB(ModelledParticipant participantB)	setParticipantB.

Method parameters in psidev.psi.mi.jami.xml.model.extension.binary.xml30 with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
boolean	XmlModelledBinaryInteractionWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlModelledBinaryInteractionWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.

Constructors in psidev.psi.mi.jami.xml.model.extension.binary.xml30 with parameters of type ModelledParticipant

Constructor	Description
XmlModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, CvTerm type, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(String shortName, ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB)	Constructor for XmlModelledBinaryInteraction.
XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)	Constructor for XmlModelledBinaryInteraction.

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.model.extension.factory.xml25

Methods in psidev.psi.mi.jami.xml.model.extension.factory.xml25 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
ModelledBinaryInteraction	XmlBinaryInteractionFactory.createModelledBinaryInteractionFrom(ModelledInteraction interaction, ModelledParticipant p1, ModelledParticipant p2, CvTerm expansionMethod)	Create a new ModelledBinaryInteraction object from a ModelledInteraction parent and two modelled participants

Uses of ModelledParticipant in psidev.psi.mi.jami.xml.model.extension.factory.xml30

Methods in psidev.psi.mi.jami.xml.model.extension.factory.xml30 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
ModelledBinaryInteraction	XmlBinaryInteractionFactory.createModelledBinaryInteractionFrom(ModelledInteraction interaction, ModelledParticipant p1, ModelledParticipant p2, CvTerm expansionMethod)	Create a new ModelledBinaryInteraction object from a ModelledInteraction parent and two modelled participants

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

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

Modifier and Type	Class	Description
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	XmlModelledParticipantPool	Xml implementation of participant pool
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 types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
List<ModelledParticipant>	AbstractXmlModelledInteraction.JAXBParticipantWrapper.getJAXBParticipants()
Collection<ModelledParticipant>	XmlBasicInteractionComplexWrapper.getParticipants()	getParticipants.
Collection<ModelledParticipant>	XmlInteractionEvidenceComplexWrapper.getParticipants()	getParticipants.
Collection<ModelledParticipant>	XmlModelledInteractionComplexWrapper.getParticipants()	getParticipants.

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

Modifier and Type	Method	Description
boolean	XmlBasicInteractionComplexWrapper.addParticipant(ModelledParticipant part)	addParticipant.
boolean	XmlInteractionEvidenceComplexWrapper.addParticipant(ModelledParticipant part)	addParticipant.
boolean	XmlModelledInteractionComplexWrapper.addParticipant(ModelledParticipant part)	addParticipant.
boolean	XmlBasicInteractionComplexWrapper.removeParticipant(ModelledParticipant part)	removeParticipant.
boolean	XmlInteractionEvidenceComplexWrapper.removeParticipant(ModelledParticipant part)	removeParticipant.
boolean	XmlModelledInteractionComplexWrapper.removeParticipant(ModelledParticipant part)	removeParticipant.

Method parameters in psidev.psi.mi.jami.xml.model.extension.xml253 with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
boolean	XmlBasicInteractionComplexWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlInteractionEvidenceComplexWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlModelledInteractionComplexWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlBasicInteractionComplexWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	XmlInteractionEvidenceComplexWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	XmlModelledInteractionComplexWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.

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

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

Modifier and Type	Class	Description
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	XmlModelledParticipantPool	Xml implementation of participant pool
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 types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
List<ModelledParticipant>	AbstractXmlModelledInteraction.JAXBParticipantWrapper.getJAXBParticipants()
Collection<ModelledParticipant>	XmlBasicInteractionComplexWrapper.getParticipants()	getParticipants.
Collection<ModelledParticipant>	XmlInteractionEvidenceComplexWrapper.getParticipants()	getParticipants.
Collection<ModelledParticipant>	XmlModelledInteractionComplexWrapper.getParticipants()	getParticipants.

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

Modifier and Type	Method	Description
boolean	XmlBasicInteractionComplexWrapper.addParticipant(ModelledParticipant part)	addParticipant.
boolean	XmlInteractionEvidenceComplexWrapper.addParticipant(ModelledParticipant part)	addParticipant.
boolean	XmlModelledInteractionComplexWrapper.addParticipant(ModelledParticipant part)	addParticipant.
boolean	XmlBasicInteractionComplexWrapper.removeParticipant(ModelledParticipant part)	removeParticipant.
boolean	XmlInteractionEvidenceComplexWrapper.removeParticipant(ModelledParticipant part)	removeParticipant.
boolean	XmlModelledInteractionComplexWrapper.removeParticipant(ModelledParticipant part)	removeParticipant.

Method parameters in psidev.psi.mi.jami.xml.model.extension.xml254 with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
boolean	XmlBasicInteractionComplexWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlInteractionEvidenceComplexWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlModelledInteractionComplexWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlBasicInteractionComplexWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	XmlInteractionEvidenceComplexWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	XmlModelledInteractionComplexWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.

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

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

Modifier and Type	Class	Description
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	XmlModelledParticipantPool	Xml implementation of participant pool
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 types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
List<ModelledParticipant>	AbstractXmlModelledInteraction.JAXBParticipantWrapper.getJAXBParticipants()
List<ModelledParticipant>	XmlModelledInteraction.JAXBParticipantWrapper.getJAXBParticipants()
Collection<ModelledParticipant>	XmlBasicInteractionComplexWrapper.getParticipants()	getParticipants.
Collection<ModelledParticipant>	XmlInteractionEvidenceComplexWrapper.getParticipants()	getParticipants.
Collection<ModelledParticipant>	XmlModelledInteractionComplexWrapper.getParticipants()	getParticipants.

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

Modifier and Type	Method	Description
boolean	XmlBasicInteractionComplexWrapper.addParticipant(ModelledParticipant part)	addParticipant.
boolean	XmlInteractionEvidenceComplexWrapper.addParticipant(ModelledParticipant part)	addParticipant.
boolean	XmlModelledInteractionComplexWrapper.addParticipant(ModelledParticipant part)	addParticipant.
boolean	XmlBasicInteractionComplexWrapper.removeParticipant(ModelledParticipant part)	removeParticipant.
boolean	XmlInteractionEvidenceComplexWrapper.removeParticipant(ModelledParticipant part)	removeParticipant.
boolean	XmlModelledInteractionComplexWrapper.removeParticipant(ModelledParticipant part)	removeParticipant.

Method parameters in psidev.psi.mi.jami.xml.model.extension.xml300 with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
boolean	XmlBasicInteractionComplexWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlInteractionEvidenceComplexWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlModelledInteractionComplexWrapper.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	XmlBasicInteractionComplexWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	XmlInteractionEvidenceComplexWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.
boolean	XmlModelledInteractionComplexWrapper.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.

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

Methods in psidev.psi.mi.jami.xml.model.reference.xml253 that return types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
Collection<ModelledParticipant>	AbstractComplexRef.getParticipants()	getParticipants.

Methods in psidev.psi.mi.jami.xml.model.reference.xml253 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
boolean	AbstractComplexRef.addParticipant(ModelledParticipant part)	addParticipant.
boolean	AbstractComplexRef.removeParticipant(ModelledParticipant part)	removeParticipant.

Method parameters in psidev.psi.mi.jami.xml.model.reference.xml253 with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
boolean	AbstractComplexRef.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	AbstractComplexRef.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.

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

Methods in psidev.psi.mi.jami.xml.model.reference.xml254 that return types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
Collection<ModelledParticipant>	AbstractComplexRef.getParticipants()	getParticipants.

Methods in psidev.psi.mi.jami.xml.model.reference.xml254 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
boolean	AbstractComplexRef.addParticipant(ModelledParticipant part)	addParticipant.
boolean	AbstractComplexRef.removeParticipant(ModelledParticipant part)	removeParticipant.

Method parameters in psidev.psi.mi.jami.xml.model.reference.xml254 with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
boolean	AbstractComplexRef.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	AbstractComplexRef.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.

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

Methods in psidev.psi.mi.jami.xml.model.reference.xml300 that return types with arguments of type ModelledParticipant

Modifier and Type	Method	Description
Collection<ModelledParticipant>	AbstractComplexRef.getParticipants()	getParticipants.

Methods in psidev.psi.mi.jami.xml.model.reference.xml300 with parameters of type ModelledParticipant

Modifier and Type	Method	Description
boolean	AbstractComplexRef.addParticipant(ModelledParticipant part)	addParticipant.
boolean	AbstractComplexRef.removeParticipant(ModelledParticipant part)	removeParticipant.

Method parameters in psidev.psi.mi.jami.xml.model.reference.xml300 with type arguments of type ModelledParticipant

Modifier and Type	Method	Description
boolean	AbstractComplexRef.addAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will add all the participant and set the interaction of the new participant to this current interaction
boolean	AbstractComplexRef.removeAllParticipants(Collection<? extends ModelledParticipant> participants)	This method will remove the participant and set the interaction of the removed participant to null.