Uses of Interface
psidev.psi.mi.jami.model.CvTerm
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Uses of CvTerm in psidev.psi.mi.jami.binary
Methods in psidev.psi.mi.jami.binary that return CvTerm Modifier and Type Method Description CvTermBinaryInteraction. getCausalRegulatoryMechanism()The causal regulatory mechanism for the binary interactionCvTermBinaryInteraction. getComplexExpansion()The complex expansion method if this binary interaction is expanded from a complex or n-ary interaction.Methods in psidev.psi.mi.jami.binary with parameters of type CvTerm Modifier and Type Method Description voidBinaryInteraction. setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)Sets the causal regulatory mechanism of this binary interactionvoidBinaryInteraction. setComplexExpansion(CvTerm expansion)Sets the complex expansion of this binary interaction -
Uses of CvTerm in psidev.psi.mi.jami.binary.expansion
Methods in psidev.psi.mi.jami.binary.expansion that return CvTerm Modifier and Type Method Description CvTermAbstractComplexExpansionMethod. getMethod()The CvTerm that describe the method used to expand.CvTermComplexExpansionMethod. getMethod()The method represented by the ComplexExpansionMethod object.Constructors in psidev.psi.mi.jami.binary.expansion with parameters of type CvTerm Constructor Description AbstractComplexExpansionMethod(CvTerm method)Constructor for AbstractComplexExpansionMethod. -
Uses of CvTerm in psidev.psi.mi.jami.binary.impl
Methods in psidev.psi.mi.jami.binary.impl that return CvTerm Modifier and Type Method Description CvTermAbstractBinaryInteraction. getCausalRegulatoryMechanism()Getter for the fieldcausalRegulatoryMechanism.CvTermAbstractBinaryInteractionWrapper. getCausalRegulatoryMechanism()Getter for the fieldcausalRegulatoryMechanismCvTermAbstractBinaryInteraction. getComplexExpansion()Getter for the fieldcomplexExpansion.CvTermAbstractBinaryInteractionWrapper. getComplexExpansion()Getter for the fieldcomplexExpansion.CvTermDefaultModelledBinaryInteraction. getEvidenceType()getEvidenceTypeCvTermModelledBinaryInteractionWrapper. getEvidenceType()getEvidenceTypeCvTermAbstractBinaryInteractionWrapper. getInteractionType()getInteractionTypeMethods in psidev.psi.mi.jami.binary.impl with parameters of type CvTerm Modifier and Type Method Description voidAbstractBinaryInteraction. setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)Setter for the fieldcausalRegulatoryMechanism.voidAbstractBinaryInteractionWrapper. setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)Setter for the fieldcausalRegulatoryMechanism.voidAbstractBinaryInteraction. setComplexExpansion(CvTerm expansion)Sets the complex expansion of this binary interactionvoidAbstractBinaryInteractionWrapper. setComplexExpansion(CvTerm expansion)Sets the complex expansion of this binary interactionvoidDefaultModelledBinaryInteraction. setEvidenceType(CvTerm eco)Sets the evidence typevoidModelledBinaryInteractionWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidAbstractBinaryInteractionWrapper. setInteractionType(CvTerm term)Sets the interaction type.Constructors in psidev.psi.mi.jami.binary.impl with parameters of type CvTerm Constructor Description AbstractBinaryInteraction(String shortName, CvTerm type)Constructor for AbstractBinaryInteraction.AbstractBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for AbstractBinaryInteraction.AbstractBinaryInteraction(String shortName, CvTerm type, T participantA, T participantB)Constructor for AbstractBinaryInteraction.AbstractBinaryInteraction(String shortName, CvTerm type, T participantA, T participantB, CvTerm complexExpansion)Constructor for AbstractBinaryInteraction.AbstractBinaryInteraction(String shortName, CvTerm type, T participantA, T participantB, CvTerm complexExpansion, CvTerm causalRegulatoryMechanism)Constructor for AbstractBinaryInteraction.AbstractBinaryInteraction(String shortName, T participantA, T participantB, CvTerm complexExpansion)Constructor for AbstractBinaryInteraction.AbstractBinaryInteraction(CvTerm complexExpansion)Constructor for AbstractBinaryInteraction.AbstractBinaryInteraction(T participantA, T participantB, CvTerm complexExpansion)Constructor for AbstractBinaryInteraction.AbstractBinaryInteractionWrapper(I interaction, CvTerm complexExpansion)Constructor for AbstractBinaryInteractionWrapper.BinaryInteractionEvidenceWrapper(InteractionEvidence interaction, CvTerm complexExpansion)Constructor for BinaryInteractionEvidenceWrapper.BinaryInteractionWrapper(Interaction interaction, CvTerm complexExpansion)Constructor for BinaryInteractionWrapper.DefaultBinaryInteraction(String shortName, CvTerm type)Constructor for DefaultBinaryInteraction.DefaultBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for DefaultBinaryInteraction.DefaultBinaryInteraction(String shortName, CvTerm type, Participant participantA, Participant participantB)Constructor for DefaultBinaryInteraction.DefaultBinaryInteraction(String shortName, CvTerm type, Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for DefaultBinaryInteraction.DefaultBinaryInteraction(String shortName, Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for DefaultBinaryInteraction.DefaultBinaryInteraction(CvTerm complexExpansion)Constructor for DefaultBinaryInteraction.DefaultBinaryInteraction(Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for DefaultBinaryInteraction.DefaultBinaryInteractionEvidence(String shortName, CvTerm type)Constructor for DefaultBinaryInteractionEvidence.DefaultBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for DefaultBinaryInteractionEvidence.DefaultBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)Constructor for DefaultBinaryInteractionEvidence.DefaultBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for DefaultBinaryInteractionEvidence.DefaultBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for DefaultBinaryInteractionEvidence.DefaultBinaryInteractionEvidence(CvTerm complexExpansion)Constructor for DefaultBinaryInteractionEvidence.DefaultBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for DefaultBinaryInteractionEvidence.DefaultModelledBinaryInteraction(String shortName, CvTerm type)Constructor for DefaultModelledBinaryInteraction.DefaultModelledBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for DefaultModelledBinaryInteraction.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, CvTerm complexExpansion)Constructor for DefaultModelledBinaryInteraction.DefaultModelledBinaryInteraction(CvTerm complexExpansion)Constructor for DefaultModelledBinaryInteraction.DefaultModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)Constructor for DefaultModelledBinaryInteraction.DefaultNamedBinaryInteraction(String shortName, CvTerm type)Constructor for DefaultNamedBinaryInteraction.DefaultNamedBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteraction.DefaultNamedBinaryInteraction(String shortName, CvTerm type, Participant participantA, Participant participantB)Constructor for DefaultNamedBinaryInteraction.DefaultNamedBinaryInteraction(String shortName, CvTerm type, Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteraction.DefaultNamedBinaryInteraction(String shortName, Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteraction.DefaultNamedBinaryInteraction(CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteraction.DefaultNamedBinaryInteraction(Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteraction.DefaultNamedBinaryInteractionEvidence(String shortName, CvTerm type)Constructor for DefaultNamedBinaryInteractionEvidence.DefaultNamedBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteractionEvidence.DefaultNamedBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)Constructor for DefaultNamedBinaryInteractionEvidence.DefaultNamedBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteractionEvidence.DefaultNamedBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteractionEvidence.DefaultNamedBinaryInteractionEvidence(CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteractionEvidence.DefaultNamedBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for DefaultNamedBinaryInteractionEvidence.DefaultNamedModelledBinaryInteraction(String shortName, CvTerm type)Constructor for DefaultNamedModelledBinaryInteraction.DefaultNamedModelledBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for DefaultNamedModelledBinaryInteraction.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, CvTerm complexExpansion)Constructor for DefaultNamedModelledBinaryInteraction.DefaultNamedModelledBinaryInteraction(CvTerm complexExpansion)Constructor for DefaultNamedModelledBinaryInteraction.DefaultNamedModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)Constructor for DefaultNamedModelledBinaryInteraction.ModelledBinaryInteractionWrapper(ModelledInteraction interaction, CvTerm complexExpansion)Constructor for ModelledBinaryInteractionWrapper. -
Uses of CvTerm in psidev.psi.mi.jami.bridges.fetcher
Classes in psidev.psi.mi.jami.bridges.fetcher with type parameters of type CvTerm Modifier and Type Interface Description interfaceCvTermFetcher<C extends CvTerm>The interface for finding a CvTerm or extension of CvTerm.Methods in psidev.psi.mi.jami.bridges.fetcher with parameters of type CvTerm Modifier and Type Method Description CCvTermFetcher. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Collection<C>CvTermFetcher. fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Set<OntologyTerm>OntologyTermFetcher. fetchRootTerms(CvTerm database)fetchRootTerms. -
Uses of CvTerm in psidev.psi.mi.jami.bridges.fetcher.mock
Classes in psidev.psi.mi.jami.bridges.fetcher.mock with type parameters of type CvTerm Modifier and Type Class Description classCvTermCompositeFetcherTemplate<T extends CvTerm,F extends CvTermFetcher<T>>Template for a CvTermCompositeFetcher which delegates fetching to other fetcherMethods in psidev.psi.mi.jami.bridges.fetcher.mock that return CvTerm Modifier and Type Method Description CvTermFailingCvTermFetcher. fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)Uses the identifier and the name of the database to search for a complete form of the cvTerm.CvTermFailingCvTermFetcher. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)fetchByIdentifier.CvTermMockCvTermFetcher. fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)Uses the identifier and the name of the database to search for a complete form of the cvTerm.CvTermMockCvTermFetcher. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)fetchByIdentifier.CvTermFailingCvTermFetcher. fetchByName(String searchName, String ontologyDatabaseName)Uses the name of the term and the name of the database to search for a complete form of the term.CvTermMockCvTermFetcher. fetchByName(String searchName, String ontologyDatabaseName)Uses the name of the term and the name of the database to search for a complete form of the term.Methods in psidev.psi.mi.jami.bridges.fetcher.mock that return types with arguments of type CvTerm Modifier and Type Method Description Collection<CvTerm>FailingCvTermFetcher. fetchByIdentifiers(Collection<String> termIdentifiers, String ontologyDatabaseName)fetchByIdentifiers.Collection<CvTerm>FailingCvTermFetcher. fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Collection<CvTerm>MockCvTermFetcher. fetchByIdentifiers(Collection<String> termIdentifiers, String ontologyDatabaseName)fetchByIdentifiers.Collection<CvTerm>MockCvTermFetcher. fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Collection<CvTerm>FailingCvTermFetcher. fetchByName(String searchName)Uses the name of the term and the name of the database to search for a complete form of the term.Collection<CvTerm>MockCvTermFetcher. fetchByName(String searchName)Uses the name of the term and the name of the database to search for a complete form of the term.Collection<CvTerm>FailingCvTermFetcher. fetchByNames(Collection<String> searchNames)Finds the CvTerms which match the exact names provided.Collection<CvTerm>FailingCvTermFetcher. fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)Uses the name of the term and the name of the database to search for a complete form of the term.Collection<CvTerm>MockCvTermFetcher. fetchByNames(Collection<String> searchNames)Finds the CvTerms which match the exact names provided.Collection<CvTerm>MockCvTermFetcher. fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)Uses the name of the term and the name of the database to search for a complete form of the term.Methods in psidev.psi.mi.jami.bridges.fetcher.mock with parameters of type CvTerm Modifier and Type Method Description TCvTermCompositeFetcherTemplate. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)fetchByIdentifier.CvTermFailingCvTermFetcher. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)fetchByIdentifier.CvTermMockCvTermFetcher. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)fetchByIdentifier.OntologyTermMockOntologyTermFetcher. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)fetchByIdentifier.SourceMockSourceFetcher. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)fetchByIdentifier.Collection<T>CvTermCompositeFetcherTemplate. fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Collection<CvTerm>FailingCvTermFetcher. fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Collection<CvTerm>MockCvTermFetcher. fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Collection<OntologyTerm>MockOntologyTermFetcher. fetchByIdentifiers(Collection<String> identifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Collection<Source>MockSourceFetcher. fetchByIdentifiers(Collection<String> identifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Set<OntologyTerm>MockOntologyTermFetcher. fetchRootTerms(CvTerm database)fetchRootTerms.Set<OntologyTerm>OntologyTermCompositeFetcher. fetchRootTerms(CvTerm database)fetchRootTerms. -
Uses of CvTerm in psidev.psi.mi.jami.bridges.obo
Classes in psidev.psi.mi.jami.bridges.obo with type parameters of type CvTerm Modifier and Type Class Description classAbstractOboLoader<T extends CvTerm>Abstract obo loaderclassOboFetcherTemplate<T extends CvTerm>Template fetcher for OBO filesMethods in psidev.psi.mi.jami.bridges.obo that return CvTerm Modifier and Type Method Description protected CvTermAbstractOboLoader. getOntologyDatabase()Getter for the fieldontologyDatabase.protected CvTermOboFetcherTemplate. getOntologyDatabase()Getter for the fieldontologyDatabase.protected CvTermCvOboLoader. instantiateNewTerm(String name, Xref identity)instantiateNewTerm.Methods in psidev.psi.mi.jami.bridges.obo with parameters of type CvTerm Modifier and Type Method Description protected voidCvOboLoader. createDefinitionFor(String def, CvTerm term)createDefinitionFor.TOboFetcherTemplate. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)fetchByIdentifier.Collection<T>OboFetcherTemplate. fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Set<OntologyTerm>OboOntologyTermFetcher. fetchRootTerms(CvTerm database)fetchRootTerms.Constructors in psidev.psi.mi.jami.bridges.obo with parameters of type CvTerm Constructor Description AbstractOboLoader(CvTerm database)Constructor for AbstractOboLoader.CvOboLoader(CvTerm database)Constructor for CvOboLoader.OboCvTermFetcher(CvTerm database, String filePath)Constructor for OboCvTermFetcher.OboFetcherTemplate(CvTerm database, AbstractOboLoader<T> oboLoader, String filePath)Constructor for OboFetcherTemplate.OboOntologyTermFetcher(CvTerm database, String filePath)Constructor for OboOntologyTermFetcher.OboSourceFetcher(CvTerm database, String filePath)Constructor for OboSourceFetcher.OntologyOboLoader(CvTerm database)Constructor for OntologyOboLoader.SourceOboLoader(CvTerm database)Constructor for SourceOboLoader. -
Uses of CvTerm in psidev.psi.mi.jami.bridges.ols
Classes in psidev.psi.mi.jami.bridges.ols with type parameters of type CvTerm Modifier and Type Class Description classAbstractOlsFetcher<T extends CvTerm>Abstract class for OlsCvTermFetcherclassCachedOlsFetcher<T extends CvTerm>Generic implementation for CachedOlsServiceClasses in psidev.psi.mi.jami.bridges.ols that implement CvTerm Modifier and Type Class Description classLazyCvTermA lazy cvTerm which will only fetch metadata when required.classLazyOntologyTermA lazy ontology term, which only checks for parents of children when required.classLazySourceA lazy cvTerm which will only fetch metadata when required.Methods in psidev.psi.mi.jami.bridges.ols that return CvTerm Modifier and Type Method Description protected CvTermOlsCvTermFetcher. instantiateCvTerm(String termName, Xref identity, String ontologyName)instantiateCvTerm.Methods in psidev.psi.mi.jami.bridges.ols with parameters of type CvTerm Modifier and Type Method Description TAbstractOlsFetcher. fetchByIdentifier(String termIdentifier, CvTerm ontologyCvTerm)fetchByIdentifier.TCachedOlsFetcher. fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Collection<T>AbstractOlsFetcher. fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Collection<T>CachedOlsFetcher. fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.Set<OntologyTerm>CachedOlsOntologyTermFetcher. fetchRootTerms(CvTerm database)fetchRootTerms.Set<OntologyTerm>OlsOntologyTermFetcher. fetchRootTerms(CvTerm database)fetchRootTerms. -
Uses of CvTerm in psidev.psi.mi.jami.bridges.uniprot
Methods in psidev.psi.mi.jami.bridges.uniprot that return types with arguments of type CvTerm Modifier and Type Method Description Map<uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType,CvTerm>UniprotProteinFetcher. getSelectedDatabases()Getter for the fieldselectedDatabases.Method parameters in psidev.psi.mi.jami.bridges.uniprot with type arguments of type CvTerm Modifier and Type Method Description voidUniprotProteinFetcher. setSelectedDatabases(Map<uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType,CvTerm> selectedDatabases)Setter for the fieldselectedDatabases. -
Uses of CvTerm in psidev.psi.mi.jami.crosslink.extension
Constructors in psidev.psi.mi.jami.crosslink.extension with parameters of type CvTerm Constructor Description CsvBinaryInteractionEvidence(String shortName, CvTerm type)Constructor for CsvBinaryInteractionEvidence.CsvBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for CsvBinaryInteractionEvidence.CsvBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)Constructor for CsvBinaryInteractionEvidence.CsvBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for CsvBinaryInteractionEvidence.CsvBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for CsvBinaryInteractionEvidence.CsvBinaryInteractionEvidence(CvTerm complexExpansion)Constructor for CsvBinaryInteractionEvidence.CsvBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for CsvBinaryInteractionEvidence.CsvExperimentalParticipantPool(String poolName, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(String poolName, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvExperimentalParticipantPool.CsvFeatureEvidence(String shortName, String fullName, CvTerm type)Constructor for CsvFeatureEvidence.CsvFeatureEvidence(CvTerm type)Constructor for CsvFeatureEvidence.CsvFeatureEvidence(ParticipantEvidence participant, String shortName, String fullName, CvTerm type)Constructor for CsvFeatureEvidence.CsvFeatureEvidence(ParticipantEvidence participant, CvTerm type)Constructor for CsvFeatureEvidence.CsvInteractionEvidence(String shortName, CvTerm type)Constructor for CsvInteractionEvidence.CsvInteractionEvidence(String shortName, CvTerm type, Xref imexId)Constructor for CsvInteractionEvidence.CsvInteractionEvidence(Experiment experiment, String shortName, CvTerm type)Constructor for CsvInteractionEvidence.CsvInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)Constructor for CsvInteractionEvidence.CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(Interactor interactor, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvParticipantEvidence(Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for CsvParticipantEvidence.CsvProtein(String name, String fullName, CvTerm type)Constructor for CsvProtein.CsvProtein(String name, String fullName, CvTerm type, Organism organism)Constructor for CsvProtein.CsvProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for CsvProtein.CsvProtein(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for CsvProtein.CsvProtein(String name, CvTerm type)Constructor for CsvProtein.CsvProtein(String name, CvTerm type, Organism organism)Constructor for CsvProtein.CsvProtein(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for CsvProtein.CsvProtein(String name, CvTerm type, Xref uniqueId)Constructor for CsvProtein.CsvXref(CvTerm database, String id)Constructor for CsvXref.CsvXref(CvTerm database, String id, String version)Constructor for CsvXref.CsvXref(CvTerm database, String id, String version, CvTerm qualifier)Constructor for CsvXref.CsvXref(CvTerm database, String id, CvTerm qualifier)Constructor for CsvXref. -
Uses of CvTerm in psidev.psi.mi.jami.crosslink.extension.datasource
Methods in psidev.psi.mi.jami.crosslink.extension.datasource with parameters of type CvTerm Modifier and Type Method Description voidAbstractCsvSource. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.voidAbstractCsvStreamSource. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.voidCsvMixedEvidenceSource. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.voidCsvNaryEvidenceSource. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names. -
Uses of CvTerm in psidev.psi.mi.jami.datasource
Methods in psidev.psi.mi.jami.datasource that return types with arguments of type CvTerm Modifier and Type Method Description Iterator<CvTerm>CvTermStream. getCvTermsIterator()The CV terms iterator for this datasource. -
Uses of CvTerm in psidev.psi.mi.jami.enricher
Classes in psidev.psi.mi.jami.enricher with type parameters of type CvTerm Modifier and Type Interface Description interfaceCvTermEnricher<C extends CvTerm>The CvTerm enricher is an enricher which can enrich either single cvTerm or a collection.Methods in psidev.psi.mi.jami.enricher that return types with arguments of type CvTerm Modifier and Type Method Description CvTermEnricher<CvTerm>ExperimentEnricher. getCvTermEnricher()Gets the subEnricher for CvTerms.CvTermEnricher<CvTerm>FeatureEnricher. getCvTermEnricher()Gets the subEnricher for CvTerms.CvTermEnricher<CvTerm>InteractionEnricher. getCvTermEnricher()Sets the sub enricher for CvTerms.CvTermEnricher<CvTerm>InteractorEnricher. getCvTermEnricher()getCvTermEnricher.CvTermEnricher<CvTerm>OrganismEnricher. getCvTermEnricher()getCvTermEnricher.CvTermEnricher<CvTerm>ParticipantEnricher. getCvTermEnricher()The current CvTerm enricher, If null, CvTerms will not be enriched.Method parameters in psidev.psi.mi.jami.enricher with type arguments of type CvTerm Modifier and Type Method Description voidExperimentEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> cvEnricher)setCvTermEnricher.voidFeatureEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> cvEnricher)setCvTermEnricher.voidInteractionEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> enricher)setCvTermEnricher.voidInteractorEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> enricher)setCvTermEnricher.voidOrganismEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> enricher)setCvTermEnricher.voidParticipantEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> enricher)setCvTermEnricher. -
Uses of CvTerm in psidev.psi.mi.jami.enricher.impl
Methods in psidev.psi.mi.jami.enricher.impl that return types with arguments of type CvTerm Modifier and Type Method Description CvTermEnricher<CvTerm>AbstractInteractorEnricher. getCvTermEnricher()Getter for the fieldcvTermEnricher.CvTermEnricher<CvTerm>CompositeInteractorEnricher. getCvTermEnricher()getCvTermEnricher.CvTermEnricher<CvTerm>CompositeModelledParticipantEnricher. getCvTermEnricher()getCvTermEnricher.CvTermEnricher<CvTerm>CompositeParticipantEnricher. getCvTermEnricher()getCvTermEnricher.CvTermEnricher<CvTerm>CompositeParticipantEvidenceEnricher. getCvTermEnricher()getCvTermEnricher.Method parameters in psidev.psi.mi.jami.enricher.impl with type arguments of type CvTerm Modifier and Type Method Description voidAbstractInteractorEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)setCvTermEnricher.voidCompositeInteractorEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> enricher)setCvTermEnricher.voidCompositeModelledParticipantEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> enricher)setCvTermEnricher.voidCompositeParticipantEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> enricher)setCvTermEnricher.voidCompositeParticipantEvidenceEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> enricher)setCvTermEnricher. -
Uses of CvTerm in psidev.psi.mi.jami.enricher.impl.full
Classes in psidev.psi.mi.jami.enricher.impl.full with type parameters of type CvTerm Modifier and Type Class Description classFullCvTermEnricher<C extends CvTerm>Provides full enrichment of cv term.classFullCvTermUpdater<C extends CvTerm>Provides full update of cv term.Methods in psidev.psi.mi.jami.enricher.impl.full that return types with arguments of type CvTerm Modifier and Type Method Description CvTermEnricher<CvTerm>FullInteractionEvidenceEnricher. getCvTermEnricher()Sets the sub enricher for CvTerms.CvTermEnricher<CvTerm>FullInteractionUpdater. getCvTermEnricher()Sets the sub enricher for CvTerms.CvTermEnricher<CvTerm>FullModelledInteractionEnricher. getCvTermEnricher()Sets the sub enricher for CvTerms.CvTermEnricher<CvTerm>FullOrganismEnricher. getCvTermEnricher()getCvTermEnricher.CvTermEnricher<CvTerm>FullOrganismUpdater. getCvTermEnricher()getCvTermEnricher.CvTermEnricher<CvTerm>FullParticipantEvidenceUpdater. getCvTermEnricher()The current CvTerm enricher, If null, CvTerms will not be enriched.Methods in psidev.psi.mi.jami.enricher.impl.full with parameters of type CvTerm Modifier and Type Method Description voidFullFeatureEvidenceEnricher. onInteractorTypeUpdate(Protein interactor, CvTerm old)Listen to the event where the interactor type has been initialised.voidFullFeatureEvidenceUpdater. onInteractorTypeUpdate(Protein interactor, CvTerm old)Listen to the event where the interactor type has been initialised.voidFullFeatureUpdater. onInteractorTypeUpdate(Protein interactor, CvTerm old)Listen to the event where the interactor type has been initialised.Method parameters in psidev.psi.mi.jami.enricher.impl.full with type arguments of type CvTerm Modifier and Type Method Description protected voidFullParticipantEvidenceEnricher. mergeExperimentalPreparations(P termToEnrich, Collection<CvTerm> toEnrichTerms, Collection<CvTerm> fetchedTerms, boolean remove)mergeExperimentalPreparations.voidFullInteractionUpdater. setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)setCvTermEnricher.voidFullOrganismEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> cvEnricher)setCvTermEnricher.voidFullOrganismUpdater. setCvTermEnricher(CvTermEnricher<CvTerm> cvEnricher)setCvTermEnricher.voidFullParticipantEvidenceUpdater. setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)setCvTermEnricher. -
Uses of CvTerm in psidev.psi.mi.jami.enricher.impl.minimal
Classes in psidev.psi.mi.jami.enricher.impl.minimal with type parameters of type CvTerm Modifier and Type Class Description classMinimalCvTermEnricher<C extends CvTerm>Provides minimal enrichment of cv term.classMinimalCvTermUpdater<C extends CvTerm>Provides minimal update of cv term.Methods in psidev.psi.mi.jami.enricher.impl.minimal that return types with arguments of type CvTerm Modifier and Type Method Description CvTermEnricher<CvTerm>MinimalInteractionEnricher. getCvTermEnricher()Sets the sub enricher for CvTerms.CvTermEnricher<CvTerm>MinimalInteractionEvidenceUpdater. getCvTermEnricher()Sets the sub enricher for CvTerms.CvTermEnricher<CvTerm>MinimalModelledInteractionUpdater. getCvTermEnricher()Sets the sub enricher for CvTerms.CvTermEnricher<CvTerm>MinimalOrganismEnricher. getCvTermEnricher()getCvTermEnricher.CvTermEnricher<CvTerm>MinimalParticipantEnricher. getCvTermEnricher()The current CvTerm enricher, If null, CvTerms will not be enriched.CvTermEnricher<CvTerm>MinimalParticipantEvidenceUpdater. getCvTermEnricher()The current CvTerm enricher, If null, CvTerms will not be enriched.Methods in psidev.psi.mi.jami.enricher.impl.minimal with parameters of type CvTerm Modifier and Type Method Description voidMinimalFeatureEnricher. onInteractorTypeUpdate(Protein interactor, CvTerm old)Listen to the event where the interactor type has been initialised.voidMinimalFeatureEvidenceUpdater. onInteractorTypeUpdate(Protein interactor, CvTerm old)Listen to the event where the interactor type has been initialised.protected voidMinimalFeatureEnricher. processRangeStatus(CvTerm status)processRangeStatus.Method parameters in psidev.psi.mi.jami.enricher.impl.minimal with type arguments of type CvTerm Modifier and Type Method Description protected voidMinimalFeatureEvidenceEnricher. mergeDetectionMethods(FeatureEvidence termToEnrich, Collection<CvTerm> toEnrichTerms, Collection<CvTerm> fetchedTerms, boolean remove)Takes two lists of detection methods and produces a list of those to add and those to remove.protected voidMinimalParticipantEvidenceEnricher. mergeIdentificationMethods(P termToEnrich, Collection<CvTerm> toEnrichTerms, Collection<CvTerm> fetchedTerms, boolean remove)mergeIdentificationMethods.voidMinimalInteractionEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)setCvTermEnricher.voidMinimalInteractionEvidenceUpdater. setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)setCvTermEnricher.voidMinimalModelledInteractionUpdater. setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)setCvTermEnricher.voidMinimalOrganismEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> enricher)setCvTermEnricher.voidMinimalParticipantEnricher. setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)setCvTermEnricher.voidMinimalParticipantEvidenceUpdater. setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)setCvTermEnricher. -
Uses of CvTerm in psidev.psi.mi.jami.enricher.listener
Classes in psidev.psi.mi.jami.enricher.listener with type parameters of type CvTerm Modifier and Type Interface Description interfaceCvTermEnricherListener<C extends CvTerm>An extension of the CvTermChangeListener with specific methods related to the process of enriching. -
Uses of CvTerm in psidev.psi.mi.jami.enricher.listener.impl
Classes in psidev.psi.mi.jami.enricher.listener.impl with type parameters of type CvTerm Modifier and Type Class Description classCvTermEnricherListenerManager<C extends CvTerm>A manager for listeners which holds a list of listeners.Methods in psidev.psi.mi.jami.enricher.listener.impl with parameters of type CvTerm Modifier and Type Method Description voidCvTermEnricherListenerManager. onAddedAlias(CvTerm cv, Alias added)Listen to the event where an alias has been added to the object aliases.voidCvTermEnricherListenerManager. onAddedAnnotation(CvTerm o, Annotation added)Listen to the event where an annotation has been added to the object annotations.voidFeatureEvidenceEnricherListenerManager. onAddedDetectionMethod(FeatureEvidence feature, CvTerm added)onAddedDetectionMethodvoidParticipantEvidenceEnricherListenerManager. onAddedExperimentalPreparation(P participant, CvTerm added)onAddedExperimentalPreparationvoidParticipantEvidenceEnricherListenerManager. onAddedIdentificationMethod(P participant, CvTerm added)onAddedIdentificationMethodvoidCvTermEnricherListenerManager. onAddedIdentifier(CvTerm cv, Xref added)Listen to the event where an identifier has been added to the protein identifiers.voidCvTermEnricherListenerManager. onAddedXref(CvTerm cv, Xref added)Listen to the event where a xref has been added to the protein xrefs.voidParticipantEnricherListenerManager. onBiologicalRoleUpdate(P participant, CvTerm oldType)onBiologicalRoleUpdatevoidOrganismEnricherListenerManager. onCellTypeUpdate(Organism organism, CvTerm oldType)Listen to the event where the cell type has been initialised.voidOrganismEnricherListenerManager. onCompartmentUpdate(Organism organism, CvTerm oldType)Listen to the event where the organism compartment has been initialised.voidModelledInteractionEnricherListenerManager. onEvidenceTypeUpdate(I interaction, CvTerm oldType)onEvidenceTypeUpdatevoidParticipantEvidenceEnricherListenerManager. onExperimentalRoleUpdate(P participant, CvTerm oldType)onExperimentalRoleUpdatevoidCvTermEnricherListenerManager. onFullNameUpdate(CvTerm cv, String oldFullName)Listen to the event where the fullName of a cv term has been changed.voidExperimentEnricherListenerManager. onInteractionDetectionMethodUpdate(Experiment experiment, CvTerm oldCv)onInteractionDetectionMethodUpdatevoidInteractionEnricherListenerManager. onInteractionTypeUpdate(I interaction, CvTerm oldType)onInteractionTypeUpdatevoidComplexEnricherListenerManager. onInteractorTypeUpdate(Complex interactor, CvTerm oldType)Listen to the event where the interactor type has been initialised.voidInteractorEnricherListenerManager. onInteractorTypeUpdate(T interactor, CvTerm old)Listen to the event where the interactor type has been initialised.voidCvTermEnricherListenerManager. onMIIdentifierUpdate(CvTerm cv, String oldMI)Listen to the event where the MI identifier of a cv term has been changed.voidCvTermEnricherListenerManager. onMODIdentifierUpdate(CvTerm cv, String oldMOD)Listen to the event where the MOD identifier of a cv term has been changed.voidCvTermEnricherListenerManager. onPARIdentifierUpdate(CvTerm cv, String oldPAR)Listen to the event where the PAR identifier of a cv term has been changed.voidCvTermEnricherListenerManager. onRemovedAlias(CvTerm o, Alias removed)Listen to the event where an alias has been removed from the object aliases.voidCvTermEnricherListenerManager. onRemovedAnnotation(CvTerm o, Annotation removed)Listen to the event where an annotation has been removed from the object annotations.voidFeatureEvidenceEnricherListenerManager. onRemovedDetectionMethod(FeatureEvidence feature, CvTerm removed)onRemovedDetectionMethodvoidParticipantEvidenceEnricherListenerManager. onRemovedExperimentalPreparation(P participant, CvTerm removed)onRemovedExperimentalPreparationvoidParticipantEvidenceEnricherListenerManager. onRemovedIdentificationMethod(P participant, CvTerm removed)onRemovedIdentificationMethodvoidCvTermEnricherListenerManager. onRemovedIdentifier(CvTerm cv, Xref removed)Listen to the event where an identifier has been removed from the protein identifiers.voidCvTermEnricherListenerManager. onRemovedXref(CvTerm cv, Xref removed)Listen to the event where a xref has been removed from the interactor xrefs.voidFeatureEnricherListenerManager. onRoleUpdate(T feature, CvTerm oldDependency)onRoleUpdatevoidCvTermEnricherListenerManager. onShortNameUpdate(CvTerm cv, String oldShortName)Listen to the event where the shortName of a cv term has been changed.voidOrganismEnricherListenerManager. onTissueUpdate(Organism organism, CvTerm oldType)Listen to the event where the organism tissue has been initialised.voidExperimentalParticipantPoolEnricherListenerManager. onTypeUpdate(ExperimentalParticipantPool participant, CvTerm oldType)onTypeUpdatevoidFeatureEnricherListenerManager. onTypeUpdate(T feature, CvTerm oldType)onTypeUpdatevoidParticipantPoolEnricherListenerManager. onTypeUpdate(P participant, CvTerm oldType)onTypeUpdate -
Uses of CvTerm in psidev.psi.mi.jami.enricher.listener.impl.log
Methods in psidev.psi.mi.jami.enricher.listener.impl.log with parameters of type CvTerm Modifier and Type Method Description voidCvTermEnricherLogger. onEnrichmentComplete(CvTerm cvTerm, EnrichmentStatus status, String message)onEnrichmentComplete.voidCvTermEnricherLogger. onEnrichmentError(CvTerm object, String message, Exception e)onEnrichmentError.voidExperimentalParticipantPoolEnricherLogger. onTypeUpdate(ExperimentalParticipantPool entity, CvTerm oldTerm)onTypeUpdate -
Uses of CvTerm in psidev.psi.mi.jami.enricher.listener.impl.writer
Classes in psidev.psi.mi.jami.enricher.listener.impl.writer with type parameters of type CvTerm Modifier and Type Class Description classCvTermEnricherStatisticsWriter<C extends CvTerm>A statistics logger which records changes made by the enricher.Methods in psidev.psi.mi.jami.enricher.listener.impl.writer with parameters of type CvTerm Modifier and Type Method Description voidCvTermEnricherStatisticsWriter. onAddedAlias(CvTerm cv, Alias added)Listen to the event where an alias has been added to the object aliases.voidCvTermEnricherStatisticsWriter. onAddedAnnotation(CvTerm o, Annotation added)Listen to the event where an annotation has been added to the object annotations.voidFeatureEvidenceEnricherStatisticsWriter. onAddedDetectionMethod(FeatureEvidence feature, CvTerm added)onAddedDetectionMethodvoidParticipantEvidenceEnricherStatisticsWriter. onAddedExperimentalPreparation(P participant, CvTerm added)onAddedExperimentalPreparationvoidParticipantEvidenceEnricherStatisticsWriter. onAddedIdentificationMethod(P participant, CvTerm added)onAddedIdentificationMethodvoidCvTermEnricherStatisticsWriter. onAddedIdentifier(CvTerm cv, Xref added)Listen to the event where an identifier has been added to the protein identifiers.voidCvTermEnricherStatisticsWriter. onAddedXref(CvTerm cv, Xref added)Listen to the event where a xref has been added to the protein xrefs.voidParticipantEnricherStatisticsWriter. onBiologicalRoleUpdate(P participant, CvTerm oldType)onBiologicalRoleUpdatevoidOrganismEnricherStatisticsWriter. onCellTypeUpdate(Organism organism, CvTerm oldType)Listen to the event where the cell type has been initialised.voidOrganismEnricherStatisticsWriter. onCompartmentUpdate(Organism organism, CvTerm oldType)Listen to the event where the organism compartment has been initialised.voidModelledInteractionEnricherStatisticsWriter. onEvidenceTypeUpdate(I interaction, CvTerm oldType)onEvidenceTypeUpdatevoidParticipantEvidenceEnricherStatisticsWriter. onExperimentalRoleUpdate(P participant, CvTerm oldType)onExperimentalRoleUpdatevoidCvTermEnricherStatisticsWriter. onFullNameUpdate(CvTerm cv, String oldFullName)Listen to the event where the fullName of a cv term has been changed.voidExperimentEnricherStatisticsWriter. onInteractionDetectionMethodUpdate(Experiment experiment, CvTerm oldCv)onInteractionDetectionMethodUpdatevoidInteractionEnricherStatisticsWriter. onInteractionTypeUpdate(I interaction, CvTerm oldType)onInteractionTypeUpdatevoidComplexEnricherStatisticsWriter. onInteractorTypeUpdate(Complex interactor, CvTerm oldType)Listen to the event where the interactor type has been initialised.voidInteractorEnricherStatisticsWriter. onInteractorTypeUpdate(T interactor, CvTerm old)Listen to the event where the interactor type has been initialised.voidCvTermEnricherStatisticsWriter. onMIIdentifierUpdate(CvTerm cv, String oldMI)Listen to the event where the MI identifier of a cv term has been changed.voidCvTermEnricherStatisticsWriter. onMODIdentifierUpdate(CvTerm cv, String oldMOD)Listen to the event where the MOD identifier of a cv term has been changed.voidCvTermEnricherStatisticsWriter. onPARIdentifierUpdate(CvTerm cv, String oldPAR)Listen to the event where the PAR identifier of a cv term has been changed.voidCvTermEnricherStatisticsWriter. onRemovedAlias(CvTerm cv, Alias removed)Listen to the event where an alias has been removed from the object aliases.voidCvTermEnricherStatisticsWriter. onRemovedAnnotation(CvTerm o, Annotation removed)Listen to the event where an annotation has been removed from the object annotations.voidFeatureEvidenceEnricherStatisticsWriter. onRemovedDetectionMethod(FeatureEvidence feature, CvTerm removed)onRemovedDetectionMethodvoidParticipantEvidenceEnricherStatisticsWriter. onRemovedExperimentalPreparation(P participant, CvTerm removed)onRemovedExperimentalPreparationvoidParticipantEvidenceEnricherStatisticsWriter. onRemovedIdentificationMethod(P participant, CvTerm removed)onRemovedIdentificationMethodvoidCvTermEnricherStatisticsWriter. onRemovedIdentifier(CvTerm cv, Xref removed)Listen to the event where an identifier has been removed from the protein identifiers.voidCvTermEnricherStatisticsWriter. onRemovedXref(CvTerm cv, Xref removed)Listen to the event where a xref has been removed from the interactor xrefs.voidFeatureEnricherStatisticsWriter. onRoleUpdate(T feature, CvTerm oldRole)onRoleUpdatevoidCvTermEnricherStatisticsWriter. onShortNameUpdate(CvTerm cv, String oldShortName)Listen to the event where the shortName of a cv term has been changed.voidOrganismEnricherStatisticsWriter. onTissueUpdate(Organism organism, CvTerm oldType)Listen to the event where the organism tissue has been initialised.voidExperimentalParticipantPoolEnricherStatisticsWriter. onTypeUpdate(ExperimentalParticipantPool participant, CvTerm oldType)onTypeUpdatevoidFeatureEnricherStatisticsWriter. onTypeUpdate(T feature, CvTerm oldType)onTypeUpdatevoidParticipantPoolEnricherStatisticsWriter. onTypeUpdate(P participant, CvTerm oldType)onTypeUpdate -
Uses of CvTerm in psidev.psi.mi.jami.factory
Methods in psidev.psi.mi.jami.factory with parameters of type CvTerm Modifier and Type Method Description BinaryInteractionBinaryInteractionFactory. createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)Create a new BinaryInteraction object from an Interaction parent and two participantsBinaryInteractionDefaultBinaryInteractionFactory. createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)Create a new BinaryInteraction object from an Interaction parent and two participantsBinaryInteractionEvidenceBinaryInteractionFactory. createBinaryInteractionEvidenceFrom(InteractionEvidence interaction, ParticipantEvidence p1, ParticipantEvidence p2, CvTerm expansionMethod)Create a new BinaryInteractionEvidence object from an InteractionEvidence parent and two participants evidencesBinaryInteractionEvidenceDefaultBinaryInteractionFactory. createBinaryInteractionEvidenceFrom(InteractionEvidence interaction, ParticipantEvidence p1, ParticipantEvidence p2, CvTerm expansionMethod)Create a new BinaryInteractionEvidence object from an InteractionEvidence parent and two participants evidencesBioactiveEntityDefaultInteractorFactory. createBioactiveEntity(String name, CvTerm type)Creates a new BioactiveEntity with the name and interactor typeBioactiveEntityInteractorFactory. createBioactiveEntity(String name, CvTerm type)Creates a new BioactiveEntity with the name and interactor typeComplexDefaultInteractorFactory. createComplex(String name, CvTerm type)Creates a new Complex with the name and interactor typeComplexInteractorFactory. createComplex(String name, CvTerm type)Creates a new Complex with the name and interactor typeInteractorDefaultInteractorFactory. createInteractor(String name, CvTerm type)Creates a default interactor from the name and interactor typeInteractorInteractorFactory. createInteractor(String name, CvTerm type)Creates a default interactor from the name and interactor typeInteractorDefaultInteractorFactory. createInteractorFromDatabase(CvTerm database, String name)Return the proper instance of the interactor if the database is recognized.InteractorInteractorFactory. createInteractorFromDatabase(CvTerm database, String name)Return the proper instance of the interactor if the database is recognized.InteractorDefaultInteractorFactory. createInteractorFromInteractorType(CvTerm type, String name)Return the proper instance of the interactor if the type is recognized and not null.InteractorInteractorFactory. createInteractorFromInteractorType(CvTerm type, String name)Return the proper instance of the interactor if the type is recognized and not null.protected InteractorDefaultInteractorFactory. createInteractorFromRecognizedCategory(InteractorCategory category, String name, CvTerm type)Creates an interactor from a given category (should be the canonical name of an Interactor interface)InteractorPoolDefaultInteractorFactory. createInteractorSet(String name, CvTerm type)Creates an interactor pool from the name and interactor typeInteractorPoolInteractorFactory. createInteractorSet(String name, CvTerm type)Creates an interactor pool from the name and interactor typeModelledBinaryInteractionBinaryInteractionFactory. createModelledBinaryInteractionFrom(ModelledInteraction interaction, ModelledParticipant p1, ModelledParticipant p2, CvTerm expansionMethod)Create a new ModelledBinaryInteraction object from a ModelledInteraction parent and two modelled participantsModelledBinaryInteractionDefaultBinaryInteractionFactory. createModelledBinaryInteractionFrom(ModelledInteraction interaction, ModelledParticipant p1, ModelledParticipant p2, CvTerm expansionMethod)Create a new ModelledBinaryInteraction object from a ModelledInteraction parent and two modelled participantsNucleicAcidDefaultInteractorFactory. createNucleicAcid(String name, CvTerm type)Creates a new NucleicAcid with the name and interactor typeNucleicAcidInteractorFactory. createNucleicAcid(String name, CvTerm type)Creates a new NucleicAcid with the name and interactor typePolymerDefaultInteractorFactory. createPolymer(String name, CvTerm type)Creates a new Polymer with the name and interactor typePolymerInteractorFactory. createPolymer(String name, CvTerm type)Creates a new Polymer with the name and interactor typeProteinDefaultInteractorFactory. createProtein(String name, CvTerm type)Creates a new Protein with the name and interactor typeProteinInteractorFactory. createProtein(String name, CvTerm type)Creates a new Protein with the name and interactor type -
Uses of CvTerm in psidev.psi.mi.jami.html
Methods in psidev.psi.mi.jami.html with parameters of type CvTerm Modifier and Type Method Description protected voidAbstractMIHtmlWriter. writeCvTerm(String label, CvTerm term)writeCvTerm -
Uses of CvTerm in psidev.psi.mi.jami.json.elements
Methods in psidev.psi.mi.jami.json.elements that return types with arguments of type CvTerm Modifier and Type Method Description JsonElementWriter<CvTerm>SimpleJsonExperimentWriter. getCvWriter()Getter for the fieldcvWriter.JsonElementWriter<CvTerm>SimpleJsonFeatureWriter. getCvWriter()Getter for the fieldcvWriter.JsonElementWriter<CvTerm>SimpleJsonHostOrganismWriter. getCvWriter()Getter for the fieldcvWriter.JsonElementWriter<CvTerm>SimpleJsonInteractionWriter. getCvWriter()Getter for the fieldcvWriter.JsonElementWriter<CvTerm>SimpleJsonInteractorWriter. getCvWriter()Getter for the fieldcvWriter.JsonElementWriter<CvTerm>SimpleJsonParticipantWriter. getCvWriter()Getter for the fieldcvWriter.JsonElementWriter<CvTerm>SimpleJsonPublicationWriter. getCvWriter()Getter for the fieldcvWriter.Methods in psidev.psi.mi.jami.json.elements with parameters of type CvTerm Modifier and Type Method Description voidSimpleJsonCvTermWriter. write(CvTerm object)write.protected voidSimpleJsonInteractionWriter. writeExpansionMethod(CvTerm expansion)writeExpansionMethod.Method parameters in psidev.psi.mi.jami.json.elements with type arguments of type CvTerm Modifier and Type Method Description voidSimpleJsonExperimentWriter. setCvWriter(JsonElementWriter<CvTerm> cvWriter)Setter for the fieldcvWriter.voidSimpleJsonFeatureWriter. setCvWriter(JsonElementWriter<CvTerm> cvWriter)Setter for the fieldcvWriter.voidSimpleJsonHostOrganismWriter. setCvWriter(JsonElementWriter<CvTerm> cvWriter)Setter for the fieldcvWriter.voidSimpleJsonInteractionWriter. setCvWriter(JsonElementWriter<CvTerm> cvWriter)Setter for the fieldcvWriter.voidSimpleJsonInteractorWriter. setCvWriter(JsonElementWriter<CvTerm> cvWriter)Setter for the fieldcvWriter.voidSimpleJsonParticipantWriter. setCvWriter(JsonElementWriter<CvTerm> cvWriter)Setter for the fieldcvWriter.voidSimpleJsonPublicationWriter. setCvWriter(JsonElementWriter<CvTerm> cvWriter)Setter for the fieldcvWriter. -
Uses of CvTerm in psidev.psi.mi.jami.listener
Methods in psidev.psi.mi.jami.listener with parameters of type CvTerm Modifier and Type Method Description voidFeatureEvidenceChangeListener. onAddedDetectionMethod(FeatureEvidence feature, CvTerm added)onAddedDetectionMethodvoidParticipantEvidenceChangeListener. onAddedExperimentalPreparation(F participant, CvTerm added)onAddedExperimentalPreparationvoidParticipantEvidenceChangeListener. onAddedIdentificationMethod(F participant, CvTerm added)onAddedIdentificationMethodvoidParticipantChangeListener. onBiologicalRoleUpdate(F participant, CvTerm oldType)onBiologicalRoleUpdatevoidOrganismChangeListener. onCellTypeUpdate(Organism organism, CvTerm oldType)Listen to the event where the cell type has been initialised.voidOrganismChangeListener. onCompartmentUpdate(Organism organism, CvTerm oldType)Listen to the event where the organism compartment has been initialised.voidModelledInteractionChangeListener. onEvidenceTypeUpdate(I interaction, CvTerm oldType)onEvidenceTypeUpdatevoidParticipantEvidenceChangeListener. onExperimentalRoleUpdate(F participant, CvTerm oldType)onExperimentalRoleUpdatevoidCvTermChangeListener. onFullNameUpdate(CvTerm cv, String oldFullName)Listen to the event where the fullName of a cv term has been changed.voidExperimentChangeListener. onInteractionDetectionMethodUpdate(Experiment experiment, CvTerm oldCv)onInteractionDetectionMethodUpdatevoidInteractionChangeListener. onInteractionTypeUpdate(I interaction, CvTerm oldType)onInteractionTypeUpdatevoidInteractorChangeListener. onInteractorTypeUpdate(T interactor, CvTerm oldType)Listen to the event where the interactor type has been initialised.voidCvTermChangeListener. onMIIdentifierUpdate(CvTerm cv, String oldMI)Listen to the event where the MI identifier of a cv term has been changed.voidMIFileParserListener. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.voidCvTermChangeListener. onMODIdentifierUpdate(CvTerm cv, String oldMOD)Listen to the event where the MOD identifier of a cv term has been changed.voidCvTermChangeListener. onPARIdentifierUpdate(CvTerm cv, String oldPAR)Listen to the event where the PAR identifier of a cv term has been changed.voidFeatureEvidenceChangeListener. onRemovedDetectionMethod(FeatureEvidence feature, CvTerm removed)onRemovedDetectionMethodvoidParticipantEvidenceChangeListener. onRemovedExperimentalPreparation(F participant, CvTerm removed)onRemovedExperimentalPreparationvoidParticipantEvidenceChangeListener. onRemovedIdentificationMethod(F participant, CvTerm removed)onRemovedIdentificationMethodvoidFeatureChangeListener. onRoleUpdate(F feature, CvTerm oldRole)onRoleUpdatevoidCvTermChangeListener. onShortNameUpdate(CvTerm cv, String oldShortName)Listen to the event where the shortName of a cv term has been changed.voidOrganismChangeListener. onTissueUpdate(Organism organism, CvTerm oldType)Listen to the event where the organism tissue has been initialised.voidFeatureChangeListener. onTypeUpdate(F feature, CvTerm oldType)onTypeUpdatevoidParticipantPoolChangeListener. onTypeUpdate(F participant, CvTerm oldType)onTypeUpdate -
Uses of CvTerm in psidev.psi.mi.jami.listener.impl
Methods in psidev.psi.mi.jami.listener.impl with parameters of type CvTerm Modifier and Type Method Description voidCvTermChangeLogger. onAddedAlias(CvTerm cv, Alias added)Listen to the event where an alias has been added to the object aliases.voidCvTermChangeLogger. onAddedAnnotation(CvTerm cv, Annotation added)Listen to the event where an annotation has been added to the object annotations.voidFeatureEvidenceChangeLogger. onAddedDetectionMethod(FeatureEvidence feature, CvTerm added)onAddedDetectionMethodvoidParticipantEvidenceChangeLogger. onAddedExperimentalPreparation(T entity, CvTerm added)onAddedExperimentalPreparationvoidParticipantEvidenceChangeLogger. onAddedIdentificationMethod(T entity, CvTerm added)onAddedIdentificationMethodvoidCvTermChangeLogger. onAddedIdentifier(CvTerm cv, Xref added)Listen to the event where an identifier has been added to the protein identifiers.voidCvTermChangeLogger. onAddedXref(CvTerm cv, Xref added)Listen to the event where a xref has been added to the protein xrefs.voidParticipantChangeLogger. onBiologicalRoleUpdate(T entity, CvTerm oldTerm)onBiologicalRoleUpdatevoidOrganismChangeLogger. onCellTypeUpdate(Organism organism, CvTerm oldType)Listen to the event where the cell type has been initialised.voidOrganismChangeLogger. onCompartmentUpdate(Organism organism, CvTerm oldType)Listen to the event where the organism compartment has been initialised.voidComplexChangeLogger. onEvidenceTypeUpdate(Complex interaction, CvTerm oldType)onEvidenceTypeUpdatevoidModelledInteractionChangeLogger. onEvidenceTypeUpdate(I interaction, CvTerm oldType)onEvidenceTypeUpdatevoidParticipantEvidenceChangeLogger. onExperimentalRoleUpdate(T entity, CvTerm oldTerm)onExperimentalRoleUpdatevoidCvTermChangeLogger. onFullNameUpdate(CvTerm cv, String oldFullName)Listen to the event where the fullName of a cv term has been changed.voidExperimentChangeLogger. onInteractionDetectionMethodUpdate(Experiment experiment, CvTerm oldCv)onInteractionDetectionMethodUpdatevoidComplexChangeLogger. onInteractionTypeUpdate(Complex interaction, CvTerm oldType)onInteractionTypeUpdatevoidInteractionChangeLogger. onInteractionTypeUpdate(T interaction, CvTerm old)onInteractionTypeUpdatevoidInteractorChangeLogger. onInteractorTypeUpdate(T protein, CvTerm old)Listen to the event where the interactor type has been initialised.voidCvTermChangeLogger. onMIIdentifierUpdate(CvTerm cv, String oldMI)Listen to the event where the MI identifier of a cv term has been changed.voidMIFileParserCompositeListener. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.voidMIFileParserLogger. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.voidCvTermChangeLogger. onMODIdentifierUpdate(CvTerm cv, String oldMOD)Listen to the event where the MOD identifier of a cv term has been changed.voidCvTermChangeLogger. onPARIdentifierUpdate(CvTerm cv, String oldPAR)Listen to the event where the PAR identifier of a cv term has been changed.voidCvTermChangeLogger. onRemovedAlias(CvTerm cv, Alias removed)Listen to the event where an alias has been removed from the object aliases.voidCvTermChangeLogger. onRemovedAnnotation(CvTerm cv, Annotation removed)Listen to the event where an annotation has been removed from the object annotations.voidFeatureEvidenceChangeLogger. onRemovedDetectionMethod(FeatureEvidence feature, CvTerm removed)onRemovedDetectionMethodvoidParticipantEvidenceChangeLogger. onRemovedExperimentalPreparation(T entity, CvTerm removed)onRemovedExperimentalPreparationvoidParticipantEvidenceChangeLogger. onRemovedIdentificationMethod(T entity, CvTerm removed)onRemovedIdentificationMethodvoidCvTermChangeLogger. onRemovedIdentifier(CvTerm cv, Xref removed)Listen to the event where an identifier has been removed from the protein identifiers.voidCvTermChangeLogger. onRemovedXref(CvTerm cv, Xref removed)Listen to the event where a xref has been removed from the interactor xrefs.voidFeatureChangeLogger. onRoleUpdate(T protein, CvTerm oldRole)onRoleUpdatevoidCvTermChangeLogger. onShortNameUpdate(CvTerm cv, String oldShortName)Listen to the event where the shortName of a cv term has been changed.voidOrganismChangeLogger. onTissueUpdate(Organism organism, CvTerm oldType)Listen to the event where the organism tissue has been initialised.voidExperimentalParticipantPoolChangeLogger. onTypeUpdate(ExperimentalParticipantPool entity, CvTerm oldTerm)onTypeUpdatevoidFeatureChangeLogger. onTypeUpdate(T protein, CvTerm old)onTypeUpdatevoidParticipantPoolChangeLogger. onTypeUpdate(T entity, CvTerm oldTerm)onTypeUpdate -
Uses of CvTerm in psidev.psi.mi.jami.model
Subinterfaces of CvTerm in psidev.psi.mi.jami.model Modifier and Type Interface Description interfaceOntologyTermOntology term with definition, parents and childreninterfaceSourceSource of the data.Methods in psidev.psi.mi.jami.model with type parameters of type CvTerm Modifier and Type Method Description <C extends CvTerm>
Collection<C>FeatureEvidence. getDetectionMethods()The collection of feature detection methods.<T extends CvTerm>
Collection<T>CooperativityEvidence. getEvidenceMethods()The collection of methods used to infer the cooperative effect.<C extends CvTerm>
Collection<C>ParticipantEvidence. getExperimentalPreparations()The experimental preparations for this participant.<C extends CvTerm>
Collection<C>ParticipantEvidence. getIdentificationMethods()The identification methods for this participant.Methods in psidev.psi.mi.jami.model that return CvTerm Modifier and Type Method Description CvTermAllostery. getAllostericMechanism()The process that mediates the allosteric response of a molecule upon allosteric post-translational modification or binding of an allosteric effector.CvTermAllostery. getAllosteryType()The allosteric type indicates the chemical relationship between the two ligands whose binding is allosterically coupled.CvTermParticipant. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermParticipant. getBiologicalRole()The biological role of the participant.CvTermOrganism. getCellType()Cell type of the organism.CvTermOrganism. getCompartment()The subcellular compartment of the organism.CvTermXref. getDatabase()The database is a controlled vocabulary term.CvTermModelledInteraction. getEvidenceType()The evidence type for this modelled interactions.CvTermParticipantEvidence. getExperimentalRole()The experimental role of the participant.CvTermExperiment. getInteractionDetectionMethod()The experimental method to determine the interaction.CvTermInteraction. getInteractionType()The interaction type is a controlled vocabulary term.CvTermInteractor. getInteractorType()The molecule type of this interactor.CvTermChecksum. getMethod()The method is a controlled vocabulary term and cannot be null Ex: ROGID, CROGID, RIGID, CRC64, ...CvTermCooperativeEffect. getOutCome()For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e.CvTermXref. getQualifier()The qualifier of the xref is the reference type and is a controlled vocabulary term.CvTermCausalRelationship. getRelationType()The relation type with the participant target.CvTermCooperativeEffect. getResponse()This term describes the cooperative effect on the interactions.CvTermFeature. getRole()The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature.CvTermPosition. getStatus()The range status is a controlled vocabulary term which cannot be null.CvTermOrganism. getTissue()The source tissue.CvTermAnnotation. getTopic()The annotation topic is a controlled vocabulary term and it cannot be null.CvTermAlias. getType()The alias type is a controlled vocabulary term.CvTermConfidence. getType()Method used to compute the confidence value.CvTermFeature. getType()The type for this feature.CvTermParameter. getType()The parameter type is a controlled vocabulary term and it cannot be null.CvTermParticipantPool. getType()The pool type of this participant pool.CvTermParameter. getUnit()Unit of the parameter is a controlled vocabulary term.CvTermVariableParameter. getUnit()The unit of the variableParameter if relevant.Methods in psidev.psi.mi.jami.model with parameters of type CvTerm Modifier and Type Method Description voidAllostery. setAllostericMechanism(CvTerm mechanism)Sets the allosteric mechanism.voidAllostery. setAllosteryType(CvTerm type)Sets the allostery type.voidParticipant. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidParticipant. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidOrganism. setCellType(CvTerm cellType)Sets the cell typevoidOrganism. setCompartment(CvTerm compartment)Sets the compartment.voidModelledInteraction. setEvidenceType(CvTerm eco)Sets the evidence typevoidParticipantEvidence. setExperimentalRole(CvTerm expRole)Sets the experimental role.voidExperiment. setInteractionDetectionMethod(CvTerm term)Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).voidInteraction. setInteractionType(CvTerm term)Sets the interaction type.voidInteractor. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidCooperativeEffect. setOutCome(CvTerm effect)Sets the cooperative effect outcomevoidCooperativeEffect. setResponse(CvTerm response)Sets the response.voidFeature. setRole(CvTerm role)Sets the interaction effect/role for this feature.voidOrganism. setTissue(CvTerm tissue)Sets the tissuevoidFeature. setType(CvTerm type)Sets the feature type.voidParticipantPool. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidVariableParameter. setUnit(CvTerm unit)Sets the unit of this variableParameter. -
Uses of CvTerm in psidev.psi.mi.jami.model.impl
Classes in psidev.psi.mi.jami.model.impl that implement CvTerm Modifier and Type Class Description classDefaultCvTermDefault implementation for CvTerm Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousCvTermComparatorclassDefaultOntologyTermDefault implementation for ontology term Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousCvTermComparatorclassDefaultSourceDefault implementation for Source Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousCvTermComparatorMethods in psidev.psi.mi.jami.model.impl that return CvTerm Modifier and Type Method Description CvTermDefaultAllostery. getAllostericMechanism()Getter for the fieldallostericMechanism.CvTermDefaultAllostery. getAllosteryType()Getter for the fieldallosteryType.CvTermAbstractParticipant. getBiologicalEffect()Getter for the fieldbiologicalEffect.CvTermAbstractParticipant. getBiologicalRole()Getter for the fieldbiologicalRole.CvTermDefaultOrganism. getCellType()Getter for the fieldcellType.CvTermDefaultOrganism. getCompartment()Getter for the fieldcompartment.CvTermDefaultXref. getDatabase()Getter for the fielddatabase.CvTermDefaultComplex. getEvidenceType()Getter for the fieldevidenceType.CvTermDefaultModelledInteraction. getEvidenceType()Getter for the fieldevidenceType.CvTermDefaultExperimentalParticipantPool. getExperimentalRole()Getter for the fieldexperimentalRole.CvTermDefaultParticipantEvidence. getExperimentalRole()Getter for the fieldexperimentalRole.CvTermDefaultExperiment. getInteractionDetectionMethod()Getter for the fieldinteractionDetectionMethod.CvTermAbstractInteraction. getInteractionType()Getter for the fieldinteractionType.CvTermDefaultComplex. getInteractionType()Getter for the fieldinteractionType.CvTermDefaultInteractor. getInteractorType()Getter for the fieldinteractorType.CvTermDefaultChecksum. getMethod()Getter for the fieldmethod.CvTermDefaultCooperativeEffect. getOutCome()getOutComeCvTermDefaultXref. getQualifier()Getter for the fieldqualifier.CvTermDefaultCausalRelationship. getRelationType()Getter for the fieldrelationType.CvTermDefaultCooperativeEffect. getResponse()Getter for the fieldresponse.CvTermAbstractFeature. getRole()Getter for the fieldrole.CvTermDefaultPosition. getStatus()Getter for the fieldstatus.CvTermDefaultOrganism. getTissue()Getter for the fieldtissue.CvTermDefaultAnnotation. getTopic()Getter for the fieldtopic.CvTermAbstractFeature. getType()Getter for the fieldtype.CvTermAbstractParticipantPool. getType()Getter for the fieldtype.CvTermDefaultAlias. getType()Getter for the fieldtype.CvTermDefaultConfidence. getType()Getter for the fieldtype.CvTermDefaultParameter. getType()Getter for the fieldtype.CvTermDefaultParameter. getUnit()Getter for the fieldunit.CvTermDefaultVariableParameter. getUnit()Getter for the fieldunit.Methods in psidev.psi.mi.jami.model.impl that return types with arguments of type CvTerm Modifier and Type Method Description Collection<CvTerm>DefaultFeatureEvidence. getDetectionMethods()Getter for the fielddetectionMethods.Collection<CvTerm>DefaultCooperativityEvidence. getEvidenceMethods()Getter for the fieldevidenceMethods.Collection<CvTerm>DefaultExperimentalParticipantPool. getExperimentalPreparations()Getter for the fieldexperimentalPreparations.Collection<CvTerm>DefaultParticipantEvidence. getExperimentalPreparations()Getter for the fieldexperimentalPreparations.Collection<CvTerm>DefaultExperimentalParticipantPool. getIdentificationMethods()Getter for the fieldidentificationMethods.Collection<CvTerm>DefaultParticipantEvidence. getIdentificationMethods()Getter for the fieldidentificationMethods.Methods in psidev.psi.mi.jami.model.impl with parameters of type CvTerm Modifier and Type Method Description voidDefaultAllostery. setAllostericMechanism(CvTerm mechanism)Sets the allosteric mechanism.voidDefaultAllostery. setAllosteryType(CvTerm type)Sets the allostery type.voidAbstractParticipant. setBiologicalEffect(CvTerm biologicalEffect)setBiologicalEffectvoidAbstractParticipant. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidDefaultOrganism. setCellType(CvTerm cellType)Sets the cell typevoidDefaultOrganism. setCompartment(CvTerm compartment)Sets the compartment.voidDefaultComplex. setEvidenceType(CvTerm eco)Sets the evidence typevoidDefaultModelledInteraction. setEvidenceType(CvTerm eco)Sets the evidence typevoidDefaultExperimentalParticipantPool. setExperimentalRole(CvTerm expRole)Sets the experimental role.voidDefaultParticipantEvidence. setExperimentalRole(CvTerm expRole)Sets the experimental role.voidDefaultExperiment. setInteractionDetectionMethod(CvTerm term)Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).voidAbstractInteraction. setInteractionType(CvTerm term)Sets the interaction type.voidDefaultComplex. setInteractionType(CvTerm term)Sets the interaction type.voidDefaultBioactiveEntity. setInteractorType(CvTerm interactorType)Sets the interactor type of this bioactive entity.voidDefaultComplex. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidDefaultGene. setInteractorType(CvTerm type)voidDefaultInteractor. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidDefaultInteractorPool. setInteractorType(CvTerm type)voidDefaultNucleicAcid. setInteractorType(CvTerm interactorType)Sets the interactor type of this NucleicAcid.voidDefaultPolymer. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidDefaultProtein. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidDefaultCooperativeEffect. setOutCome(CvTerm effect)Sets the cooperative effect outcomevoidDefaultCooperativeEffect. setResponse(CvTerm response)Sets the response.voidAbstractFeature. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidDefaultOrganism. setTissue(CvTerm tissue)Sets the tissuevoidAbstractFeature. setType(CvTerm type)Sets the feature type.voidAbstractParticipantPool. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidDefaultVariableParameter. setUnit(CvTerm unit)Sets the unit of this variableParameter.Method parameters in psidev.psi.mi.jami.model.impl with type arguments of type CvTerm Modifier and Type Method Description protected voidDefaultFeatureEvidence. initialiseDetectionMethodsWith(Collection<CvTerm> methods)initialiseDetectionMethodsWithprotected voidDefaultCooperativityEvidence. initialiseEvidenceMethodsWith(Collection<CvTerm> methods)initialiseEvidenceMethodsWithprotected voidDefaultExperimentalParticipantPool. initialiseExperimentalPreparationsWith(Collection<CvTerm> expPreparations)initialiseExperimentalPreparationsWithprotected voidDefaultParticipantEvidence. initialiseExperimentalPreparationsWith(Collection<CvTerm> expPreparations)initialiseExperimentalPreparationsWithprotected voidDefaultExperimentalParticipantPool. initialiseIdentificationMethodsWith(Collection<CvTerm> methods)initialiseIdentificationMethodsWithprotected voidDefaultParticipantEvidence. initialiseIdentificationMethodsWith(Collection<CvTerm> methods)initialiseIdentificationMethodsWithConstructors in psidev.psi.mi.jami.model.impl with parameters of type CvTerm Constructor Description AbstractFeature(String shortName, String fullName, CvTerm type)Constructor for AbstractFeature.AbstractFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for AbstractFeature.AbstractFeature(CvTerm type)Constructor for AbstractFeature.AbstractFeature(CvTerm type, String interpro)Constructor for AbstractFeature.AbstractInteraction(String shortName, CvTerm type)Constructor for AbstractInteraction.AbstractParticipant(Interactor interactor, CvTerm bioRole)Constructor for AbstractParticipant.AbstractParticipant(Interactor interactor, CvTerm bioRole, CvTerm biologicalEffect, Stoichiometry stoichiometry)Constructor for AbstractParticipant.AbstractParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for AbstractParticipant.AbstractParticipantPool(String poolName, CvTerm bioRole)Constructor for AbstractParticipantPool.AbstractParticipantPool(String poolName, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for AbstractParticipantPool.DefaultAlias(CvTerm type, String name)Constructor for DefaultAlias.DefaultAllostery(CvTerm outcome, CvTerm response, ModelledParticipant allostericMolecule, T allostericEffector)Constructor for DefaultAllostery.DefaultAllostery(CvTerm outcome, ModelledParticipant allostericMolecule, T allostericEffector)Constructor for DefaultAllostery.DefaultAnnotation(CvTerm topic)Constructor for DefaultAnnotation.DefaultAnnotation(CvTerm topic, String value)Constructor for DefaultAnnotation.DefaultBioactiveEntity(String name, String fullName, CvTerm type)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, String fullName, CvTerm type, String uniqueChebi)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, String uniqueChebi)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, CvTerm type)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, CvTerm type, Organism organism)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, CvTerm type, Organism organism, String uniqueChebi)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, CvTerm type, Xref uniqueId)Constructor for DefaultBioactiveEntity.DefaultCausalRelationship(CvTerm relationType, Participant target)Constructor for DefaultCausalRelationship.DefaultChecksum(CvTerm method, String value)Constructor for DefaultChecksum.DefaultComplex(String name, String fullName, CvTerm interactorType)Constructor for DefaultComplex.DefaultComplex(String name, String fullName, CvTerm interactorType, Organism organism)Constructor for DefaultComplex.DefaultComplex(String name, String fullName, CvTerm interactorType, Organism organism, Xref uniqueId)Constructor for DefaultComplex.DefaultComplex(String name, String fullName, CvTerm interactorType, Xref uniqueId)Constructor for DefaultComplex.DefaultComplex(String name, CvTerm interactorType)Constructor for DefaultComplex.DefaultComplex(String name, CvTerm interactorType, Organism organism)Constructor for DefaultComplex.DefaultComplex(String name, CvTerm interactorType, Organism organism, Xref uniqueId)Constructor for DefaultComplex.DefaultComplex(String name, CvTerm interactorType, Xref uniqueId)Constructor for DefaultComplex.DefaultConfidence(CvTerm type, String value)Constructor for DefaultConfidence.DefaultCooperativeEffect(CvTerm outcome)Constructor for DefaultCooperativeEffect.DefaultCooperativeEffect(CvTerm outcome, CvTerm response)Constructor for DefaultCooperativeEffect.DefaultExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for DefaultExperiment.DefaultExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for DefaultExperiment.DefaultExperimentalParticipantPool(String poolName, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(String poolName, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(InteractionEvidence interaction, String poolName, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultExperimentalParticipantPool.DefaultFeature(String shortName, String fullName, CvTerm type)Constructor for DefaultFeature.DefaultFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for DefaultFeature.DefaultFeature(CvTerm type)Constructor for DefaultFeature.DefaultFeature(CvTerm type, String interpro)Constructor for DefaultFeature.DefaultFeatureEvidence(String shortName, String fullName, CvTerm type)Constructor for DefaultFeatureEvidence.DefaultFeatureEvidence(CvTerm type)Constructor for DefaultFeatureEvidence.DefaultFeatureEvidence(ParticipantEvidence participant, String shortName, String fullName, CvTerm type)Constructor for DefaultFeatureEvidence.DefaultFeatureEvidence(ParticipantEvidence participant, CvTerm type)Constructor for DefaultFeatureEvidence.DefaultGene(String name, String fullName, CvTerm type)Constructor for DefaultGene.DefaultGene(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultGene.DefaultGene(String name, String fullName, CvTerm type, Organism organism, Xref ensembl)Constructor for DefaultGene.DefaultGene(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)Constructor for DefaultGene.DefaultGene(String name, String fullName, CvTerm type, Xref ensembl)Constructor for DefaultGene.DefaultGene(String name, String fullName, CvTerm type, Xref uniqueId, Xref ensembl)Constructor for DefaultGene.DefaultGene(String name, CvTerm type)Constructor for DefaultGene.DefaultGene(String name, CvTerm type, Organism organism)Constructor for DefaultGene.DefaultGene(String name, CvTerm type, Organism organism, Xref ensembl)Constructor for DefaultGene.DefaultGene(String name, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)Constructor for DefaultGene.DefaultGene(String name, CvTerm type, Xref ensembl)Constructor for DefaultGene.DefaultGene(String name, CvTerm type, Xref uniqueId, Xref ensembl)Constructor for DefaultGene.DefaultInteraction(String shortName, CvTerm type)Constructor for DefaultInteraction.DefaultInteractionEvidence(String shortName, CvTerm type)Constructor for DefaultInteractionEvidence.DefaultInteractionEvidence(String shortName, CvTerm type, Xref imexId)Constructor for DefaultInteractionEvidence.DefaultInteractionEvidence(Experiment experiment, String shortName, CvTerm type)Constructor for DefaultInteractionEvidence.DefaultInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)Constructor for DefaultInteractionEvidence.DefaultInteractor(String name, String fullName, CvTerm type)Constructor for DefaultInteractor.DefaultInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultInteractor.DefaultInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultInteractor.DefaultInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultInteractor.DefaultInteractor(String name, CvTerm type)Constructor for DefaultInteractor.DefaultInteractor(String name, CvTerm type, Organism organism)Constructor for DefaultInteractor.DefaultInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultInteractor.DefaultInteractor(String name, CvTerm type, Xref uniqueId)Constructor for DefaultInteractor.DefaultInteractorPool(String name, String fullName, CvTerm type)Constructor for DefaultInteractorPool.DefaultInteractorPool(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultInteractorPool.DefaultInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultInteractorPool.DefaultInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultInteractorPool.DefaultInteractorPool(String name, CvTerm type)Constructor for DefaultInteractorPool.DefaultInteractorPool(String name, CvTerm type, Organism organism)Constructor for DefaultInteractorPool.DefaultInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultInteractorPool.DefaultInteractorPool(String name, CvTerm type, Xref uniqueId)Constructor for DefaultInteractorPool.DefaultModelledConfidence(CvTerm type, String value)Constructor for DefaultModelledConfidence.DefaultModelledConfidence(CvTerm type, String value, Publication publication)Constructor for DefaultModelledConfidence.DefaultModelledFeature(String shortName, String fullName, CvTerm type)Constructor for DefaultModelledFeature.DefaultModelledFeature(CvTerm type)Constructor for DefaultModelledFeature.DefaultModelledFeature(ModelledParticipant participant, String shortName, String fullName, CvTerm type)Constructor for DefaultModelledFeature.DefaultModelledFeature(ModelledParticipant participant, CvTerm type)Constructor for DefaultModelledFeature.DefaultModelledInteraction(String shortName, CvTerm type)Constructor for DefaultModelledInteraction.DefaultModelledInteraction(String shortName, Source source, CvTerm type)Constructor for DefaultModelledInteraction.DefaultModelledParameter(CvTerm type, String value)Constructor for DefaultModelledParameter.DefaultModelledParameter(CvTerm type, String value, CvTerm unit)Constructor for DefaultModelledParameter.DefaultModelledParameter(CvTerm type, ParameterValue value)Constructor for DefaultModelledParameter.DefaultModelledParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty)Constructor for DefaultModelledParameter.DefaultModelledParameter(CvTerm type, ParameterValue value, CvTerm unit)Constructor for DefaultModelledParameter.DefaultModelledParameter(CvTerm type, ParameterValue value, CvTerm unit, BigDecimal uncertainty)Constructor for DefaultModelledParameter.DefaultModelledParticipant(Interactor interactor, CvTerm bioRole)Constructor for DefaultModelledParticipant.DefaultModelledParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for DefaultModelledParticipant.DefaultModelledParticipantPool(String poolName, CvTerm bioRole)Constructor for DefaultModelledParticipantPool.DefaultModelledParticipantPool(String poolName, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for DefaultModelledParticipantPool.DefaultMolecule(String name, String fullName, CvTerm type)Constructor for DefaultMolecule.DefaultMolecule(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultMolecule.DefaultMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultMolecule.DefaultMolecule(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultMolecule.DefaultMolecule(String name, CvTerm type)Constructor for DefaultMolecule.DefaultMolecule(String name, CvTerm type, Organism organism)Constructor for DefaultMolecule.DefaultMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultMolecule.DefaultMolecule(String name, CvTerm type, Xref uniqueId)Constructor for DefaultMolecule.DefaultNamedExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for DefaultNamedExperiment.DefaultNamedExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for DefaultNamedExperiment.DefaultNamedInteraction(String shortName, CvTerm type)Constructor for DefaultNamedInteraction.DefaultNamedInteractionEvidence(String shortName, CvTerm type)Constructor for DefaultNamedInteractionEvidence.DefaultNamedInteractionEvidence(String shortName, CvTerm type, Xref imexId)Constructor for DefaultNamedInteractionEvidence.DefaultNamedInteractionEvidence(Experiment experiment, String shortName, CvTerm type)Constructor for DefaultNamedInteractionEvidence.DefaultNamedInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)Constructor for DefaultNamedInteractionEvidence.DefaultNamedModelledInteraction(String shortName, CvTerm type)Constructor for DefaultNamedModelledInteraction.DefaultNamedModelledInteraction(String shortName, Source source, CvTerm type)Constructor for DefaultNamedModelledInteraction.DefaultNamedModelledParticipant(Interactor interactor, CvTerm bioRole)Constructor for DefaultNamedModelledParticipant.DefaultNamedModelledParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for DefaultNamedModelledParticipant.DefaultNamedParticipant(Interactor interactor, CvTerm bioRole)Constructor for DefaultNamedParticipant.DefaultNamedParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for DefaultNamedParticipant.DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(InteractionEvidence interaction, Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(Interactor interactor, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNamedParticipantEvidence(Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultNamedParticipantEvidence.DefaultNucleicAcid(String name, String fullName, CvTerm type)Constructor for DefaultNucleicAcid.DefaultNucleicAcid(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultNucleicAcid.DefaultNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultNucleicAcid.DefaultNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultNucleicAcid.DefaultNucleicAcid(String name, CvTerm type)Constructor for DefaultNucleicAcid.DefaultNucleicAcid(String name, CvTerm type, Organism organism)Constructor for DefaultNucleicAcid.DefaultNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultNucleicAcid.DefaultNucleicAcid(String name, CvTerm type, Xref uniqueId)Constructor for DefaultNucleicAcid.DefaultOrganism(int taxId, String commonName, String scientificName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for DefaultOrganism.DefaultOrganism(int taxId, String commonName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for DefaultOrganism.DefaultOrganism(int taxId, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for DefaultOrganism.DefaultParameter(CvTerm type, String value)Constructor for DefaultParameter.DefaultParameter(CvTerm type, String value, CvTerm unit)Constructor for DefaultParameter.DefaultParameter(CvTerm type, ParameterValue value)Constructor for DefaultParameter.DefaultParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty)Constructor for DefaultParameter.DefaultParameter(CvTerm type, ParameterValue value, CvTerm unit)Constructor for DefaultParameter.DefaultParameter(CvTerm type, ParameterValue value, CvTerm unit, BigDecimal uncertainty)Constructor for DefaultParameter.DefaultParticipant(Interactor interactor, CvTerm bioRole)Constructor for DefaultParticipant.DefaultParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for DefaultParticipant.DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(InteractionEvidence interaction, Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(Interactor interactor, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantEvidence(Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for DefaultParticipantEvidence.DefaultParticipantPool(String poolName, CvTerm bioRole)Constructor for DefaultParticipantPool.DefaultParticipantPool(String poolName, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for DefaultParticipantPool.DefaultPolymer(String name, String fullName, CvTerm type)Constructor for DefaultPolymer.DefaultPolymer(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultPolymer.DefaultPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultPolymer.DefaultPolymer(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultPolymer.DefaultPolymer(String name, CvTerm type)Constructor for DefaultPolymer.DefaultPolymer(String name, CvTerm type, Organism organism)Constructor for DefaultPolymer.DefaultPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultPolymer.DefaultPolymer(String name, CvTerm type, Xref uniqueId)Constructor for DefaultPolymer.DefaultPosition(CvTerm status, long position)Constructor for DefaultPosition.DefaultPosition(CvTerm status, long start, long end)Constructor for DefaultPosition.DefaultPreassemby(CvTerm outcome)Constructor for DefaultPreassemby.DefaultPreassemby(CvTerm outcome, CvTerm response)Constructor for DefaultPreassemby.DefaultProtein(String name, String fullName, CvTerm type)Constructor for DefaultProtein.DefaultProtein(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultProtein.DefaultProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultProtein.DefaultProtein(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultProtein.DefaultProtein(String name, CvTerm type)Constructor for DefaultProtein.DefaultProtein(String name, CvTerm type, Organism organism)Constructor for DefaultProtein.DefaultProtein(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultProtein.DefaultProtein(String name, CvTerm type, Xref uniqueId)Constructor for DefaultProtein.DefaultVariableParameter(String description, CvTerm unit)Constructor for DefaultVariableParameter.DefaultVariableParameter(String description, Experiment experiment, CvTerm unit)Constructor for DefaultVariableParameter.DefaultXref(CvTerm database, String id)Constructor for DefaultXref.DefaultXref(CvTerm database, String id, String version)Constructor for DefaultXref.DefaultXref(CvTerm database, String id, String version, CvTerm qualifier)Constructor for DefaultXref.DefaultXref(CvTerm database, String id, CvTerm qualifier)Constructor for DefaultXref. -
Uses of CvTerm in psidev.psi.mi.jami.tab.extension
Classes in psidev.psi.mi.jami.tab.extension that implement CvTerm Modifier and Type Class Description classMitabCvTermMitab extension for CvTerm.classMitabSourceMitab extension of DefaultMitabSource It contains a FileSourceLocatorMethods in psidev.psi.mi.jami.tab.extension that return CvTerm Modifier and Type Method Description CvTermMitabXref. getDatabase()Getter for the fielddatabase.CvTermMitabXref. getQualifier()Getter for the fieldqualifier.Methods in psidev.psi.mi.jami.tab.extension with parameters of type CvTerm Modifier and Type Method Description voidMitabXref. setQualifier(CvTerm qualifier)Setter for the fieldqualifier.Constructors in psidev.psi.mi.jami.tab.extension with parameters of type CvTerm Constructor Description DefaultMitabFeature(CvTerm type)Constructor for DefaultMitabFeature.DefaultMitabFeature(CvTerm type, String interpro)Constructor for DefaultMitabFeature.MitabAlias(String dbSource, CvTerm type, String name)Constructor for MitabAlias.MitabAlias(String dbSource, CvTerm type, String name, FileSourceLocator locator)Constructor for MitabAlias.MitabAnnotation(CvTerm topic)Constructor for MitabAnnotation.MitabAnnotation(CvTerm topic, String value)Constructor for MitabAnnotation.MitabAnnotation(CvTerm topic, String value, FileSourceLocator sourceLocator)Constructor for MitabAnnotation.MitabAnnotation(CvTerm topic, FileSourceLocator sourceLocator)Constructor for MitabAnnotation.MitabBinaryInteraction(String shortName, CvTerm type)Constructor for MitabBinaryInteraction.MitabBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for MitabBinaryInteraction.MitabBinaryInteraction(String shortName, CvTerm type, Participant participantA, Participant participantB)Constructor for MitabBinaryInteraction.MitabBinaryInteraction(String shortName, CvTerm type, Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for MitabBinaryInteraction.MitabBinaryInteraction(String shortName, Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for MitabBinaryInteraction.MitabBinaryInteraction(CvTerm complexExpansion)Constructor for MitabBinaryInteraction.MitabBinaryInteraction(Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for MitabBinaryInteraction.MitabBinaryInteractionEvidence(String shortName, CvTerm type)Constructor for MitabBinaryInteractionEvidence.MitabBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for MitabBinaryInteractionEvidence.MitabBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)Constructor for MitabBinaryInteractionEvidence.MitabBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for MitabBinaryInteractionEvidence.MitabBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for MitabBinaryInteractionEvidence.MitabBinaryInteractionEvidence(CvTerm complexExpansion)Constructor for MitabBinaryInteractionEvidence.MitabBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for MitabBinaryInteractionEvidence.MitabBioactiveEntity(String name, String fullName, CvTerm type)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, String fullName, CvTerm type, String uniqueChebi)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, String fullName, CvTerm type, Organism organism)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, String uniqueChebi)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, CvTerm type)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, CvTerm type, Organism organism)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, CvTerm type, Organism organism, String uniqueChebi)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, CvTerm type, Xref uniqueId)Constructor for MitabBioactiveEntity.MitabCausalRelationship(CvTerm relationType, Participant target)Constructor for MitabCausalRelationship.MitabChecksum(CvTerm method, String value)Constructor for MitabChecksum.MitabChecksum(CvTerm method, String value, FileSourceLocator locator)Constructor for MitabChecksum.MitabComplex(String name, String fullName, CvTerm interactorType)Constructor for MitabComplex.MitabComplex(String name, String fullName, CvTerm interactorType, Organism organism)Constructor for MitabComplex.MitabComplex(String name, String fullName, CvTerm interactorType, Organism organism, Xref uniqueId)Constructor for MitabComplex.MitabComplex(String name, String fullName, CvTerm interactorType, Xref uniqueId)Constructor for MitabComplex.MitabComplex(String name, CvTerm interactorType)Constructor for MitabComplex.MitabComplex(String name, CvTerm interactorType, Organism organism)Constructor for MitabComplex.MitabComplex(String name, CvTerm interactorType, Organism organism, Xref uniqueId)Constructor for MitabComplex.MitabComplex(String name, CvTerm interactorType, Xref uniqueId)Constructor for MitabComplex.MitabConfidence(CvTerm type, String value)Constructor for MitabConfidence.MitabConfidence(CvTerm type, String value, String text)Constructor for MitabConfidence.MitabExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for MitabExperiment.MitabExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for MitabExperiment.MitabFeatureEvidence(String shortName, String fullName, CvTerm type)Constructor for MitabFeatureEvidence.MitabFeatureEvidence(CvTerm type)Constructor for MitabFeatureEvidence.MitabFeatureEvidence(ParticipantEvidence participant, String shortName, String fullName, CvTerm type)Constructor for MitabFeatureEvidence.MitabFeatureEvidence(ParticipantEvidence participant, CvTerm type)Constructor for MitabFeatureEvidence.MitabInteraction(String shortName, CvTerm type)Constructor for MitabInteraction.MitabInteractionEvidence(String shortName, CvTerm type)Constructor for MitabInteractionEvidence.MitabInteractionEvidence(String shortName, CvTerm type, Xref imexId)Constructor for MitabInteractionEvidence.MitabInteractionEvidence(Experiment experiment, String shortName, CvTerm type)Constructor for MitabInteractionEvidence.MitabInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)Constructor for MitabInteractionEvidence.MitabInteractor(String name, String fullName, CvTerm type)Constructor for MitabInteractor.MitabInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for MitabInteractor.MitabInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabInteractor.MitabInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for MitabInteractor.MitabInteractor(String name, CvTerm type)Constructor for MitabInteractor.MitabInteractor(String name, CvTerm type, Organism organism)Constructor for MitabInteractor.MitabInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabInteractor.MitabInteractor(String name, CvTerm type, Xref uniqueId)Constructor for MitabInteractor.MitabInteractorPool(String name, String fullName, CvTerm type)Constructor for MitabInteractorPool.MitabInteractorPool(String name, String fullName, CvTerm type, Organism organism)Constructor for MitabInteractorPool.MitabInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabInteractorPool.MitabInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for MitabInteractorPool.MitabInteractorPool(String name, CvTerm type)Constructor for MitabInteractorPool.MitabInteractorPool(String name, CvTerm type, Organism organism)Constructor for MitabInteractorPool.MitabInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabInteractorPool.MitabInteractorPool(String name, CvTerm type, Xref uniqueId)Constructor for MitabInteractorPool.MitabModelledBinaryInteraction(String shortName, CvTerm type)Constructor for MitabModelledBinaryInteraction.MitabModelledBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for MitabModelledBinaryInteraction.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, CvTerm complexExpansion)Constructor for MitabModelledBinaryInteraction.MitabModelledBinaryInteraction(CvTerm complexExpansion)Constructor for MitabModelledBinaryInteraction.MitabModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)Constructor for MitabModelledBinaryInteraction.MitabModelledFeature(String shortName, String fullName, CvTerm type)Constructor for MitabModelledFeature.MitabModelledFeature(CvTerm type)Constructor for MitabModelledFeature.MitabModelledFeature(ModelledParticipant participant, String shortName, String fullName, CvTerm type)Constructor for MitabModelledFeature.MitabModelledFeature(ModelledParticipant participant, CvTerm type)Constructor for MitabModelledFeature.MitabModelledInteraction(String shortName, CvTerm type)Constructor for MitabModelledInteraction.MitabModelledInteraction(String shortName, Source source, CvTerm type)Constructor for MitabModelledInteraction.MitabModelledParticipant(Interactor interactor, CvTerm bioRole)Constructor for MitabModelledParticipant.MitabModelledParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for MitabModelledParticipant.MitabMolecule(String name, String fullName, CvTerm type)Constructor for MitabMolecule.MitabMolecule(String name, String fullName, CvTerm type, Organism organism)Constructor for MitabMolecule.MitabMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabMolecule.MitabMolecule(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for MitabMolecule.MitabMolecule(String name, CvTerm type)Constructor for MitabMolecule.MitabMolecule(String name, CvTerm type, Organism organism)Constructor for MitabMolecule.MitabMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabMolecule.MitabMolecule(String name, CvTerm type, Xref uniqueId)Constructor for MitabMolecule.MitabNucleicAcid(String name, String fullName, CvTerm type)Constructor for MitabNucleicAcid.MitabNucleicAcid(String name, String fullName, CvTerm type, Organism organism)Constructor for MitabNucleicAcid.MitabNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabNucleicAcid.MitabNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for MitabNucleicAcid.MitabNucleicAcid(String name, CvTerm type)Constructor for MitabNucleicAcid.MitabNucleicAcid(String name, CvTerm type, Organism organism)Constructor for MitabNucleicAcid.MitabNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabNucleicAcid.MitabNucleicAcid(String name, CvTerm type, Xref uniqueId)Constructor for MitabNucleicAcid.MitabOrganism(int taxId, String commonName, String scientificName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for MitabOrganism.MitabOrganism(int taxId, String commonName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for MitabOrganism.MitabOrganism(int taxId, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for MitabOrganism.MitabParameter(CvTerm type, String value)Constructor for MitabParameter.MitabParameter(CvTerm type, String value, CvTerm unit)Constructor for MitabParameter.MitabParameter(CvTerm type, ParameterValue value)Constructor for MitabParameter.MitabParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty)Constructor for MitabParameter.MitabParameter(CvTerm type, ParameterValue value, CvTerm unit)Constructor for MitabParameter.MitabParameter(CvTerm type, ParameterValue value, CvTerm unit, BigDecimal uncertainty)Constructor for MitabParameter.MitabParticipant(Interactor interactor, CvTerm bioRole)Constructor for MitabParticipant.MitabParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for MitabParticipant.MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(InteractionEvidence interaction, Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(Interactor interactor, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabParticipantEvidence(Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)Constructor for MitabParticipantEvidence.MitabPolymer(String name, String fullName, CvTerm type)Constructor for MitabPolymer.MitabPolymer(String name, String fullName, CvTerm type, Organism organism)Constructor for MitabPolymer.MitabPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabPolymer.MitabPolymer(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for MitabPolymer.MitabPolymer(String name, CvTerm type)Constructor for MitabPolymer.MitabPolymer(String name, CvTerm type, Organism organism)Constructor for MitabPolymer.MitabPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabPolymer.MitabPolymer(String name, CvTerm type, Xref uniqueId)Constructor for MitabPolymer.MitabProtein(String name, String fullName, CvTerm type)Constructor for MitabProtein.MitabProtein(String name, String fullName, CvTerm type, Organism organism)Constructor for MitabProtein.MitabProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabProtein.MitabProtein(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for MitabProtein.MitabProtein(String name, CvTerm type)Constructor for MitabProtein.MitabProtein(String name, CvTerm type, Organism organism)Constructor for MitabProtein.MitabProtein(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for MitabProtein.MitabProtein(String name, CvTerm type, Xref uniqueId)Constructor for MitabProtein.MitabXref(String database, String id, CvTerm qualifier)Constructor for MitabXref.MitabXref(CvTerm database, String id)Constructor for MitabXref.MitabXref(CvTerm database, String id, String version)Constructor for MitabXref.MitabXref(CvTerm database, String id, String version, CvTerm qualifier)Constructor for MitabXref.MitabXref(CvTerm database, String id, CvTerm qualifier)Constructor for MitabXref. -
Uses of CvTerm in psidev.psi.mi.jami.tab.extension.datasource
Methods in psidev.psi.mi.jami.tab.extension.datasource with parameters of type CvTerm Modifier and Type Method Description voidAbstractMitabSource. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.voidAbstractMitabStreamSource. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.voidDefaultMitabStreamSource. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names. -
Uses of CvTerm in psidev.psi.mi.jami.tab.extension.factory
Methods in psidev.psi.mi.jami.tab.extension.factory with parameters of type CvTerm Modifier and Type Method Description MitabBioactiveEntityMitabInteractorFactory. createBioactiveEntity(String name, CvTerm type)Creates a new BioactiveEntity with the name and interactor typeMitabComplexMitabInteractorFactory. createComplex(String name, CvTerm type)Creates a new Complex with the name and interactor typeMitabInteractorMitabInteractorFactory. createInteractor(String name, CvTerm type)Creates a default interactor from the name and interactor typeMitabInteractorPoolMitabInteractorFactory. createInteractorSet(String name, CvTerm type)Creates an interactor pool from the name and interactor typeMitabNucleicAcidMitabInteractorFactory. createNucleicAcid(String name, CvTerm type)Creates a new NucleicAcid with the name and interactor typeMitabPolymerMitabInteractorFactory. createPolymer(String name, CvTerm type)Creates a new Polymer with the name and interactor typeMitabProteinMitabInteractorFactory. createProtein(String name, CvTerm type)Creates a new Protein with the name and interactor type -
Uses of CvTerm in psidev.psi.mi.jami.tab.io.parser
Methods in psidev.psi.mi.jami.tab.io.parser with parameters of type CvTerm Modifier and Type Method Description MitabXrefMitabLineParser. id(CvTerm qualifier, boolean recognizeImexPrimary, int columnNumber)Collection<MitabXref>MitabLineParser. ids(CvTerm qualifier, boolean recognizeImex, int column) -
Uses of CvTerm in psidev.psi.mi.jami.tab.io.writer.feeder
Methods in psidev.psi.mi.jami.tab.io.writer.feeder with parameters of type CvTerm Modifier and Type Method Description voidAbstractMitabColumnFeeder. writeCvTerm(CvTerm cv)Write the CvTerm.voidMitabColumnFeeder. writeCvTerm(CvTerm cv)Write the CvTerm.protected voidAbstractMitabColumnFeeder. writeCvTermName(CvTerm cv)Write full name if not null, otherwise write shortname -
Uses of CvTerm in psidev.psi.mi.jami.utils
Methods in psidev.psi.mi.jami.utils that return CvTerm Modifier and Type Method Description static CvTermCvTermUtils. createAllosteryCooperativeMechanism()createAllosteryCooperativeMechanismstatic CvTermCvTermUtils. createAuthorAssignedName()createAuthorAssignedNamestatic CvTermCvTermUtils. createBioactiveEntityType()createBioactiveEntityTypestatic CvTermCvTermUtils. createBiologicalFeatureType()createBiologicalFeatureTypestatic CvTermCvTermUtils. createCertainStatus()createCertainStatusstatic CvTermCvTermUtils. createChebiDatabase()createChebiDatabasestatic CvTermCvTermUtils. createComplexInteractorType()createComplexInteractorTypestatic CvTermCvTermUtils. createComplexPhysicalProperties()createComplexPhysicalPropertiesstatic CvTermCvTermUtils. createComplexPortalDatabase()createComplexPortalDatabasestatic CvTermCvTermUtils. createComplexPortalPrimaryQualifier()createComplexPortalPrimaryQualifierstatic CvTermCvTermUtils. createComplexRecommendedName()createComplexRecommendedNamestatic CvTermCvTermUtils. createComplexSynonym()createComplexSynonymstatic CvTermCvTermUtils. createComplexSystematicName()createComplexSystematicNamestatic CvTermCvTermUtils. createCTerminalRangeStatus()createCTerminalRangeStatusstatic CvTermCvTermUtils. createCTerminalStatus()createCTerminalStatusstatic CvTermCvTermUtils. createDdbjEmblGenbankDatabase()createDdbjEmblGenbankDatabasestatic CvTermCvTermUtils. createDoiDatabase()createDoiDatabasestatic CvTermCvTermUtils. createECOCvTerm(String name, String ecoId)createECOCvTermstatic CvTermCvTermUtils. createEnsemblDatabase()createEnsemblDatabasestatic CvTermCvTermUtils. createEnsemblGenomesDatabase()createEnsemblGenomesDatabasestatic CvTermCvTermUtils. createEntrezGeneIdDatabase()createEntrezGeneIdDatabasestatic CvTermCvTermUtils. createGeneInteractorType()createGeneInteractorTypestatic CvTermCvTermUtils. createGeneNameAliasType()createGeneNameAliasTypestatic CvTermCvTermUtils. createGeneNameSynonym()createGeneNameSynonymstatic CvTermCvTermUtils. createGOCvTerm(String name, String goId)createGOCvTermstatic CvTermCvTermUtils. createGreaterThanRangeStatus()createGreaterThanRangeStatusstatic CvTermCvTermUtils. createIdentityQualifier()createIdentityQualifierstatic CvTermCvTermUtils. createIdentityQualifier(CvTerm psiMi)createIdentityQualifierstatic CvTermCvTermUtils. createIdentityQualifierNameOnly()createIdentityQualifierNameOnlystatic CvTermCvTermUtils. createIdentityXrefQualifier()createIdentityXrefQualifierstatic CvTermCvTermUtils. createImexDatabase()createImexDatabasestatic CvTermCvTermUtils. createImexPrimaryQualifier()createImexPrimaryQualifierstatic CvTermCvTermUtils. createInterproDatabase()createInterproDatabasestatic CvTermCvTermUtils. createIsoformSynonym()createIsoformSynonymstatic CvTermCvTermUtils. createLessThanRangeStatus()createLessThanRangeStatusstatic CvTermCvTermUtils. createLocusName()createLocusNamestatic CvTermCvTermUtils. createMICvTerm(String name, String MI)createMICvTermstatic CvTermCvTermUtils. createMODCvTerm(String name, String MOD)createMODCvTermstatic CvTermCvTermUtils. createMoleculeSetType()createMoleculeSetTypestatic CvTermCvTermUtils. createNTerminalRangeStatus()createNTerminalRangeStatusstatic CvTermCvTermUtils. createNTerminalStatus()createNTerminalStatusstatic CvTermCvTermUtils. createNucleicAcidInteractorType()createNucleicAcidInteractorTypestatic CvTermCvTermUtils. createOrfName()createOrfNamestatic CvTermCvTermUtils. createPARCvTerm(String name, String PAR)createPARCvTermstatic CvTermCvTermUtils. createPolymerInteractorType()createPolymerInteractorTypestatic CvTermCvTermUtils. createProteinInteractorType()createProteinInteractorTypestatic CvTermCvTermUtils. createPsiMiDatabase()createPsiMiDatabasestatic CvTermCvTermUtils. createPsiMiDatabase(CvTerm identity)createPsiMiDatabasestatic CvTermCvTermUtils. createPsiMiDatabaseNameOnly()createPsiMiDatabaseNameOnlystatic CvTermCvTermUtils. createPsiModDatabase()createPsiModDatabasestatic CvTermCvTermUtils. createPsiParDatabase()createPsiParDatabasestatic CvTermCvTermUtils. createPubmedDatabase()createPubmedDatabasestatic CvTermCvTermUtils. createPutativeSelf()createPutativeSelfstatic CvTermCvTermUtils. createRaggedNTerminalStatus()createRaggedNTerminalStatusstatic CvTermCvTermUtils. createRangeStatus()createRangeStatusstatic CvTermCvTermUtils. createRefseqDatabase()createRefseqDatabasestatic CvTermCvTermUtils. createRigid()createRigidstatic CvTermCvTermUtils. createRogid()createRogidstatic CvTermCvTermUtils. createSecondaryXrefQualifier()createSecondaryXrefQualifierstatic CvTermCvTermUtils. createSelf()createSelfstatic CvTermCvTermUtils. createSmile()createSmilestatic CvTermCvTermUtils. createStandardInchi()createStandardInchistatic CvTermCvTermUtils. createStandardInchiKey()createStandardInchiKeystatic CvTermCvTermUtils. createUndeterminedStatus()createUndeterminedStatusstatic CvTermCvTermUtils. createUniprotkbDatabase()createUniprotkbDatabasestatic CvTermCvTermUtils. createUnknownInteractorType()createUnknownInteractorTypestatic CvTermCvTermUtils. createUnspecifiedMethod()createUnspecifiedMethodstatic CvTermCvTermUtils. createUnspecifiedRole()createUnspecifiedRolestatic CvTermExperimentUtils. extractMostCommonParticipantDetectionMethodFrom(Experiment exp)Compare all participant identification methods in all participant evidences from all the interactions evidences.static CvTermCvTermUtils. getAllosteryMechanism()Getter for the fieldallosteryMechanism.static CvTermCvTermUtils. getCertain()Getter for the fieldcertain.static CvTermCvTermUtils. getCTerminal()Getter for the fieldcTerminal.static CvTermCvTermUtils. getCTerminalRange()Getter for the fieldcTerminalRange.static CvTermCvTermUtils. getFuzzyRange()getFuzzyRangestatic CvTermCvTermUtils. getGene()Getter for the fieldgene.static CvTermCvTermUtils. getGreaterThan()Getter for the fieldgreaterThan.static CvTermCvTermUtils. getIdentity()Getter for the fieldidentity.static CvTermCvTermUtils. getImexPrimary()Getter for the fieldimexPrimary.static CvTermCvTermUtils. getLessThan()Getter for the fieldlessThan.static CvTermCvTermUtils. getNTerminal()Getter for the fieldnTerminal.static CvTermCvTermUtils. getNTerminalRagged()Getter for the fieldnTerminalRagged.static CvTermCvTermUtils. getNTerminalRange()Getter for the fieldnTerminalRange.static CvTermCvTermUtils. getPsimi()Getter for the fieldpsimi.static CvTermCvTermUtils. getPsimod()Getter for the fieldpsimod.static CvTermCvTermUtils. getPsipar()Getter for the fieldpsipar.static CvTermCvTermUtils. getPutativeSelf()getPutativeSelfstatic CvTermCvTermUtils. getSecondary()Getter for the fieldsecondary.static CvTermCvTermUtils. getSelf()Getter for the fieldself.static CvTermCvTermUtils. getUndetermined()Getter for the fieldundetermined.static CvTermCvTermUtils. getUnknownInteractorType()Getter for the fieldunknownInteractorType.Methods in psidev.psi.mi.jami.utils with parameters of type CvTerm Modifier and Type Method Description static FeatureFeatureUtils. createDefaultFeature(String name, CvTerm featureType, Collection<Range> ranges)createDefaultFeaturestatic FeatureFeatureUtils. createDefaultFeature(String name, CvTerm featureType, Range range)createDefaultFeaturestatic NamedExperimentExperimentUtils. createExperiment(String name, String pubmedId, CvTerm interactionDetectionMethod, Organism hostOrganism)createExperimentstatic ExperimentExperimentUtils. createExperiment(String pubmedId, CvTerm interactionDetectionMethod, Organism hostOrganism)createExperimentstatic FeatureEvidenceFeatureUtils. createFeatureEvidence(String name, CvTerm featureType, Collection<CvTerm> detectionMethods, Collection<Range> ranges)createFeatureEvidencestatic FeatureEvidenceFeatureUtils. createFeatureEvidence(String name, CvTerm featureType, Collection<CvTerm> detectionMethods, Range range)createFeatureEvidencestatic FeatureEvidenceFeatureUtils. createFeatureEvidence(String name, CvTerm featureType, Collection<Range> ranges)createFeatureEvidencestatic FeatureEvidenceFeatureUtils. createFeatureEvidence(String name, CvTerm featureType, CvTerm detectionMethod, Collection<Range> ranges)createFeatureEvidencestatic FeatureEvidenceFeatureUtils. createFeatureEvidence(String name, CvTerm featureType, CvTerm detectionMethod, Range range)createFeatureEvidencestatic FeatureEvidenceFeatureUtils. createFeatureEvidence(String name, CvTerm featureType, Range range)createFeatureEvidencestatic CvTermCvTermUtils. createIdentityQualifier(CvTerm psiMi)createIdentityQualifierstatic ModelledFeatureFeatureUtils. createModelledFeature(String name, CvTerm featureType, Collection<Range> ranges)createModelledFeaturestatic ModelledFeatureFeatureUtils. createModelledFeature(String name, CvTerm featureType, Range range)createModelledFeaturestatic ParameterParameterUtils. createParameterFromString(CvTerm type, String value)createParameterFromStringstatic ParameterParameterUtils. createParameterFromString(CvTerm type, String value, CvTerm unit)createParameterFromStringstatic CvTermCvTermUtils. createPsiMiDatabase(CvTerm identity)createPsiMiDatabasestatic StringCvTermUtils. getBestIdentifier(CvTerm cvObject)Gets the unique identifier of a CvObject.static XrefCvTermUtils. getPsiMiReference(CvTerm term)getPsiMiReferencestatic XrefCvTermUtils. getPsiModReference(CvTerm term)getPsiModReferencestatic XrefCvTermUtils. getPsiParReference(CvTerm term)getPsiParReferencestatic booleanCvTermUtils. isCvTerm(CvTerm term, String mi, String name)Check if the CvTerm natches the MI term and/or the name if no MI term existMethod parameters in psidev.psi.mi.jami.utils with type arguments of type CvTerm Modifier and Type Method Description static FeatureEvidenceFeatureUtils. createFeatureEvidence(String name, CvTerm featureType, Collection<CvTerm> detectionMethods, Collection<Range> ranges)createFeatureEvidencestatic FeatureEvidenceFeatureUtils. createFeatureEvidence(String name, CvTerm featureType, Collection<CvTerm> detectionMethods, Range range)createFeatureEvidence -
Uses of CvTerm in psidev.psi.mi.jami.utils.clone
Methods in psidev.psi.mi.jami.utils.clone with parameters of type CvTerm Modifier and Type Method Description static voidCvTermCloner. copyAndOverrideCvTermProperties(CvTerm source, CvTerm target)This method will copy properties of cv term source in cv term target and will override all the other properties of Target cv term. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator
Method parameters in psidev.psi.mi.jami.utils.comparator with type arguments of type CvTerm Modifier and Type Method Description static booleanComparatorUtils. areCvTermsEqual(Collection<? extends CvTerm> method1, Collection<? extends CvTerm> method2)areCvTermsEqual -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.alias
Methods in psidev.psi.mi.jami.utils.comparator.alias that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>AliasComparator. getTypeComparator()Getter for the fieldtypeComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.alias with type arguments of type CvTerm Constructor Description AliasComparator(Comparator<CvTerm> typeComparator)Creates a new AliasComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.annotation
Methods in psidev.psi.mi.jami.utils.comparator.annotation that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>AnnotationComparator. getTopicComparator()Getter for the fieldtopicComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.annotation with type arguments of type CvTerm Constructor Description AnnotationComparator(Comparator<CvTerm> topicComparator)Creates a new AnnotationComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.checksum
Methods in psidev.psi.mi.jami.utils.comparator.checksum that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>ChecksumComparator. getMethodComparator()Getter for the fieldmethodComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.checksum with type arguments of type CvTerm Constructor Description ChecksumComparator(Comparator<CvTerm> termComparator)Creates a new ChecksumComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.confidence
Methods in psidev.psi.mi.jami.utils.comparator.confidence that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>ConfidenceComparator. getCvTermComparator()Getter for the fieldcvTermComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.confidence with type arguments of type CvTerm Constructor Description ConfidenceComparator(Comparator<CvTerm> termComparator)Creates a new ConfidenceComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.cooperativity
Methods in psidev.psi.mi.jami.utils.comparator.cooperativity that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>CooperativeEffectBaseComparator. getCvTermComparator()Getter for the fieldcvTermComparator.CollectionComparator<CvTerm>CooperativityEvidenceComparator. getCvTermsCollectionComparator()Getter for the fieldcvTermsCollectionComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.cooperativity with type arguments of type CvTerm Constructor Description CooperativeEffectBaseComparator(Comparator<CvTerm> cvTermComparator, CollectionComparator<CooperativityEvidence> cooperativityEvidenceComparator, CollectionComparator<ModelledInteraction> modelledInteractionComparator)Constructor for CooperativeEffectBaseComparator.CooperativeEffectBaseComparator(Comparator<CvTerm> cvTermComparator, CooperativityEvidenceComparator cooperativityEvidenceComparator, ModelledInteractionComparator modelledInteractionComparator)Constructor for CooperativeEffectBaseComparator.CooperativityEvidenceComparator(Comparator<CvTerm> cvTermComparator, Comparator<Publication> publicationComparator)Constructor for CooperativityEvidenceComparator.CooperativityEvidenceComparator(CollectionComparator<CvTerm> cvTermComparator, Comparator<Publication> publicationComparator)Constructor for CooperativityEvidenceComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.cv
Methods in psidev.psi.mi.jami.utils.comparator.cv with parameters of type CvTerm Modifier and Type Method Description static booleanCvTermIdentifierComparator. areEquals(CvTerm cv1, CvTerm cv2)Use UnambiguousCvTermComparator to know if two CvTerms are equals.static booleanCvTermNameComparator. areEquals(CvTerm cv1, CvTerm cv2)Use UnambiguousCvTermComparator to know if two CvTerms are equals.static booleanDefaultCvTermComparator. areEquals(CvTerm cvTerm1, CvTerm cvTerm2)Use DefaultCvTermComparator to know if two CvTerms are equals.static booleanUnambiguousCvTermComparator. areEquals(CvTerm cv1, CvTerm cv2)Use UnambiguousCvTermComparator to know if two CvTerms are equals.intCvTermComparator. compare(CvTerm cvTerm1, CvTerm cvTerm2)If one CvTerm does not have any identifiers, it will only compare the short names (case insensitive).intCvTermIdentifierComparator. compare(CvTerm cvTerm1, CvTerm cvTerm2)If one CvTerm does not have any identifiers, it will only compare the short names (case insensitive).intCvTermNameComparator. compare(CvTerm cvTerm1, CvTerm cvTerm2)Only compares the shortname of two cv terms.static intCvTermIdentifierComparator. hashCode(CvTerm cv1)hashCodestatic intCvTermNameComparator. hashCode(CvTerm cv1)hashCodestatic intUnambiguousCvTermComparator. hashCode(CvTerm cv1)hashCodeConstructor parameters in psidev.psi.mi.jami.utils.comparator.cv with type arguments of type CvTerm Constructor Description CvTermsCollectionComparator(Comparator<CvTerm> cvTermComparator)Creates a new cvTerm CollectionComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.experiment
Methods in psidev.psi.mi.jami.utils.comparator.experiment that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>ExperimentComparator. getCvTermComparator()Getter for the fieldcvTermComparator.Comparator<CvTerm>VariableParameterComparator. getCvTermComparator()Getter for the fieldcvTermComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.experiment with type arguments of type CvTerm Constructor Description VariableParameterComparator(Comparator<CvTerm> cvTermComparator)Constructor for VariableParameterComparator.VariableParameterComparator(Comparator<CvTerm> cvTermComparator, CollectionComparator<VariableParameterValue> variablecomparator)Constructor for VariableParameterComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.feature
Methods in psidev.psi.mi.jami.utils.comparator.feature that return types with arguments of type CvTerm Modifier and Type Method Description CollectionComparator<CvTerm>FeatureEvidenceComparator. getCvTermCollectionComparators()Getter for the fieldcvTermCollectionComparators.Comparator<CvTerm>FeatureBaseComparator. getCvTermComparator()Getter for the fieldcvTermComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.feature with type arguments of type CvTerm Constructor Description FeatureBaseComparator(Comparator<CvTerm> cvComparator, Comparator<Xref> identifierComparator, RangeComparator rangeComparator)Creates a new UnambiguousFeatureBaseComparator.FeatureBaseComparator(Comparator<CvTerm> cvComparator, CollectionComparator<Xref> identifierComparator, CollectionComparator<Range> rangeComparator)Constructor for FeatureBaseComparator.FeatureEvidenceComparator(Comparator<Feature> featureComparator, CollectionComparator<CvTerm> cvTermComparator)Constructor for FeatureEvidenceComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.interaction
Methods in psidev.psi.mi.jami.utils.comparator.interaction that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>InteractionBaseComparator. getCvTermComparator()Getter for the fieldcvTermComparator.Comparator<CvTerm>CuratedModelledInteractionComparator. getSourceComparator()Getter for the fieldsourceComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.interaction with type arguments of type CvTerm Constructor Description InteractionBaseComparator(CollectionComparator<Xref> identifierComparator, Comparator<CvTerm> cvTermComparator)Constructor for InteractionBaseComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.interactor
Methods in psidev.psi.mi.jami.utils.comparator.interactor that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>ComplexComparator. getCvTermComparator()Getter for the fieldcvTermComparator.Comparator<CvTerm>ExactInteractorBaseComparator. getTypeComparator()Getter for the fieldtypeComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.interactor with type arguments of type CvTerm Constructor Description ExactInteractorBaseComparator(OrganismTaxIdComparator organismComparator, Comparator<CvTerm> typeComparator, InteractorBaseComparator interactorBaseComparator)Creates a new UnambiguousExactInteractorBaseComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.organism
Methods in psidev.psi.mi.jami.utils.comparator.organism that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>OrganismComparator. getCvTermComparator()Constructor parameters in psidev.psi.mi.jami.utils.comparator.organism with type arguments of type CvTerm Constructor Description OrganismComparator(Comparator<CvTerm> cvTermComparator)Creates a new OrganismComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.parameter
Methods in psidev.psi.mi.jami.utils.comparator.parameter that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>ParameterComparator. getCvTermComparator()Getter for the fieldcvTermComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.parameter with type arguments of type CvTerm Constructor Description ParameterComparator(Comparator<CvTerm> cvTermComparator)Creates a new ParameterComparatorParameterComparator(Comparator<CvTerm> cvTermComparator, ParameterValueComparator valueComparator)Creates a new ParameterComparator -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.participant
Methods in psidev.psi.mi.jami.utils.comparator.participant that return types with arguments of type CvTerm Modifier and Type Method Description CollectionComparator<CvTerm>ExperimentalParticipantPoolComparator. getCvTermCollectionComparator()Getter for the fieldcvTermCollectionComparator.Comparator<CvTerm>CausalRelationshipComparator. getCvTermComparator()Getter for the fieldcvTermComparator.Comparator<CvTerm>ParticipantBaseComparator. getCvTermComparator()Getter for the fieldcvTermComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.participant with type arguments of type CvTerm Constructor Description CausalRelationshipComparator(Comparator<CvTerm> cvTermComparator, EntityComparator participantComparator)Constructor for CausalRelationshipComparator.ParticipantBaseComparator(EntityBaseComparator interactorComparator, Comparator<CvTerm> cvTermComparator)Creates a new ParticipantBaseComparator -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.publication
Methods in psidev.psi.mi.jami.utils.comparator.publication that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>CuratedPublicationComparator. getSourceComparator()Getter for the fieldsourceComparator. -
Uses of CvTerm in psidev.psi.mi.jami.utils.comparator.range
Methods in psidev.psi.mi.jami.utils.comparator.range that return types with arguments of type CvTerm Modifier and Type Method Description Comparator<CvTerm>PositionComparator. getStatusComparator()Getter for the fieldstatusComparator.Constructor parameters in psidev.psi.mi.jami.utils.comparator.range with type arguments of type CvTerm Constructor Description PositionComparator(Comparator<CvTerm> statusComparator)Creates a new positionComparator -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements
Methods in psidev.psi.mi.jami.xml.io.writer.elements that return CvTerm Modifier and Type Method Description CvTermPsiXmlExperimentWriter. extractDefaultParticipantIdentificationMethod(Experiment exp)extractDefaultParticipantIdentificationMethod.CvTermPsiXmlExperimentWriter. writeExperiment(Experiment exp)writeExperiment.Methods in psidev.psi.mi.jami.xml.io.writer.elements that return types with arguments of type CvTerm Modifier and Type Method Description static PsiXmlVariableNameWriter<CvTerm>PsiXmlElementWriterFactory. createCvWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlXrefWriter primaryRefWriter)createCvWriter.static PsiXmlVariableNameWriter<CvTerm>PsiXmlElementWriterFactory. createExperimentalCvWriter(XMLStreamWriter streamWriter, PsiXmlVersion version, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlXrefWriter primaryRefWriter)createExperimentalCvWriter.static PsiXmlVariableNameWriter<CvTerm>PsiXmlElementWriterFactory. createOpenCvWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter)createOpenCvWriter.Methods in psidev.psi.mi.jami.xml.io.writer.elements with parameters of type CvTerm Modifier and Type Method Description voidPsiXmlParticipantWriter. writeParticipant(T participant, CvTerm generalParticipantDetectionMethod)writeParticipant.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements with type arguments of type CvTerm Modifier and Type Method Description static PsiXmlElementWriter<Allostery>PsiXmlElementWriterFactory. createAllosteryWriter(XMLStreamWriter streamWriter, boolean expanded, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlPublicationWriter publicationWriter)createAllosteryWriter.static PsiXmlCausalRelationshipWriterPsiXmlElementWriterFactory. createCausalRelationshipWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter)createCausalRelationshipWriter.static PsiXmlElementWriter<Confidence>[]PsiXmlElementWriterFactory. createConfidenceWriters(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlVariableNameWriter<CvTerm> confidenceTypeWriter, PsiXmlPublicationWriter publicationWriter)createConfidenceWriters.static PsiXmlElementWriter<CooperativityEvidence>PsiXmlElementWriterFactory. createCooperativityEvidenceWriter(XMLStreamWriter streamWriter, boolean expanded, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlPublicationWriter publicationWriter)createCooperativityEvidenceWriter.static PsiXmlInteractionWriter[]PsiXmlElementWriterFactory. createDefaultPsiXmlInteractionWriters(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlParameterWriter[] parameterWriters, PsiXmlParticipantWriter[] participantWriters, PsiXmlElementWriter inferredInteractionWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)createDefaultPsiXmlInteractionWriters.static PsiXmlExperimentWriterPsiXmlElementWriterFactory. createExperimentWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, boolean named, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlElementWriter<Organism> nonExperimentalHostOrganismWriter, PsiXmlVariableNameWriter<CvTerm> detectionMethodWriter, PsiXmlElementWriter<Confidence> confidenceWriter)createExperimentWriter.static PsiXmlInteractionWriter[]PsiXmlElementWriterFactory. createExtendedPsiXmlInteractionWriters(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlParameterWriter[] parameterWriters, PsiXmlParticipantWriter[] participantWriters, PsiXmlElementWriter inferredInteractionWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)createExtendedPsiXmlInteractionWriters.static <F extends Feature>
PsiXmlElementWriter<F>[]PsiXmlElementWriterFactory. createFeatureWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, InteractionCategory category, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlVariableNameWriter<CvTerm> featureTypeWriter, PsiXmlParameterWriter parameterWriter)createFeatureWriter.static PsiXmlElementWriter<Organism>PsiXmlElementWriterFactory. createHostOrganismWriter(XMLStreamWriter streamWriter, PsiXmlVersion version, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> annotationWriter, PsiXmlXrefWriter xrefWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)createHostOrganismWriter.static PsiXmlInteractionWriter[]PsiXmlElementWriterFactory. createInteractionWritersFor(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, boolean extended, boolean named, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlElementWriter<Interactor> interactorWriter, PsiXmlPublicationWriter publicationWriter)createInteractionWritersFor.static PsiXmlElementWriter<Interactor>PsiXmlElementWriterFactory. createInteractorWriter(PsiXmlVersion version, XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlVariableNameWriter<CvTerm> interactorTypeWriter, PsiXmlElementWriter<Organism> organismWriter, PsiXmlElementWriter<Checksum> checksumWriter)createInteractorWriter.static PsiXmlInteractionWriter[]PsiXmlElementWriterFactory. createNamedPsiXmlInteractionWriters(XMLStreamWriter streamWriter, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory interactionCategory, ComplexType complexType, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter[] confidenceWriters, PsiXmlElementWriter<Checksum> checksumWriter, PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter, PsiXmlExperimentWriter experimentWriter, PsiXmlElementWriter<String> availabilityWriter, PsiXmlParameterWriter[] parameterWriters, PsiXmlParticipantWriter[] participantWriters, PsiXmlElementWriter inferredInteractionWriter, PsiXmlPublicationWriter publicationWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)createNamedPsiXmlInteractionWriters.static PsiXmlElementWriter<Organism>PsiXmlElementWriterFactory. createOrganismWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> annotationWriter, PsiXmlXrefWriter xrefWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)createOrganismWriter.static <P extends Participant>
PsiXmlParticipantWriter<P>[]PsiXmlElementWriterFactory. createParticipantWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlType xmlType, InteractionCategory category, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlXrefWriter primaryRefWriter, PsiXmlElementWriter<Confidence> confidenceWriter, PsiXmlElementWriter<Interactor> interactorWriter, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter, PsiXmlParameterWriter parameterWriter)createParticipantWriter.static PsiXmlElementWriter<Position>[]PsiXmlElementWriterFactory. createPositionsWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlVariableNameWriter<CvTerm> statusWriter)createPositionsWriter.static PsiXmlElementWriter<Preassembly>PsiXmlElementWriterFactory. createPreassemblyWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter, PsiXmlElementWriter<Annotation> attributeWriter, PsiXmlPublicationWriter publicationWriter)createPreassemblyWriter.static PsiXmlElementWriter<Range>PsiXmlElementWriterFactory. createRangeWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlXrefWriter refWriter, PsiXmlVariableNameWriter<CvTerm> statusWriter)createRangeWriter.static PsiXmlElementWriter<VariableParameter>PsiXmlElementWriterFactory. createVariableParameterWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVariableNameWriter<CvTerm> cvWriter)createVariableParameterWriter. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl that return types with arguments of type CvTerm Modifier and Type Method Description PsiXmlVariableNameWriter<CvTerm>XmlInteractorWriter. getInteractorTypeWriter()Getter for the fieldinteractorTypeWriter.PsiXmlVariableNameWriter<CvTerm>XmlConfidenceWriter. getTypeWriter()Getter for the fieldtypeWriter.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl with parameters of type CvTerm Modifier and Type Method Description voidXmlCvTermWriter. write(CvTerm object, String name)write.protected voidXmlCvTermWriter. writeOtherProperties(CvTerm term)writeOtherProperties.protected voidXmlOpenCvTermWriter. writeOtherProperties(CvTerm object)writeOtherProperties.protected voidXmlCvTermWriter. writeXrefFromCvIdentifiers(CvTerm object)writeXrefFromCvIdentifiers.protected voidXmlCvTermWriter. writeXrefFromCvXrefs(CvTerm object)writeXrefFromCvXrefs.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl with type arguments of type CvTerm Modifier and Type Method Description voidXmlInteractorWriter. setInteractorTypeWriter(PsiXmlVariableNameWriter<CvTerm> interactorTypeWriter)Setter for the fieldinteractorTypeWriter.voidXmlConfidenceWriter. setTypeWriter(PsiXmlVariableNameWriter<CvTerm> typeWriter)Setter for the fieldtypeWriter. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts that return CvTerm Modifier and Type Method Description CvTermAbstractXmlExperimentWriter. extractDefaultParticipantIdentificationMethod(Experiment exp)extractDefaultParticipantIdentificationMethod.protected CvTermAbstractXmlInteractionWriter. newXmlCvTerm(String shortName, CvTerm database, String id, CvTerm qualifier)CvTermAbstractXmlExperimentWriter. writeExperiment(Experiment object)writeExperiment.protected CvTermAbstractXmlInteractionWriter. writeExperimentDescription()writeExperimentDescription.protected CvTermAbstractXmlInteractionWriter. writeExperimentRef()writeExperimentRef.protected CvTermAbstractXmlInteractionEvidenceWriter. writeExperiments(I object)writeExperiments.protected abstract CvTermAbstractXmlInteractionWriter. writeExperiments(T object)writeExperiments.protected CvTermAbstractXmlModelledInteractionWriter. writeExperiments(I object)writeExperiments.protected CvTermAbstractXmlExperimentWriter. writeParticipantIdentificationMethod(Experiment object)writeParticipantIdentificationMethod.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts that return types with arguments of type CvTerm Modifier and Type Method Description PsiXmlVariableNameWriter<CvTerm>AbstractXmlParticipantWriter. getBiologicalRoleWriter()Getter for the fieldbiologicalRoleWriter.PsiXmlVariableNameWriter<CvTerm>AbstractXmlOrganismWriter. getCvWriter()Getter for the fieldcvWriter.PsiXmlVariableNameWriter<CvTerm>AbstractXmlExperimentWriter. getDetectionMethodWriter()Getter for the fielddetectionMethodWriter.PsiXmlVariableNameWriter<CvTerm>AbstractXmlParticipantEvidenceWriter. getExperimentalCvWriter()getExperimentalCvWriter.PsiXmlVariableNameWriter<CvTerm>AbstractXmlFeatureWriter. getFeatureTypeWriter()Getter for the fieldfeatureTypeWriter.PsiXmlVariableNameWriter<CvTerm>AbstractXmlInteractionWriter. getInteractionTypeWriter()Getter for the fieldinteractionTypeWriter.PsiXmlVariableNameWriter<CvTerm>AbstractXmlPositionWriter. getStatusWriter()Getter for the fieldstatusWriter.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with parameters of type CvTerm Modifier and Type Method Description protected CvTermAbstractXmlInteractionWriter. newXmlCvTerm(String shortName, CvTerm database, String id, CvTerm qualifier)voidAbstractXmlParticipantWriter. writeParticipant(P object, CvTerm detectionMethod)writeParticipant.protected voidAbstractXmlModelledParticipantWriter. writeParticipantIdentificationMethods(ModelledParticipant object, CvTerm method)writeParticipantIdentificationMethods.protected voidAbstractXmlParticipantEvidenceWriter. writeParticipantIdentificationMethods(ParticipantEvidence object, CvTerm experimentMethod)writeParticipantIdentificationMethods.protected abstract voidAbstractXmlParticipantWriter. writeParticipantIdentificationMethods(P object, CvTerm method)writeParticipantIdentificationMethods.protected voidAbstractXmlInteractionWriter. writeParticipants(T object, CvTerm method)writeParticipants.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with type arguments of type CvTerm Modifier and Type Method Description voidAbstractXmlParticipantWriter. setBiologicalRoleWriter(PsiXmlVariableNameWriter<CvTerm> biologicalRoleWriter)Setter for the fieldbiologicalRoleWriter.voidAbstractXmlOrganismWriter. setCvWriter(PsiXmlVariableNameWriter<CvTerm> cvWriter)Setter for the fieldcvWriter.voidAbstractXmlExperimentWriter. setDetectionMethodWriter(PsiXmlVariableNameWriter<CvTerm> detectionMethodWriter)Setter for the fielddetectionMethodWriter.voidAbstractXmlParticipantEvidenceWriter. setExperimentalCvWriter(PsiXmlVariableNameWriter<CvTerm> cvWriter)setExperimentalCvWriter.voidAbstractXmlFeatureWriter. setFeatureTypeWriter(PsiXmlVariableNameWriter<CvTerm> featureTypeWriter)Setter for the fieldfeatureTypeWriter.voidAbstractXmlInteractionWriter. setInteractionTypeWriter(PsiXmlVariableNameWriter<CvTerm> interactionTypeWriter)Setter for the fieldinteractionTypeWriter.voidAbstractXmlPositionWriter. setStatusWriter(PsiXmlVariableNameWriter<CvTerm> statusWriter)Setter for the fieldstatusWriter. -
Uses of CvTerm 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 CvTerm Modifier and Type Method Description protected voidAbstractXmlParticipantWriter. writeParticipantIdentificationMethods(Participant object, CvTerm method)writeParticipantIdentificationMethods. -
Uses of CvTerm 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 that return CvTerm Modifier and Type Method Description protected CvTermAbstractXmlModelledInteractionWriter. writeExperimentDescription()writeExperimentDescription.protected CvTermAbstractXmlModelledInteractionWriter. writeExperimentRef()writeExperimentRef.protected CvTermAbstractXmlModelledInteractionWriter. writeExperiments(I object)writeExperiments.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30 that return types with arguments of type CvTerm Modifier and Type Method Description PsiXmlVariableNameWriter<CvTerm>AbstractXmlCooperativeEffectWriter. getCvWriter()Getter for the fieldcvWriter.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30 with parameters of type CvTerm Modifier and Type Method Description protected voidAbstractXmlModelledParticipantWriter. writeParticipantIdentificationMethods(ModelledParticipant object, CvTerm method)writeParticipantIdentificationMethods.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30 with type arguments of type CvTerm Modifier and Type Method Description voidAbstractXmlCooperativeEffectWriter. setCvWriter(PsiXmlVariableNameWriter<CvTerm> cvWriter)Setter for the fieldcvWriter. -
Uses of CvTerm 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 that return CvTerm Modifier and Type Method Description protected CvTermXmlBasicBinaryInteractionWriter. writeExperiments(BinaryInteraction object)writeExperiments.protected CvTermXmlBasicInteractionWriter. writeExperiments(Interaction object)writeExperiments.protected CvTermXmlBinaryInteractionEvidenceWriter. writeExperiments(BinaryInteractionEvidence object)writeExperiments.protected CvTermXmlComplexWriter. writeExperiments(Complex object)writeExperiments.protected CvTermXmlInteractionEvidenceWriter. writeExperiments(InteractionEvidence object)writeExperiments.protected CvTermXmlModelledBinaryInteractionWriter. writeExperiments(ModelledBinaryInteraction object)writeExperiments.protected CvTermXmlModelledInteractionWriter. writeExperiments(ModelledInteraction object)writeExperiments. -
Uses of CvTerm 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 that return CvTerm Modifier and Type Method Description protected CvTermXmlBinaryInteractionEvidenceWriter. writeExperiments(BinaryInteractionEvidence object)writeExperiments.protected CvTermXmlInteractionEvidenceWriter. writeExperiments(InteractionEvidence object)writeExperiments.protected CvTermXmlModelledBinaryInteractionWriter. writeExperiments(ModelledBinaryInteraction object)writeExperiments.protected CvTermXmlModelledInteractionWriter. writeExperiments(ModelledInteraction object)writeExperiments. -
Uses of CvTerm 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 that return CvTerm Modifier and Type Method Description protected CvTermXmlBasicBinaryInteractionWriter. writeExperiments(BinaryInteraction object)writeExperiments.protected CvTermXmlBasicInteractionWriter. writeExperiments(Interaction object)writeExperiments.protected CvTermXmlBinaryInteractionEvidenceWriter. writeExperiments(BinaryInteractionEvidence object)writeExperiments.protected CvTermXmlComplexWriter. writeExperiments(Complex object)writeExperiments.protected CvTermXmlInteractionEvidenceWriter. writeExperiments(InteractionEvidence object)writeExperiments.protected CvTermXmlModelledBinaryInteractionWriter. writeExperiments(ModelledBinaryInteraction object)writeExperiments.protected CvTermXmlModelledInteractionWriter. writeExperiments(ModelledInteraction object)writeExperiments. -
Uses of CvTerm 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 that return CvTerm Modifier and Type Method Description protected CvTermXmlBinaryInteractionEvidenceWriter. writeExperiments(BinaryInteractionEvidence object)writeExperiments.protected CvTermXmlInteractionEvidenceWriter. writeExperiments(InteractionEvidence object)writeExperiments.protected CvTermXmlModelledBinaryInteractionWriter. writeExperiments(ModelledBinaryInteraction object)writeExperiments.protected CvTermXmlModelledInteractionWriter. writeExperiments(ModelledInteraction object)writeExperiments. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended that return CvTerm Modifier and Type Method Description protected CvTermAbstractXmlInteractionEvidenceWriter. writeExperimentDescription()writeExperimentDescription.protected CvTermAbstractXmlInteractionEvidenceWriter. writeExperimentRef()writeExperimentRef.protected CvTermAbstractXmlInteractionEvidenceWriter. writeExperiments(I object)writeExperiments. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml25
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml25 that return CvTerm Modifier and Type Method Description protected CvTermXmlBasicBinaryInteractionWriter. writeExperiments(BinaryInteraction object)writeExperiments.protected CvTermXmlBasicInteractionWriter. writeExperiments(Interaction object)writeExperiments.protected CvTermXmlBinaryInteractionEvidenceWriter. writeExperiments(BinaryInteractionEvidence object)writeExperiments.protected CvTermXmlComplexWriter. writeExperiments(Complex object)writeExperiments.protected CvTermXmlInteractionEvidenceWriter. writeExperiments(InteractionEvidence object)writeExperiments.protected CvTermXmlModelledBinaryInteractionWriter. writeExperiments(ModelledBinaryInteraction object)writeExperiments.protected CvTermXmlModelledInteractionWriter. writeExperiments(ModelledInteraction object)writeExperiments. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml30
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml30 that return CvTerm Modifier and Type Method Description protected CvTermXmlBinaryInteractionEvidenceWriter. writeExperiments(BinaryInteractionEvidence object)writeExperiments.protected CvTermXmlInteractionEvidenceWriter. writeExperiments(InteractionEvidence object)writeExperiments. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml25
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml25 that return CvTerm Modifier and Type Method Description protected CvTermXmlBasicBinaryInteractionWriter. writeExperiments(BinaryInteraction object)writeExperiments.protected CvTermXmlBasicInteractionWriter. writeExperiments(Interaction object)writeExperiments.protected CvTermXmlBinaryInteractionEvidenceWriter. writeExperiments(BinaryInteractionEvidence object)writeExperiments.protected CvTermXmlComplexWriter. writeExperiments(Complex object)writeExperiments.protected CvTermXmlInteractionEvidenceWriter. writeExperiments(InteractionEvidence object)writeExperiments.protected CvTermXmlModelledBinaryInteractionWriter. writeExperiments(ModelledBinaryInteraction object)writeExperiments.protected CvTermXmlModelledInteractionWriter. writeExperiments(ModelledInteraction object)writeExperiments. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml30
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml30 that return CvTerm Modifier and Type Method Description protected CvTermXmlBinaryInteractionEvidenceWriter. writeExperiments(BinaryInteractionEvidence object)writeExperiments.protected CvTermXmlInteractionEvidenceWriter. writeExperiments(InteractionEvidence object)writeExperiments. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25 that return CvTerm Modifier and Type Method Description CvTermXmlExperimentWriter. extractDefaultParticipantIdentificationMethod(Experiment exp)extractDefaultParticipantIdentificationMethod.protected CvTermAbstractXmlInteractionWriter. writeExperimentDescription()writeExperimentDescription.protected CvTermAbstractXmlModelledInteractionWriter. writeExperimentDescription()writeExperimentDescription.protected CvTermAbstractXmlInteractionWriter. writeExperimentRef()writeExperimentRef.protected CvTermAbstractXmlModelledInteractionWriter. writeExperimentRef()writeExperimentRef.protected CvTermAbstractXmlModelledInteractionWriter. writeExperiments(I object)writeExperiments.protected CvTermXmlExperimentWriter. writeParticipantIdentificationMethod(Experiment object)writeParticipantIdentificationMethod. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml253
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml253 that return types with arguments of type CvTerm Modifier and Type Method Description PsiXmlVariableNameWriter<CvTerm>XmlConfidenceWriter. getTypeWriter()Getter for the fieldtypeWriter.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml253 with parameters of type CvTerm Modifier and Type Method Description protected voidXmlExperimentalCvTermWriter. writeOtherProperties(CvTerm object)writeOtherProperties.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml253 with type arguments of type CvTerm Modifier and Type Method Description voidXmlConfidenceWriter. setTypeWriter(PsiXmlVariableNameWriter<CvTerm> typeWriter)Setter for the fieldtypeWriter. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml254
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml254 that return types with arguments of type CvTerm Modifier and Type Method Description PsiXmlVariableNameWriter<CvTerm>XmlConfidenceWriter. getTypeWriter()Getter for the fieldtypeWriter.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml254 with parameters of type CvTerm Modifier and Type Method Description protected voidXmlExperimentalCvTermWriter. writeOtherProperties(CvTerm object)writeOtherProperties.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml254 with type arguments of type CvTerm Modifier and Type Method Description voidXmlConfidenceWriter. setTypeWriter(PsiXmlVariableNameWriter<CvTerm> typeWriter)Setter for the fieldtypeWriter. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30 that return CvTerm Modifier and Type Method Description CvTermXmlExperimentWriter. extractDefaultParticipantIdentificationMethod(Experiment exp)extractDefaultParticipantIdentificationMethod.protected CvTermAbstractXmlModelledInteractionWriter. writeExperimentDescription()writeExperimentDescription.protected CvTermAbstractXmlModelledInteractionWriter. writeExperimentRef()writeExperimentRef.protected CvTermAbstractXmlModelledInteractionWriter. writeExperiments(I object)writeExperiments.protected CvTermXmlExperimentWriter. writeParticipantIdentificationMethod(Experiment object)writeParticipantIdentificationMethod.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30 that return types with arguments of type CvTerm Modifier and Type Method Description PsiXmlVariableNameWriter<CvTerm>XmlConfidenceWriter. getTypeWriter()Getter for the fieldtypeWriter.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30 with parameters of type CvTerm Modifier and Type Method Description protected voidXmlExperimentalCvTermWriter. writeOtherProperties(CvTerm object)writeOtherProperties.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30 with type arguments of type CvTerm Modifier and Type Method Description voidXmlConfidenceWriter. setTypeWriter(PsiXmlVariableNameWriter<CvTerm> typeWriter)Setter for the fieldtypeWriter. -
Uses of CvTerm in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30
Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 that return types with arguments of type CvTerm Modifier and Type Method Description PsiXmlVariableNameWriter<CvTerm>XmlCausalRelationshipWriter. getCausalStatementWriter()Getter for the fieldcausalStatementWriter.PsiXmlVariableNameWriter<CvTerm>XmlCooperativityEvidenceWriter. getCvWriter()Getter for the fieldcvWriter.PsiXmlVariableNameWriter<CvTerm>XmlVariableParameterWriter. getUnitWriter()Getter for the fieldunitWriter.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 with type arguments of type CvTerm Modifier and Type Method Description voidXmlCausalRelationshipWriter. setCausalStatementWriter(PsiXmlVariableNameWriter<CvTerm> causalStatementWriter)Setter for the fieldcausalStatementWriter.voidXmlCooperativityEvidenceWriter. setCvWriter(PsiXmlVariableNameWriter<CvTerm> cvWriter)Setter for the fieldcvWriter.voidXmlVariableParameterWriter. setUnitWriter(PsiXmlVariableNameWriter<CvTerm> unitWriter)Setter for the fieldunitWriter. -
Uses of CvTerm in psidev.psi.mi.jami.xml.listener
Method parameters in psidev.psi.mi.jami.xml.listener with type arguments of type CvTerm Modifier and Type Method Description voidPsiXmlParserCompositeListener. onSeveralExperimentalRolesFound(Collection<CvTerm> roles, FileSourceLocator locator)onSeveralExperimentalRolesFound.voidPsiXmlParserListener. onSeveralExperimentalRolesFound(Collection<CvTerm> roles, FileSourceLocator locator)onSeveralExperimentalRolesFound.voidPsiXmlParserLogger. onSeveralExperimentalRolesFound(Collection<CvTerm> roles, FileSourceLocator locator)onSeveralExperimentalRolesFound. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension
Subinterfaces of CvTerm in psidev.psi.mi.jami.xml.model.extension Modifier and Type Interface Description interfaceExtendedPsiXmlSourceExtended source for PSI-XML standardsMethods in psidev.psi.mi.jami.xml.model.extension that return CvTerm Modifier and Type Method Description CvTermExtendedPsiXmlExperiment. getFeatureDetectionMethod()getFeatureDetectionMethod.CvTermAbstractBaseXmlInteractor. getInteractorType()Gets the value of the interactorType property.CvTermExtendedPsiXmlExperiment. getParticipantIdentificationMethod()getParticipantIdentificationMethod.Methods in psidev.psi.mi.jami.xml.model.extension that return types with arguments of type CvTerm Modifier and Type Method Description List<CvTerm>ExtendedPsiXmlParticipantEvidence. getExperimentalRoles()getExperimentalRoles.List<CvTerm>ExtendedPsiXmlInteraction. getInteractionTypes()getInteractionTypes.Methods in psidev.psi.mi.jami.xml.model.extension with parameters of type CvTerm Modifier and Type Method Description voidExtendedPsiXmlExperiment. setFeatureDetectionMethod(CvTerm method)setFeatureDetectionMethod.voidAbstractBaseXmlInteractor. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidAbstractBaseXmlInteractor. setJAXBInteractorType(CvTerm interactorType)setJAXBInteractorType.voidExtendedPsiXmlExperiment. setParticipantIdentificationMethod(CvTerm method)setParticipantIdentificationMethod.Constructors in psidev.psi.mi.jami.xml.model.extension with parameters of type CvTerm Constructor Description AbstractBaseXmlInteractor(String name, String fullName, CvTerm type)Constructor for AbstractBaseXmlInteractor.AbstractBaseXmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for AbstractBaseXmlInteractor.AbstractBaseXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractBaseXmlInteractor.AbstractBaseXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for AbstractBaseXmlInteractor.AbstractBaseXmlInteractor(String name, CvTerm type)Constructor for AbstractBaseXmlInteractor.AbstractBaseXmlInteractor(String name, CvTerm type, Organism organism)Constructor for AbstractBaseXmlInteractor.AbstractBaseXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractBaseXmlInteractor.AbstractBaseXmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for AbstractBaseXmlInteractor.XmlChecksum(CvTerm method, String value)Constructor for XmlChecksum. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension.binary
Methods in psidev.psi.mi.jami.xml.model.extension.binary that return CvTerm Modifier and Type Method Description CvTermXmlBinaryInteractionEvidenceWrapper. getCausalRegulatoryMechanism()getCausalRegulatoryMechanism.CvTermXmlBinaryInteractionWrapper. getCausalRegulatoryMechanism()getCausalRegulatoryMechanism.CvTermXmlModelledBinaryInteractionWrapper. getCausalRegulatoryMechanism()getCausalRegulatoryMechanism.CvTermXmlBinaryInteractionEvidenceWrapper. getComplexExpansion()getComplexExpansion.CvTermXmlBinaryInteractionWrapper. getComplexExpansion()getComplexExpansion.CvTermXmlModelledBinaryInteractionWrapper. getComplexExpansion()getComplexExpansion.CvTermXmlModelledBinaryInteraction. getEvidenceType()Getter for the fieldevidenceType.CvTermXmlModelledBinaryInteractionWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermAbstractExtendedXmlBinaryInteraction. getInteractionType()Getter for the fieldinteractionType.CvTermXmlBinaryInteractionEvidenceWrapper. getInteractionType()The interaction type is a controlled vocabulary term.CvTermXmlBinaryInteractionWrapper. getInteractionType()The interaction type is a controlled vocabulary term.CvTermXmlModelledBinaryInteractionWrapper. getInteractionType()The interaction type is a controlled vocabulary term.Methods in psidev.psi.mi.jami.xml.model.extension.binary that return types with arguments of type CvTerm Modifier and Type Method Description List<CvTerm>AbstractExtendedXmlBinaryInteraction. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlBinaryInteractionEvidenceWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlBinaryInteractionWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlModelledBinaryInteractionWrapper. getInteractionTypes()getInteractionTypes.Methods in psidev.psi.mi.jami.xml.model.extension.binary with parameters of type CvTerm Modifier and Type Method Description voidXmlBinaryInteractionEvidenceWrapper. setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)Sets the causal regulatory mechanism of this binary interactionvoidXmlBinaryInteractionWrapper. setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)Sets the causal regulatory mechanism of this binary interactionvoidXmlModelledBinaryInteractionWrapper. setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)Sets the causal regulatory mechanism of this binary interactionvoidXmlBinaryInteractionEvidenceWrapper. setComplexExpansion(CvTerm expansion)Sets the complex expansion of this binary interactionvoidXmlBinaryInteractionWrapper. setComplexExpansion(CvTerm expansion)Sets the complex expansion of this binary interactionvoidXmlModelledBinaryInteractionWrapper. setComplexExpansion(CvTerm expansion)Sets the complex expansion of this binary interactionvoidXmlModelledBinaryInteraction. setEvidenceType(CvTerm evidenceType)Sets the evidence typevoidXmlModelledBinaryInteractionWrapper. setEvidenceType(CvTerm eco)Sets the evidence typeprotected abstract voidAbstractXmlBinaryInteractionEvidence. setImexId(CvTerm database, String id, CvTerm qualifier)voidAbstractExtendedXmlBinaryInteraction. setInteractionType(CvTerm term)Sets the interaction type.voidXmlBinaryInteractionEvidenceWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidXmlBinaryInteractionWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidXmlModelledBinaryInteractionWrapper. setInteractionType(CvTerm term)Sets the interaction type.Constructors in psidev.psi.mi.jami.xml.model.extension.binary with parameters of type CvTerm Constructor Description AbstractExtendedXmlBinaryInteraction(String shortName, P participantA, P participantB, CvTerm complexExpansion)Constructor for AbstractExtendedXmlBinaryInteraction.AbstractExtendedXmlBinaryInteraction(String shortName, CvTerm type)Constructor for AbstractExtendedXmlBinaryInteraction.AbstractExtendedXmlBinaryInteraction(String shortName, CvTerm type, P participantA, P participantB)Constructor for AbstractExtendedXmlBinaryInteraction.AbstractExtendedXmlBinaryInteraction(String shortName, CvTerm type, P participantA, P participantB, CvTerm complexExpansion)Constructor for AbstractExtendedXmlBinaryInteraction.AbstractExtendedXmlBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for AbstractExtendedXmlBinaryInteraction.AbstractExtendedXmlBinaryInteraction(P participantA, P participantB, CvTerm complexExpansion)Constructor for AbstractExtendedXmlBinaryInteraction.AbstractExtendedXmlBinaryInteraction(CvTerm complexExpansion)Constructor for AbstractExtendedXmlBinaryInteraction.AbstractXmlBinaryInteraction(String shortName, P participantA, P participantB, CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteraction.AbstractXmlBinaryInteraction(String shortName, CvTerm type)Constructor for AbstractXmlBinaryInteraction.AbstractXmlBinaryInteraction(String shortName, CvTerm type, P participantA, P participantB)Constructor for AbstractXmlBinaryInteraction.AbstractXmlBinaryInteraction(String shortName, CvTerm type, P participantA, P participantB, CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteraction.AbstractXmlBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteraction.AbstractXmlBinaryInteraction(P participantA, P participantB, CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteraction.AbstractXmlBinaryInteraction(CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteraction.AbstractXmlBinaryInteractionEvidence(String shortName, CvTerm type)Constructor for AbstractXmlBinaryInteractionEvidence.AbstractXmlBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteractionEvidence.AbstractXmlBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)Constructor for AbstractXmlBinaryInteractionEvidence.AbstractXmlBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteractionEvidence.AbstractXmlBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteractionEvidence.AbstractXmlBinaryInteractionEvidence(CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteractionEvidence.AbstractXmlBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for AbstractXmlBinaryInteractionEvidence.XmlBinaryInteraction(String shortName, CvTerm type)Constructor for XmlBinaryInteraction.XmlBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for XmlBinaryInteraction.XmlBinaryInteraction(String shortName, CvTerm type, Participant participantA, Participant participantB)Constructor for XmlBinaryInteraction.XmlBinaryInteraction(String shortName, CvTerm type, Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteraction.XmlBinaryInteraction(String shortName, Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteraction.XmlBinaryInteraction(CvTerm complexExpansion)Constructor for XmlBinaryInteraction.XmlBinaryInteraction(Participant participantA, Participant participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteraction.XmlBinaryInteractionEvidenceWrapper(ExtendedPsiXmlInteractionEvidence interaction, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidenceWrapper.XmlBinaryInteractionWrapper(ExtendedPsiXmlInteraction interaction, CvTerm complexExpansion)Constructor for XmlBinaryInteractionWrapper.XmlModelledBinaryInteraction(String shortName, CvTerm type)Constructor for XmlModelledBinaryInteraction.XmlModelledBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for XmlModelledBinaryInteraction.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, CvTerm complexExpansion)Constructor for XmlModelledBinaryInteraction.XmlModelledBinaryInteraction(CvTerm complexExpansion)Constructor for XmlModelledBinaryInteraction.XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)Constructor for XmlModelledBinaryInteraction.XmlModelledBinaryInteractionWrapper(ExtendedPsiXmlModelledInteraction interaction, CvTerm complexExpansion)Constructor for XmlModelledBinaryInteractionWrapper. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension.binary.xml253
Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml253 with parameters of type CvTerm Modifier and Type Method Description voidXmlBinaryInteractionEvidence. setImexId(CvTerm database, String id, CvTerm qualifier)Constructors in psidev.psi.mi.jami.xml.model.extension.binary.xml253 with parameters of type CvTerm Constructor Description XmlBinaryInteractionEvidence(String shortName, CvTerm type)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension.binary.xml254
Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml254 with parameters of type CvTerm Modifier and Type Method Description voidXmlBinaryInteractionEvidence. setImexId(CvTerm database, String id, CvTerm qualifier)Constructors in psidev.psi.mi.jami.xml.model.extension.binary.xml254 with parameters of type CvTerm Constructor Description XmlBinaryInteractionEvidence(String shortName, CvTerm type)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension.binary.xml30
Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 that return CvTerm Modifier and Type Method Description CvTermXmlModelledBinaryInteractionWrapper. getCausalRegulatoryMechanism()getCausalRegulatoryMechanism.CvTermXmlModelledBinaryInteractionWrapper. getComplexExpansion()getComplexExpansion.CvTermXmlModelledBinaryInteraction. getEvidenceType()Getter for the fieldevidenceType.CvTermXmlModelledBinaryInteractionWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlModelledBinaryInteractionWrapper. getInteractionType()The interaction type is a controlled vocabulary term.CvTermXmlModelledBinaryInteraction. getInteractorType()The molecule type of this interactor.CvTermXmlModelledBinaryInteractionWrapper. getInteractorType()The molecule type of this interactor.Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 with parameters of type CvTerm Modifier and Type Method Description voidXmlModelledBinaryInteractionWrapper. setCausalRegulatoryMechanism(CvTerm causalRegulatoryMechanism)Sets the causal regulatory mechanism of this binary interactionvoidXmlModelledBinaryInteractionWrapper. setComplexExpansion(CvTerm expansion)Sets the complex expansion of this binary interactionvoidXmlModelledBinaryInteraction. setEvidenceType(CvTerm evidenceType)Sets the evidence typevoidXmlModelledBinaryInteractionWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlBinaryInteractionEvidence. setImexId(CvTerm database, String id, CvTerm qualifier)voidXmlModelledBinaryInteractionWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidXmlModelledBinaryInteraction. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlModelledBinaryInteractionWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)Constructors in psidev.psi.mi.jami.xml.model.extension.binary.xml30 with parameters of type CvTerm Constructor Description XmlBinaryInteractionEvidence(String shortName, CvTerm type)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, CvTerm type, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(String shortName, ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidence(ParticipantEvidence participantA, ParticipantEvidence participantB, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidence.XmlBinaryInteractionEvidenceWrapper(ExtendedPsiXmlInteractionEvidence interaction, CvTerm complexExpansion)Constructor for XmlBinaryInteractionEvidenceWrapper.XmlModelledBinaryInteraction(String shortName, CvTerm type)Constructor for XmlModelledBinaryInteraction.XmlModelledBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)Constructor for XmlModelledBinaryInteraction.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, CvTerm complexExpansion)Constructor for XmlModelledBinaryInteraction.XmlModelledBinaryInteraction(CvTerm complexExpansion)Constructor for XmlModelledBinaryInteraction.XmlModelledBinaryInteraction(ModelledParticipant participantA, ModelledParticipant participantB, CvTerm complexExpansion)Constructor for XmlModelledBinaryInteraction.XmlModelledBinaryInteractionWrapper(ExtendedPsiXmlModelledInteraction interaction, CvTerm complexExpansion)Constructor for XmlModelledBinaryInteractionWrapper. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension.datasource
Methods in psidev.psi.mi.jami.xml.model.extension.datasource with parameters of type CvTerm Modifier and Type Method Description voidAbstractPsiXmlStream. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.voidDefaultPsiXmlStreamSource. onMissingCvTermName(CvTerm term, FileSourceContext context, String message)Listen to an event fired when a CvTerm is read and does not have any names.Method parameters in psidev.psi.mi.jami.xml.model.extension.datasource with type arguments of type CvTerm Modifier and Type Method Description voidAbstractPsiXmlStream. onSeveralExperimentalRolesFound(Collection<CvTerm> roles, FileSourceLocator locator)onSeveralExperimentalRolesFound.voidDefaultPsiXmlStreamSource. onSeveralExperimentalRolesFound(Collection<CvTerm> roles, FileSourceLocator locator)onSeveralExperimentalRolesFound. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension.factory
Methods in psidev.psi.mi.jami.xml.model.extension.factory with parameters of type CvTerm Modifier and Type Method Description BioactiveEntityXmlInteractorFactory. createBioactiveEntity(String name, CvTerm type)Creates a new BioactiveEntity with the name and interactor typeComplexXmlInteractorFactory. createComplex(String name, CvTerm type)Creates a new Complex with the name and interactor typeInteractorXmlInteractorFactory. createInteractor(String name, CvTerm type)Creates a default interactor from the name and interactor typeInteractorPoolXmlInteractorFactory. createInteractorSet(String name, CvTerm type)Creates an interactor pool from the name and interactor typeNucleicAcidXmlInteractorFactory. createNucleicAcid(String name, CvTerm type)Creates a new NucleicAcid with the name and interactor typePolymerXmlInteractorFactory. createPolymer(String name, CvTerm type)Creates a new Polymer with the name and interactor typeProteinXmlInteractorFactory. createProtein(String name, CvTerm type)Creates a new Protein with the name and interactor type -
Uses of CvTerm 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 CvTerm Modifier and Type Method Description BinaryInteractionXmlBinaryInteractionFactory. createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)Create a new BinaryInteraction object from an Interaction parent and two participantsBinaryInteractionEvidenceXmlBinaryInteractionFactory. createBinaryInteractionEvidenceFrom(InteractionEvidence interaction, ParticipantEvidence p1, ParticipantEvidence p2, CvTerm expansionMethod)Create a new BinaryInteractionEvidence object from an InteractionEvidence parent and two participants evidencesModelledBinaryInteractionXmlBinaryInteractionFactory. createModelledBinaryInteractionFrom(ModelledInteraction interaction, ModelledParticipant p1, ModelledParticipant p2, CvTerm expansionMethod)Create a new ModelledBinaryInteraction object from a ModelledInteraction parent and two modelled participants -
Uses of CvTerm 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 CvTerm Modifier and Type Method Description BinaryInteractionXmlBinaryInteractionFactory. createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod)Create a new BinaryInteraction object from an Interaction parent and two participantsBinaryInteractionEvidenceXmlBinaryInteractionFactory. createBinaryInteractionEvidenceFrom(InteractionEvidence interaction, ParticipantEvidence p1, ParticipantEvidence p2, CvTerm expansionMethod)Create a new BinaryInteractionEvidence object from an InteractionEvidence parent and two participants evidencesModelledBinaryInteractionXmlBinaryInteractionFactory. createModelledBinaryInteractionFrom(ModelledInteraction interaction, ModelledParticipant p1, ModelledParticipant p2, CvTerm expansionMethod)Create a new ModelledBinaryInteraction object from a ModelledInteraction parent and two modelled participants -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension.xml253
Classes in psidev.psi.mi.jami.xml.model.extension.xml253 that implement CvTerm Modifier and Type Class Description classAbstractXmlCvTermAbstract cv termclassAbstractXmlSourceDesciption of the source of the entry, usually an organisationclassDefaultXmlSourceDesciption of the source of the entry, usually an organisationclassExperimentalCvTermThis elements is controlled by the PSI-MI controlled vocabulary "experimentalPreparation", root term id MI:0346.classXmlCvTermXml implementation of CvTerm.classXmlOpenCvTermXml implementation of CvTerm.classXmlSourceDesciption of the source of the entry, usually an organisationMethods in psidev.psi.mi.jami.xml.model.extension.xml253 that return CvTerm Modifier and Type Method Description CvTermXmlAllostery. getAllostericMechanism()Getter for the fieldallostericMechanism.CvTermXmlAllostery. getAllosteryType()Getter for the fieldallosteryType.CvTermAbstractXmlParticipant. getBiologicalEffect()Gets the value of the biologicalEffect property.CvTermAbstractXmlParticipantPool. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermXmlParticipantEvidenceWrapper. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermXmlParticipantWrapper. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermAbstractXmlParticipant. getBiologicalRole()Gets the value of the biologicalRole property.CvTermAbstractXmlParticipantPool. getBiologicalRole()The biological role of the participant.CvTermXmlParticipantEvidenceWrapper. getBiologicalRole()The biological role of the participant.CvTermXmlParticipantWrapper. getBiologicalRole()The biological role of the participant.CvTermXmlOrganism. getCellType()Getter for the fieldcellType.CvTermXmlOrganism. getCompartment()Getter for the fieldcompartment.CvTermXmlXref. getDatabase()Getter for the fielddatabase.CvTermAbstractXmlModelledInteraction. getEvidenceType()Getter for the fieldevidenceType.CvTermXmlBasicInteractionComplexWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlInteractionEvidenceComplexWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlModelledInteractionComplexWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlExperimentalParticipantPool. getExperimentalRole()The experimental role of the participant.CvTermXmlParticipantEvidence. getExperimentalRole()getExperimentalRole.CvTermAbstractXmlExperiment. getFeatureDetectionMethod()Gets the value of the featureDetectionMethod property.CvTermAbstractXmlExperiment. getInteractionDetectionMethod()Gets the value of the interactionDetectionMethod property.CvTermAbstractPsiXmlInteraction. getInteractionType()getInteractionType.abstract CvTermAbstractXmlInteraction. getInteractionType()getInteractionType.CvTermXmlBasicInteractionComplexWrapper. getInteractionType()getInteractionType.CvTermXmlInteractionEvidenceComplexWrapper. getInteractionType()getInteractionType.CvTermXmlModelledInteractionComplexWrapper. getInteractionType()getInteractionType.CvTermAbstractXmlComplex. getInteractorType()The molecule type of this interactor.CvTermXmlBasicInteractionComplexWrapper. getInteractorType()The molecule type of this interactor.CvTermXmlInteractionEvidenceComplexWrapper. getInteractorType()The molecule type of this interactor.CvTermXmlModelledInteractionComplexWrapper. getInteractorType()The molecule type of this interactor.CvTermAbstractXmlExperiment. getParticipantIdentificationMethod()Gets the value of the participantIdentificationMethod property.CvTermXmlXref. getQualifier()Getter for the fieldqualifier.CvTermAbstractXmlFeature. getRole()Getter for the fieldrole.CvTermXmlFeatureEvidenceWrapper. getRole()The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature.CvTermXmlFeatureWrapper. getRole()The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature.CvTermAbstractXmlPosition. getStatus()Getter for the fieldstatus.CvTermXmlInterval. getStatus()Getter for the fieldstatus.CvTermXmlPosition. getStatus()Getter for the fieldstatus.CvTermXmlOrganism. getTissue()Getter for the fieldtissue.CvTermAbstractXmlAnnotation. getTopic()Getter for the fieldtopic.CvTermAbstractXmlConfidence. getType()Gets the value of the type property.CvTermAbstractXmlFeature. getType()Getter for the fieldtype.CvTermAbstractXmlParameter. getType()Getter for the fieldtype.CvTermAbstractXmlParticipantPool. getType()Getter for the fieldtype.CvTermXmlAlias. getType()Getter for the fieldtype.CvTermXmlConfidenceWrapper. getType()Method used to compute the confidence value.CvTermXmlExperimentalParticipantPoolWrapper. getType()The pool type of this participant pool.CvTermXmlFeatureEvidenceWrapper. getType()The type for this feature.CvTermXmlFeatureWrapper. getType()The type for this feature.CvTermXmlParameterWrapper. getType()The parameter type is a controlled vocabulary term and it cannot be null.CvTermXmlParticipantPoolWrapper. getType()The pool type of this participant pool.CvTermAbstractXmlParameter. getUnit()Getter for the fieldunit.CvTermXmlParameterWrapper. getUnit()Unit of the parameter is a controlled vocabulary term.CvTermXmlVariableParameter. getUnit()Getter for the fieldunit.Methods in psidev.psi.mi.jami.xml.model.extension.xml253 that return types with arguments of type CvTerm Modifier and Type Method Description Collection<CvTerm>XmlFeatureEvidence. getDetectionMethods()getDetectionMethods.Collection<CvTerm>XmlCooperativityEvidence. getEvidenceMethods()Getter for the fieldevidenceMethods.Collection<CvTerm>XmlExperimentalParticipantPool. getExperimentalPreparations()The experimental preparations for this participant.Collection<CvTerm>XmlParticipantEvidence. getExperimentalPreparations()getExperimentalPreparations.List<CvTerm>XmlParticipantEvidence. getExperimentalRoles()getExperimentalRoles.Collection<CvTerm>XmlExperimentalParticipantPool. getIdentificationMethods()The identification methods for this participant.Collection<CvTerm>XmlParticipantEvidence. getIdentificationMethods()getIdentificationMethods.List<CvTerm>AbstractPsiXmlInteraction. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>AbstractXmlBasicInteraction. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>AbstractXmlInteractionEvidence. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>AbstractXmlModelledInteraction. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>XmlBasicInteractionComplexWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlInteractionEvidenceComplexWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlModelledInteractionComplexWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlParticipantEvidence.JAXBExperimentalPreparationWrapper. getJAXBExperimentalPreparations()List<CvTerm>XmlParticipantEvidence.JAXBExperimentalRoleWrapper. getJAXBExperimentalRoles()List<CvTerm>XmlFeatureEvidence. getJAXBFeatureDetectionMethods()getJAXBFeatureDetectionMethods.List<CvTerm>XmlParticipantEvidence.JAXBParticipantIdentificationWrapper. getJAXBParticipantIdentificationMethods()Methods in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type CvTerm Modifier and Type Method Description voidXmlAllostery. setAllostericMechanism(CvTerm mechanism)Sets the allosteric mechanism.voidXmlAllostery. setAllosteryType(CvTerm type)Sets the allostery type.voidAbstractXmlParticipant. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidAbstractXmlParticipantPool. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidXmlParticipantEvidenceWrapper. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidXmlParticipantWrapper. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidAbstractXmlParticipant. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidAbstractXmlParticipantPool. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidXmlParticipantEvidenceWrapper. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidXmlParticipantWrapper. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidXmlOrganism. setCellType(CvTerm cellType)Sets the cell typevoidXmlOrganism. setCompartment(CvTerm compartment)Sets the compartment.voidAbstractXmlModelledInteraction. setEvidenceType(CvTerm evidenceType)Sets the evidence typevoidXmlBasicInteractionComplexWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlInteractionEvidenceComplexWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlModelledInteractionComplexWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlExperimentalParticipantPool. setExperimentalRole(CvTerm expRole)Sets the experimental role.voidXmlParticipantEvidence. setExperimentalRole(CvTerm expRole)Sets the experimental role.voidAbstractXmlExperiment. setFeatureDetectionMethod(CvTerm value)setFeatureDetectionMethod.voidAbstractXmlExperiment. setInteractionDetectionMethod(CvTerm value)Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).voidAbstractPsiXmlInteraction. setInteractionType(CvTerm term)Sets the interaction type.abstract voidAbstractXmlInteraction. setInteractionType(CvTerm term)Sets the interaction type.voidXmlBasicInteractionComplexWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidXmlInteractionEvidenceComplexWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidXmlModelledInteractionComplexWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidAbstractXmlComplex. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlBasicInteractionComplexWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlBioactiveEntity. setInteractorType(CvTerm interactorType)Sets the interactor type of this bioactive entity.voidXmlGene. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlInteractionEvidenceComplexWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlModelledInteractionComplexWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlNucleicAcid. setInteractorType(CvTerm interactorType)Sets the interactor type of this NucleicAcid.voidXmlProtein. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidAbstractXmlExperiment. setParticipantIdentificationMethod(CvTerm value)setParticipantIdentificationMethod.voidAbstractXmlFeature. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidXmlFeatureEvidenceWrapper. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidXmlFeatureWrapper. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidXmlOrganism. setTissue(CvTerm tissue)Sets the tissuevoidAbstractXmlFeature. setType(CvTerm type)Sets the feature type.voidAbstractXmlParticipantPool. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidXmlExperimentalParticipantPoolWrapper. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidXmlFeatureEvidenceWrapper. setType(CvTerm type)Sets the feature type.voidXmlFeatureWrapper. setType(CvTerm type)Sets the feature type.voidXmlParticipantPoolWrapper. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidXmlVariableParameter. setUnit(CvTerm unit)Sets the unit of this variableParameter.Method parameters in psidev.psi.mi.jami.xml.model.extension.xml253 with type arguments of type CvTerm Modifier and Type Method Description protected voidXmlCooperativityEvidence. initialiseEvidenceMethodsWith(Collection<CvTerm> methods)initialiseEvidenceMethodsWith.Constructors in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type CvTerm Constructor Description AbstractPsiXmlInteraction(String shortName, CvTerm type)Constructor for AbstractPsiXmlInteraction.AbstractXmlAnnotation(CvTerm topic)Constructor for AbstractXmlAnnotation.AbstractXmlAnnotation(CvTerm topic, String value)Constructor for AbstractXmlAnnotation.AbstractXmlBasicInteraction(String shortName, CvTerm type)Constructor for AbstractXmlBasicInteraction.AbstractXmlComplex(String name, String fullName, CvTerm type)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type, Organism organism)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlConfidence(CvTerm type, String value)Constructor for AbstractXmlConfidence.AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for AbstractXmlExperiment.AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for AbstractXmlExperiment.AbstractXmlFeature(String shortName, String fullName, CvTerm type)Constructor for AbstractXmlFeature.AbstractXmlFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for AbstractXmlFeature.AbstractXmlFeature(CvTerm type)Constructor for AbstractXmlFeature.AbstractXmlFeature(CvTerm type, String interpro)Constructor for AbstractXmlFeature.AbstractXmlInteraction(String shortName, CvTerm type)Constructor for AbstractXmlInteraction.AbstractXmlInteractionEvidence(String shortName, CvTerm type)Constructor for AbstractXmlInteractionEvidence.AbstractXmlInteractor(String name, String fullName, CvTerm type)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type, Organism organism)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlModelledInteraction(String shortName, CvTerm type)Constructor for AbstractXmlModelledInteraction.AbstractXmlParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty, CvTerm unit)Constructor for AbstractXmlParameter.AbstractXmlParticipant(Interactor interactor, CvTerm bioRole)Constructor for AbstractXmlParticipant.AbstractXmlParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for AbstractXmlParticipant.AbstractXmlPosition(CvTerm status, boolean positionUndetermined)Constructor for AbstractXmlPosition.DefaultXmlAnnotation(CvTerm topic)Constructor for DefaultXmlAnnotation.DefaultXmlAnnotation(CvTerm topic, String value)Constructor for DefaultXmlAnnotation.DefaultXmlBasicInteraction(String shortName, CvTerm type)Constructor for DefaultXmlBasicInteraction.DefaultXmlComplex(String name, String fullName, CvTerm type)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type, Organism organism)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for DefaultXmlExperiment.DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for DefaultXmlExperiment.DefaultXmlInteractionEvidence(String shortName, CvTerm type)Constructor for DefaultXmlInteractionEvidence.DefaultXmlInteractor(String name, String fullName, CvTerm type)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type, Organism organism)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlModelledInteraction(String shortName, CvTerm type)Constructor for DefaultXmlModelledInteraction.HostOrganism(int taxId, String commonName, String scientificName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for HostOrganism.HostOrganism(int taxId, String commonName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for HostOrganism.HostOrganism(int taxId, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for HostOrganism.XmlAlias(String name, CvTerm type)Constructor for XmlAlias.XmlAllostery(CvTerm outcome)Constructor for XmlAllostery.XmlAllostery(CvTerm outcome, CvTerm response)Constructor for XmlAllostery.XmlAnnotation(CvTerm topic)Constructor for XmlAnnotation.XmlAnnotation(CvTerm topic, String value)Constructor for XmlAnnotation.XmlBasicInteraction(String shortName, CvTerm type)Constructor for XmlBasicInteraction.XmlBioactiveEntity(String name, String fullName, CvTerm type)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, String uniqueChebi)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, String uniqueChebi)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Organism organism)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Organism organism, String uniqueChebi)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlComplex(String name, String fullName, CvTerm type)Constructor for XmlComplex.XmlComplex(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlComplex.XmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlComplex.XmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlComplex.XmlComplex(String name, CvTerm type)Constructor for XmlComplex.XmlComplex(String name, CvTerm type, Organism organism)Constructor for XmlComplex.XmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlComplex.XmlComplex(String name, CvTerm type, Xref uniqueId)Constructor for XmlComplex.XmlConfidence(CvTerm type, String value)Constructor for XmlConfidence.XmlExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for XmlExperiment.XmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for XmlExperiment.XmlFeature(String shortName, String fullName, CvTerm type)Constructor for XmlFeature.XmlFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for XmlFeature.XmlFeature(CvTerm type)Constructor for XmlFeature.XmlFeature(CvTerm type, String interpro)Constructor for XmlFeature.XmlFeatureEvidence(String shortName, String fullName, CvTerm type)Constructor for XmlFeatureEvidence.XmlFeatureEvidence(String shortName, String fullName, CvTerm type, String interpro)Constructor for XmlFeatureEvidence.XmlFeatureEvidence(CvTerm type)Constructor for XmlFeatureEvidence.XmlFeatureEvidence(CvTerm type, String interpro)Constructor for XmlFeatureEvidence.XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref ensembl)Constructor for XmlGene.XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlGene(String name, String fullName, CvTerm type, Xref ensembl)Constructor for XmlGene.XmlGene(String name, String fullName, CvTerm type, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Organism organism, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlInteractionEvidence(String shortName, CvTerm type)Constructor for XmlInteractionEvidence.XmlInteractor(String name, String fullName, CvTerm type)Constructor for XmlInteractor.XmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlInteractor.XmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractor.XmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type, Organism organism)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for XmlInteractor.XmlInteractorPool(String name, String fullName, CvTerm type)Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type, Organism organism)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type, Xref uniqueId)Constructor for XmlInteractorPool.XmlInterval(CvTerm status, boolean positionUndetermined)Constructor for XmlInterval.XmlInterval(CvTerm status, long start, long end, boolean positionUndetermined)Constructor for XmlInterval.XmlModelledFeature(String shortName, String fullName, CvTerm type)Constructor for XmlModelledFeature.XmlModelledFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for XmlModelledFeature.XmlModelledFeature(CvTerm type)Constructor for XmlModelledFeature.XmlModelledFeature(CvTerm type, String interpro)Constructor for XmlModelledFeature.XmlModelledInteraction(String shortName, CvTerm type)Constructor for XmlModelledInteraction.XmlModelledParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty, CvTerm unit)Constructor for XmlModelledParameter.XmlModelledParticipant(Interactor interactor, CvTerm bioRole)Constructor for XmlModelledParticipant.XmlModelledParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for XmlModelledParticipant.XmlMolecule(String name, String fullName, CvTerm type)Constructor for XmlMolecule.XmlMolecule(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlMolecule.XmlMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlMolecule.XmlMolecule(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type, Organism organism)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type, Xref uniqueId)Constructor for XmlMolecule.XmlNucleicAcid(String name, String fullName, CvTerm type)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type, Organism organism)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type, Xref uniqueId)Constructor for XmlNucleicAcid.XmlOrganism(int taxId, String commonName, String scientificName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for XmlOrganism.XmlOrganism(int taxId, String commonName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for XmlOrganism.XmlOrganism(int taxId, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for XmlOrganism.XmlParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty, CvTerm unit)Constructor for XmlParameter.XmlParticipant(Interactor interactor, CvTerm bioRole)Constructor for XmlParticipant.XmlParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for XmlParticipant.XmlParticipantEvidence(Interactor interactor, CvTerm bioRole)Constructor for XmlParticipantEvidence.XmlParticipantEvidence(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for XmlParticipantEvidence.XmlPolymer(String name, String fullName, CvTerm type)Constructor for XmlPolymer.XmlPolymer(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlPolymer.XmlPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlPolymer.XmlPolymer(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type, Organism organism)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type, Xref uniqueId)Constructor for XmlPolymer.XmlPosition(CvTerm status, boolean positionUndetermined)Constructor for XmlPosition.XmlPosition(CvTerm status, long pos, boolean positionUndetermined)Constructor for XmlPosition.XmlPreAssembly(CvTerm outcome)Constructor for XmlPreAssembly.XmlPreAssembly(CvTerm outcome, CvTerm response)Constructor for XmlPreAssembly.XmlProtein(String name, String fullName, CvTerm type)Constructor for XmlProtein.XmlProtein(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlProtein.XmlProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlProtein.XmlProtein(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlProtein.XmlProtein(String name, CvTerm type)Constructor for XmlProtein.XmlProtein(String name, CvTerm type, Organism organism)Constructor for XmlProtein.XmlProtein(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlProtein.XmlProtein(String name, CvTerm type, Xref uniqueId)Constructor for XmlProtein.XmlVariableParameter(String description, CvTerm unit)Constructor for XmlVariableParameter.XmlVariableParameter(String description, Experiment experiment, CvTerm unit)Constructor for XmlVariableParameter.XmlXref(CvTerm database, String id)Constructor for XmlXref.XmlXref(CvTerm database, String id, String version)Constructor for XmlXref.XmlXref(CvTerm database, String id, String version, CvTerm qualifier)Constructor for XmlXref.XmlXref(CvTerm database, String id, CvTerm qualifier)Constructor for XmlXref. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension.xml254
Classes in psidev.psi.mi.jami.xml.model.extension.xml254 that implement CvTerm Modifier and Type Class Description classAbstractXmlCvTermAbstract cv termclassAbstractXmlSourceDesciption of the source of the entry, usually an organisationclassDefaultXmlSourceDesciption of the source of the entry, usually an organisationclassExperimentalCvTermThis elements is controlled by the PSI-MI controlled vocabulary "experimentalPreparation", root term id MI:0346.classXmlCvTermXml implementation of CvTerm.classXmlOpenCvTermXml implementation of CvTerm.classXmlSourceDesciption of the source of the entry, usually an organisationMethods in psidev.psi.mi.jami.xml.model.extension.xml254 that return CvTerm Modifier and Type Method Description CvTermXmlAllostery. getAllostericMechanism()Getter for the fieldallostericMechanism.CvTermXmlAllostery. getAllosteryType()Getter for the fieldallosteryType.CvTermAbstractXmlParticipant. getBiologicalEffect()Gets the value of the biologicalEffect property.CvTermAbstractXmlParticipantPool. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermXmlParticipantEvidenceWrapper. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermXmlParticipantWrapper. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermAbstractXmlParticipant. getBiologicalRole()Gets the value of the biologicalRole property.CvTermAbstractXmlParticipantPool. getBiologicalRole()The biological role of the participant.CvTermXmlParticipantEvidenceWrapper. getBiologicalRole()The biological role of the participant.CvTermXmlParticipantWrapper. getBiologicalRole()The biological role of the participant.CvTermXmlOrganism. getCellType()Getter for the fieldcellType.CvTermXmlOrganism. getCompartment()Getter for the fieldcompartment.CvTermXmlXref. getDatabase()Getter for the fielddatabase.CvTermAbstractXmlModelledInteraction. getEvidenceType()Getter for the fieldevidenceType.CvTermXmlBasicInteractionComplexWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlInteractionEvidenceComplexWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlModelledInteractionComplexWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlExperimentalParticipantPool. getExperimentalRole()The experimental role of the participant.CvTermXmlParticipantEvidence. getExperimentalRole()getExperimentalRole.CvTermAbstractXmlExperiment. getFeatureDetectionMethod()Gets the value of the featureDetectionMethod property.CvTermAbstractXmlExperiment. getInteractionDetectionMethod()Gets the value of the interactionDetectionMethod property.CvTermAbstractPsiXmlInteraction. getInteractionType()getInteractionType.abstract CvTermAbstractXmlInteraction. getInteractionType()getInteractionType.CvTermXmlBasicInteractionComplexWrapper. getInteractionType()getInteractionType.CvTermXmlInteractionEvidenceComplexWrapper. getInteractionType()getInteractionType.CvTermXmlModelledInteractionComplexWrapper. getInteractionType()getInteractionType.CvTermAbstractXmlComplex. getInteractorType()The molecule type of this interactor.CvTermXmlBasicInteractionComplexWrapper. getInteractorType()The molecule type of this interactor.CvTermXmlInteractionEvidenceComplexWrapper. getInteractorType()The molecule type of this interactor.CvTermXmlModelledInteractionComplexWrapper. getInteractorType()The molecule type of this interactor.CvTermAbstractXmlExperiment. getParticipantIdentificationMethod()Gets the value of the participantIdentificationMethod property.CvTermXmlXref. getQualifier()Getter for the fieldqualifier.CvTermAbstractXmlFeature. getRole()Getter for the fieldrole.CvTermXmlFeatureEvidenceWrapper. getRole()The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature.CvTermXmlFeatureWrapper. getRole()The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature.CvTermAbstractXmlPosition. getStatus()Getter for the fieldstatus.CvTermXmlInterval. getStatus()Getter for the fieldstatus.CvTermXmlPosition. getStatus()Getter for the fieldstatus.CvTermXmlOrganism. getTissue()Getter for the fieldtissue.CvTermAbstractXmlAnnotation. getTopic()Getter for the fieldtopic.CvTermAbstractXmlConfidence. getType()Gets the value of the type property.CvTermAbstractXmlFeature. getType()Getter for the fieldtype.CvTermAbstractXmlParameter. getType()Getter for the fieldtype.CvTermAbstractXmlParticipantPool. getType()Getter for the fieldtype.CvTermXmlAlias. getType()Getter for the fieldtype.CvTermXmlConfidenceWrapper. getType()Method used to compute the confidence value.CvTermXmlExperimentalParticipantPoolWrapper. getType()The pool type of this participant pool.CvTermXmlFeatureEvidenceWrapper. getType()The type for this feature.CvTermXmlFeatureWrapper. getType()The type for this feature.CvTermXmlParameterWrapper. getType()The parameter type is a controlled vocabulary term and it cannot be null.CvTermXmlParticipantPoolWrapper. getType()The pool type of this participant pool.CvTermAbstractXmlParameter. getUnit()Getter for the fieldunit.CvTermXmlParameterWrapper. getUnit()Unit of the parameter is a controlled vocabulary term.CvTermXmlVariableParameter. getUnit()Getter for the fieldunit.Methods in psidev.psi.mi.jami.xml.model.extension.xml254 that return types with arguments of type CvTerm Modifier and Type Method Description Collection<CvTerm>XmlFeatureEvidence. getDetectionMethods()getDetectionMethods.Collection<CvTerm>XmlCooperativityEvidence. getEvidenceMethods()Getter for the fieldevidenceMethods.Collection<CvTerm>XmlExperimentalParticipantPool. getExperimentalPreparations()The experimental preparations for this participant.Collection<CvTerm>XmlParticipantEvidence. getExperimentalPreparations()getExperimentalPreparations.List<CvTerm>XmlParticipantEvidence. getExperimentalRoles()getExperimentalRoles.Collection<CvTerm>XmlExperimentalParticipantPool. getIdentificationMethods()The identification methods for this participant.Collection<CvTerm>XmlParticipantEvidence. getIdentificationMethods()getIdentificationMethods.List<CvTerm>AbstractPsiXmlInteraction. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>AbstractXmlBasicInteraction. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>AbstractXmlInteractionEvidence. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>AbstractXmlModelledInteraction. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>XmlBasicInteractionComplexWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlInteractionEvidenceComplexWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlModelledInteractionComplexWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlParticipantEvidence.JAXBExperimentalPreparationWrapper. getJAXBExperimentalPreparations()List<CvTerm>XmlParticipantEvidence.JAXBExperimentalRoleWrapper. getJAXBExperimentalRoles()List<CvTerm>XmlFeatureEvidence. getJAXBFeatureDetectionMethods()getJAXBFeatureDetectionMethods.List<CvTerm>XmlParticipantEvidence.JAXBParticipantIdentificationWrapper. getJAXBParticipantIdentificationMethods()Methods in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type CvTerm Modifier and Type Method Description voidXmlAllostery. setAllostericMechanism(CvTerm mechanism)Sets the allosteric mechanism.voidXmlAllostery. setAllosteryType(CvTerm type)Sets the allostery type.voidAbstractXmlParticipant. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidAbstractXmlParticipantPool. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidXmlParticipantEvidenceWrapper. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidXmlParticipantWrapper. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidAbstractXmlParticipant. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidAbstractXmlParticipantPool. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidXmlParticipantEvidenceWrapper. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidXmlParticipantWrapper. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidXmlOrganism. setCellType(CvTerm cellType)Sets the cell typevoidXmlOrganism. setCompartment(CvTerm compartment)Sets the compartment.voidAbstractXmlModelledInteraction. setEvidenceType(CvTerm evidenceType)Sets the evidence typevoidXmlBasicInteractionComplexWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlInteractionEvidenceComplexWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlModelledInteractionComplexWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlExperimentalParticipantPool. setExperimentalRole(CvTerm expRole)Sets the experimental role.voidXmlParticipantEvidence. setExperimentalRole(CvTerm expRole)Sets the experimental role.voidAbstractXmlExperiment. setFeatureDetectionMethod(CvTerm value)setFeatureDetectionMethod.voidAbstractXmlExperiment. setInteractionDetectionMethod(CvTerm value)Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).voidAbstractPsiXmlInteraction. setInteractionType(CvTerm term)Sets the interaction type.abstract voidAbstractXmlInteraction. setInteractionType(CvTerm term)Sets the interaction type.voidXmlBasicInteractionComplexWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidXmlInteractionEvidenceComplexWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidXmlModelledInteractionComplexWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidAbstractXmlComplex. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlBasicInteractionComplexWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlBioactiveEntity. setInteractorType(CvTerm interactorType)Sets the interactor type of this bioactive entity.voidXmlGene. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlInteractionEvidenceComplexWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlModelledInteractionComplexWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlNucleicAcid. setInteractorType(CvTerm interactorType)Sets the interactor type of this NucleicAcid.voidXmlProtein. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidAbstractXmlExperiment. setParticipantIdentificationMethod(CvTerm value)setParticipantIdentificationMethod.voidAbstractXmlFeature. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidXmlFeatureEvidenceWrapper. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidXmlFeatureWrapper. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidXmlOrganism. setTissue(CvTerm tissue)Sets the tissuevoidAbstractXmlFeature. setType(CvTerm type)Sets the feature type.voidAbstractXmlParticipantPool. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidXmlExperimentalParticipantPoolWrapper. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidXmlFeatureEvidenceWrapper. setType(CvTerm type)Sets the feature type.voidXmlFeatureWrapper. setType(CvTerm type)Sets the feature type.voidXmlParticipantPoolWrapper. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidXmlVariableParameter. setUnit(CvTerm unit)Sets the unit of this variableParameter.Method parameters in psidev.psi.mi.jami.xml.model.extension.xml254 with type arguments of type CvTerm Modifier and Type Method Description protected voidXmlCooperativityEvidence. initialiseEvidenceMethodsWith(Collection<CvTerm> methods)initialiseEvidenceMethodsWith.Constructors in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type CvTerm Constructor Description AbstractPsiXmlInteraction(String shortName, CvTerm type)Constructor for AbstractPsiXmlInteraction.AbstractXmlAnnotation(CvTerm topic)Constructor for AbstractXmlAnnotation.AbstractXmlAnnotation(CvTerm topic, String value)Constructor for AbstractXmlAnnotation.AbstractXmlBasicInteraction(String shortName, CvTerm type)Constructor for AbstractXmlBasicInteraction.AbstractXmlComplex(String name, String fullName, CvTerm type)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type, Organism organism)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlConfidence(CvTerm type, String value)Constructor for AbstractXmlConfidence.AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for AbstractXmlExperiment.AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for AbstractXmlExperiment.AbstractXmlFeature(String shortName, String fullName, CvTerm type)Constructor for AbstractXmlFeature.AbstractXmlFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for AbstractXmlFeature.AbstractXmlFeature(CvTerm type)Constructor for AbstractXmlFeature.AbstractXmlFeature(CvTerm type, String interpro)Constructor for AbstractXmlFeature.AbstractXmlInteraction(String shortName, CvTerm type)Constructor for AbstractXmlInteraction.AbstractXmlInteractionEvidence(String shortName, CvTerm type)Constructor for AbstractXmlInteractionEvidence.AbstractXmlInteractor(String name, String fullName, CvTerm type)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type, Organism organism)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlModelledInteraction(String shortName, CvTerm type)Constructor for AbstractXmlModelledInteraction.AbstractXmlParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty, CvTerm unit)Constructor for AbstractXmlParameter.AbstractXmlParticipant(Interactor interactor, CvTerm bioRole)Constructor for AbstractXmlParticipant.AbstractXmlParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for AbstractXmlParticipant.AbstractXmlPosition(CvTerm status, boolean positionUndetermined)Constructor for AbstractXmlPosition.DefaultXmlAnnotation(CvTerm topic)Constructor for DefaultXmlAnnotation.DefaultXmlAnnotation(CvTerm topic, String value)Constructor for DefaultXmlAnnotation.DefaultXmlBasicInteraction(String shortName, CvTerm type)Constructor for DefaultXmlBasicInteraction.DefaultXmlComplex(String name, String fullName, CvTerm type)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type, Organism organism)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for DefaultXmlExperiment.DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for DefaultXmlExperiment.DefaultXmlInteractionEvidence(String shortName, CvTerm type)Constructor for DefaultXmlInteractionEvidence.DefaultXmlInteractor(String name, String fullName, CvTerm type)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type, Organism organism)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlModelledInteraction(String shortName, CvTerm type)Constructor for DefaultXmlModelledInteraction.HostOrganism(int taxId, String commonName, String scientificName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for HostOrganism.HostOrganism(int taxId, String commonName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for HostOrganism.HostOrganism(int taxId, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for HostOrganism.XmlAlias(String name, CvTerm type)Constructor for XmlAlias.XmlAllostery(CvTerm outcome)Constructor for XmlAllostery.XmlAllostery(CvTerm outcome, CvTerm response)Constructor for XmlAllostery.XmlAnnotation(CvTerm topic)Constructor for XmlAnnotation.XmlAnnotation(CvTerm topic, String value)Constructor for XmlAnnotation.XmlBasicInteraction(String shortName, CvTerm type)Constructor for XmlBasicInteraction.XmlBioactiveEntity(String name, String fullName, CvTerm type)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, String uniqueChebi)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, String uniqueChebi)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Organism organism)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Organism organism, String uniqueChebi)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlComplex(String name, String fullName, CvTerm type)Constructor for XmlComplex.XmlComplex(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlComplex.XmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlComplex.XmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlComplex.XmlComplex(String name, CvTerm type)Constructor for XmlComplex.XmlComplex(String name, CvTerm type, Organism organism)Constructor for XmlComplex.XmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlComplex.XmlComplex(String name, CvTerm type, Xref uniqueId)Constructor for XmlComplex.XmlConfidence(CvTerm type, String value)Constructor for XmlConfidence.XmlExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for XmlExperiment.XmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for XmlExperiment.XmlFeature(String shortName, String fullName, CvTerm type)Constructor for XmlFeature.XmlFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for XmlFeature.XmlFeature(CvTerm type)Constructor for XmlFeature.XmlFeature(CvTerm type, String interpro)Constructor for XmlFeature.XmlFeatureEvidence(String shortName, String fullName, CvTerm type)Constructor for XmlFeatureEvidence.XmlFeatureEvidence(String shortName, String fullName, CvTerm type, String interpro)Constructor for XmlFeatureEvidence.XmlFeatureEvidence(CvTerm type)Constructor for XmlFeatureEvidence.XmlFeatureEvidence(CvTerm type, String interpro)Constructor for XmlFeatureEvidence.XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref ensembl)Constructor for XmlGene.XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlGene(String name, String fullName, CvTerm type, Xref ensembl)Constructor for XmlGene.XmlGene(String name, String fullName, CvTerm type, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Organism organism, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlInteractionEvidence(String shortName, CvTerm type)Constructor for XmlInteractionEvidence.XmlInteractor(String name, String fullName, CvTerm type)Constructor for XmlInteractor.XmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlInteractor.XmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractor.XmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type, Organism organism)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for XmlInteractor.XmlInteractorPool(String name, String fullName, CvTerm type)Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type, Organism organism)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type, Xref uniqueId)Constructor for XmlInteractorPool.XmlInterval(CvTerm status, boolean positionUndetermined)Constructor for XmlInterval.XmlInterval(CvTerm status, long start, long end, boolean positionUndetermined)Constructor for XmlInterval.XmlModelledFeature(String shortName, String fullName, CvTerm type)Constructor for XmlModelledFeature.XmlModelledFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for XmlModelledFeature.XmlModelledFeature(CvTerm type)Constructor for XmlModelledFeature.XmlModelledFeature(CvTerm type, String interpro)Constructor for XmlModelledFeature.XmlModelledInteraction(String shortName, CvTerm type)Constructor for XmlModelledInteraction.XmlModelledParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty, CvTerm unit)Constructor for XmlModelledParameter.XmlModelledParticipant(Interactor interactor, CvTerm bioRole)Constructor for XmlModelledParticipant.XmlModelledParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for XmlModelledParticipant.XmlMolecule(String name, String fullName, CvTerm type)Constructor for XmlMolecule.XmlMolecule(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlMolecule.XmlMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlMolecule.XmlMolecule(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type, Organism organism)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type, Xref uniqueId)Constructor for XmlMolecule.XmlNucleicAcid(String name, String fullName, CvTerm type)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type, Organism organism)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type, Xref uniqueId)Constructor for XmlNucleicAcid.XmlOrganism(int taxId, String commonName, String scientificName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for XmlOrganism.XmlOrganism(int taxId, String commonName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for XmlOrganism.XmlOrganism(int taxId, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for XmlOrganism.XmlParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty, CvTerm unit)Constructor for XmlParameter.XmlParticipant(Interactor interactor, CvTerm bioRole)Constructor for XmlParticipant.XmlParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for XmlParticipant.XmlParticipantEvidence(Interactor interactor, CvTerm bioRole)Constructor for XmlParticipantEvidence.XmlParticipantEvidence(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for XmlParticipantEvidence.XmlPolymer(String name, String fullName, CvTerm type)Constructor for XmlPolymer.XmlPolymer(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlPolymer.XmlPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlPolymer.XmlPolymer(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type, Organism organism)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type, Xref uniqueId)Constructor for XmlPolymer.XmlPosition(CvTerm status, boolean positionUndetermined)Constructor for XmlPosition.XmlPosition(CvTerm status, long pos, boolean positionUndetermined)Constructor for XmlPosition.XmlPreAssembly(CvTerm outcome)Constructor for XmlPreAssembly.XmlPreAssembly(CvTerm outcome, CvTerm response)Constructor for XmlPreAssembly.XmlProtein(String name, String fullName, CvTerm type)Constructor for XmlProtein.XmlProtein(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlProtein.XmlProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlProtein.XmlProtein(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlProtein.XmlProtein(String name, CvTerm type)Constructor for XmlProtein.XmlProtein(String name, CvTerm type, Organism organism)Constructor for XmlProtein.XmlProtein(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlProtein.XmlProtein(String name, CvTerm type, Xref uniqueId)Constructor for XmlProtein.XmlVariableParameter(String description, CvTerm unit)Constructor for XmlVariableParameter.XmlVariableParameter(String description, Experiment experiment, CvTerm unit)Constructor for XmlVariableParameter.XmlXref(CvTerm database, String id)Constructor for XmlXref.XmlXref(CvTerm database, String id, String version)Constructor for XmlXref.XmlXref(CvTerm database, String id, String version, CvTerm qualifier)Constructor for XmlXref.XmlXref(CvTerm database, String id, CvTerm qualifier)Constructor for XmlXref. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.extension.xml300
Classes in psidev.psi.mi.jami.xml.model.extension.xml300 that implement CvTerm Modifier and Type Class Description classAbstractXmlCvTermAbstract cv termclassAbstractXmlSourceDesciption of the source of the entry, usually an organisationclassDefaultXmlSourceDesciption of the source of the entry, usually an organisationclassExperimentalCvTermThis elements is controlled by the PSI-MI controlled vocabulary "experimentalPreparation", root term id MI:0346.classXmlCvTermXml implementation of CvTerm.classXmlOpenCvTermXml implementation of CvTerm.classXmlSourceDesciption of the source of the entry, usually an organisationMethods in psidev.psi.mi.jami.xml.model.extension.xml300 that return CvTerm Modifier and Type Method Description CvTermXmlAllostery. getAllostericMechanism()Getter for the fieldallostericMechanism.CvTermXmlAllostery. getAllosteryType()Getter for the fieldallosteryType.CvTermAbstractXmlParticipant. getBiologicalEffect()Gets the value of the biologicalEffect property.CvTermAbstractXmlParticipantPool. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermXmlParticipantEvidenceWrapper. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermXmlParticipantWrapper. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermAbstractXmlParticipant. getBiologicalRole()Gets the value of the biologicalRole property.CvTermAbstractXmlParticipantPool. getBiologicalRole()The biological role of the participant.CvTermXmlParticipantEvidenceWrapper. getBiologicalRole()The biological role of the participant.CvTermXmlParticipantWrapper. getBiologicalRole()The biological role of the participant.CvTermXmlOrganism. getCellType()Getter for the fieldcellType.CvTermXmlOrganism. getCompartment()Getter for the fieldcompartment.CvTermXmlXref. getDatabase()Getter for the fielddatabase.CvTermAbstractXmlModelledInteraction. getEvidenceType()Getter for the fieldevidenceType.CvTermXmlBasicInteractionComplexWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlInteractionEvidenceComplexWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlModelledInteraction. getEvidenceType()Getter for the fieldevidenceType.CvTermXmlModelledInteractionComplexWrapper. getEvidenceType()The evidence type for this modelled interactions.CvTermXmlExperimentalParticipantPool. getExperimentalRole()The experimental role of the participant.CvTermXmlParticipantEvidence. getExperimentalRole()getExperimentalRole.CvTermAbstractXmlExperiment. getFeatureDetectionMethod()Gets the value of the featureDetectionMethod property.CvTermAbstractXmlExperiment. getInteractionDetectionMethod()Gets the value of the interactionDetectionMethod property.CvTermAbstractPsiXmlInteraction. getInteractionType()getInteractionType.abstract CvTermAbstractXmlInteraction. getInteractionType()getInteractionType.CvTermXmlBasicInteractionComplexWrapper. getInteractionType()getInteractionType.CvTermXmlInteractionEvidenceComplexWrapper. getInteractionType()getInteractionType.CvTermXmlModelledInteraction. getInteractionType()getInteractionType.CvTermXmlModelledInteractionComplexWrapper. getInteractionType()getInteractionType.CvTermAbstractXmlComplex. getInteractorType()The molecule type of this interactor.CvTermXmlBasicInteractionComplexWrapper. getInteractorType()The molecule type of this interactor.CvTermXmlInteractionEvidenceComplexWrapper. getInteractorType()The molecule type of this interactor.CvTermXmlModelledInteraction. getInteractorType()Getter for the fieldinteractorType.CvTermXmlModelledInteractionComplexWrapper. getInteractorType()The molecule type of this interactor.CvTermAbstractXmlCooperativeEffect. getOutCome()getOutCome.CvTermAbstractXmlExperiment. getParticipantIdentificationMethod()Gets the value of the participantIdentificationMethod property.CvTermXmlXref. getQualifier()Getter for the fieldqualifier.CvTermXmlCausalRelationship. getRelationType()Getter for the fieldrelationType.CvTermAbstractXmlCooperativeEffect. getResponse()Getter for the fieldresponse.CvTermAbstractXmlFeature. getRole()Getter for the fieldrole.CvTermXmlFeatureEvidenceWrapper. getRole()The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature.CvTermXmlFeatureWrapper. getRole()The effect of this feature on the interaction where the feature has been reported or the interaction dependency between the interaction reporting this feature and this feature.CvTermAbstractXmlPosition. getStatus()Getter for the fieldstatus.CvTermXmlInterval. getStatus()Getter for the fieldstatus.CvTermXmlPosition. getStatus()Getter for the fieldstatus.CvTermXmlOrganism. getTissue()Getter for the fieldtissue.CvTermAbstractXmlAnnotation. getTopic()Getter for the fieldtopic.CvTermAbstractXmlConfidence. getType()Gets the value of the type property.CvTermAbstractXmlFeature. getType()Getter for the fieldtype.CvTermAbstractXmlParameter. getType()Getter for the fieldtype.CvTermAbstractXmlParticipantPool. getType()Getter for the fieldtype.CvTermXmlAlias. getType()Getter for the fieldtype.CvTermXmlConfidenceWrapper. getType()Method used to compute the confidence value.CvTermXmlExperimentalParticipantPoolWrapper. getType()The pool type of this participant pool.CvTermXmlFeatureEvidenceWrapper. getType()The type for this feature.CvTermXmlFeatureWrapper. getType()The type for this feature.CvTermXmlParameterWrapper. getType()The parameter type is a controlled vocabulary term and it cannot be null.CvTermXmlParticipantPoolWrapper. getType()The pool type of this participant pool.CvTermAbstractXmlParameter. getUnit()Getter for the fieldunit.CvTermXmlParameterWrapper. getUnit()Unit of the parameter is a controlled vocabulary term.CvTermXmlVariableParameter. getUnit()Getter for the fieldunit.Methods in psidev.psi.mi.jami.xml.model.extension.xml300 that return types with arguments of type CvTerm Modifier and Type Method Description Collection<CvTerm>XmlFeatureEvidence. getDetectionMethods()getDetectionMethods.Collection<CvTerm>XmlCooperativityEvidence. getEvidenceMethods()getEvidenceMethods.Collection<CvTerm>XmlExperimentalParticipantPool. getExperimentalPreparations()The experimental preparations for this participant.Collection<CvTerm>XmlParticipantEvidence. getExperimentalPreparations()getExperimentalPreparations.List<CvTerm>XmlParticipantEvidence. getExperimentalRoles()getExperimentalRoles.Collection<CvTerm>XmlExperimentalParticipantPool. getIdentificationMethods()The identification methods for this participant.Collection<CvTerm>XmlParticipantEvidence. getIdentificationMethods()getIdentificationMethods.List<CvTerm>AbstractPsiXmlInteraction. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>AbstractXmlBasicInteraction. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>AbstractXmlInteractionEvidence. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>AbstractXmlModelledInteraction. getInteractionTypes()Gets the value of the interactionTypeList property.List<CvTerm>XmlBasicInteractionComplexWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlInteractionEvidenceComplexWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlModelledInteractionComplexWrapper. getInteractionTypes()getInteractionTypes.List<CvTerm>XmlCooperativityEvidence.JAXBEvidenceMethodWrapper. getJAXBEvidenceMethods()List<CvTerm>XmlParticipantEvidence.JAXBExperimentalPreparationWrapper. getJAXBExperimentalPreparations()List<CvTerm>XmlParticipantEvidence.JAXBExperimentalRoleWrapper. getJAXBExperimentalRoles()List<CvTerm>XmlFeatureEvidence. getJAXBFeatureDetectionMethods()getJAXBFeatureDetectionMethods.List<CvTerm>XmlParticipantEvidence.JAXBParticipantIdentificationWrapper. getJAXBParticipantIdentificationMethods()Methods in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type CvTerm Modifier and Type Method Description voidXmlAllostery. setAllostericMechanism(CvTerm mechanism)Sets the allosteric mechanism.voidXmlAllostery. setAllosteryType(CvTerm type)Sets the allostery type.voidAbstractXmlParticipant. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidAbstractXmlParticipantPool. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidXmlParticipantEvidenceWrapper. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidXmlParticipantWrapper. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidAbstractXmlParticipant. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidAbstractXmlParticipantPool. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidXmlParticipantEvidenceWrapper. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidXmlParticipantWrapper. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidXmlOrganism. setCellType(CvTerm cellType)Sets the cell typevoidXmlOrganism. setCompartment(CvTerm compartment)Sets the compartment.voidAbstractXmlModelledInteraction. setEvidenceType(CvTerm evidenceType)Sets the evidence typevoidXmlBasicInteractionComplexWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlInteractionEvidenceComplexWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlModelledInteraction. setEvidenceType(CvTerm evidenceType)Sets the evidence typevoidXmlModelledInteractionComplexWrapper. setEvidenceType(CvTerm eco)Sets the evidence typevoidXmlExperimentalParticipantPool. setExperimentalRole(CvTerm expRole)Sets the experimental role.voidXmlParticipantEvidence. setExperimentalRole(CvTerm expRole)Sets the experimental role.voidAbstractXmlExperiment. setFeatureDetectionMethod(CvTerm value)setFeatureDetectionMethod.voidAbstractXmlExperiment. setInteractionDetectionMethod(CvTerm value)Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).voidAbstractPsiXmlInteraction. setInteractionType(CvTerm term)Sets the interaction type.abstract voidAbstractXmlInteraction. setInteractionType(CvTerm term)Sets the interaction type.voidXmlBasicInteractionComplexWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidXmlInteractionEvidenceComplexWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidXmlModelledInteraction. setInteractionType(CvTerm term)Sets the interaction type.voidXmlModelledInteractionComplexWrapper. setInteractionType(CvTerm term)Sets the interaction type.voidAbstractXmlComplex. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlBasicInteractionComplexWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlBioactiveEntity. setInteractorType(CvTerm interactorType)Sets the interactor type of this bioactive entity.voidXmlGene. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlInteractionEvidenceComplexWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlModelledInteraction. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlModelledInteractionComplexWrapper. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidXmlNucleicAcid. setInteractorType(CvTerm interactorType)Sets the interactor type of this NucleicAcid.voidXmlProtein. setInteractorType(CvTerm interactorType)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidAbstractXmlCooperativeEffect. setOutCome(CvTerm effect)Sets the cooperative effect outcomevoidAbstractXmlExperiment. setParticipantIdentificationMethod(CvTerm value)setParticipantIdentificationMethod.voidAbstractXmlCooperativeEffect. setResponse(CvTerm response)Sets the response.voidAbstractXmlFeature. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidXmlFeatureEvidenceWrapper. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidXmlFeatureWrapper. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidXmlOrganism. setTissue(CvTerm tissue)Sets the tissuevoidAbstractXmlFeature. setType(CvTerm type)Sets the feature type.voidAbstractXmlParticipantPool. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidXmlExperimentalParticipantPoolWrapper. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidXmlFeatureEvidenceWrapper. setType(CvTerm type)Sets the feature type.voidXmlFeatureWrapper. setType(CvTerm type)Sets the feature type.voidXmlParticipantPoolWrapper. setType(CvTerm type)Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)voidXmlVariableParameter. setUnit(CvTerm unit)Sets the unit of this variableParameter.Constructors in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type CvTerm Constructor Description AbstractPsiXmlInteraction(String shortName, CvTerm type)Constructor for AbstractPsiXmlInteraction.AbstractXmlAnnotation(CvTerm topic)Constructor for AbstractXmlAnnotation.AbstractXmlAnnotation(CvTerm topic, String value)Constructor for AbstractXmlAnnotation.AbstractXmlBasicInteraction(String shortName, CvTerm type)Constructor for AbstractXmlBasicInteraction.AbstractXmlComplex(String name, String fullName, CvTerm type)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type, Organism organism)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, CvTerm type, Xref uniqueId)Constructor for AbstractXmlComplex.AbstractXmlConfidence(CvTerm type, String value)Constructor for AbstractXmlConfidence.AbstractXmlCooperativeEffect(CvTerm outcome)Constructor for AbstractXmlCooperativeEffect.AbstractXmlCooperativeEffect(CvTerm outcome, CvTerm response)Constructor for AbstractXmlCooperativeEffect.AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for AbstractXmlExperiment.AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for AbstractXmlExperiment.AbstractXmlFeature(String shortName, String fullName, CvTerm type)Constructor for AbstractXmlFeature.AbstractXmlFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for AbstractXmlFeature.AbstractXmlFeature(CvTerm type)Constructor for AbstractXmlFeature.AbstractXmlFeature(CvTerm type, String interpro)Constructor for AbstractXmlFeature.AbstractXmlInteraction(String shortName, CvTerm type)Constructor for AbstractXmlInteraction.AbstractXmlInteractionEvidence(String shortName, CvTerm type)Constructor for AbstractXmlInteractionEvidence.AbstractXmlInteractor(String name, String fullName, CvTerm type)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type, Organism organism)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for AbstractXmlInteractor.AbstractXmlModelledInteraction(String shortName, CvTerm type)Constructor for AbstractXmlModelledInteraction.AbstractXmlParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty, CvTerm unit)Constructor for AbstractXmlParameter.AbstractXmlParticipant(Interactor interactor, CvTerm bioRole)Constructor for AbstractXmlParticipant.AbstractXmlParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for AbstractXmlParticipant.AbstractXmlPosition(CvTerm status, boolean positionUndetermined)Constructor for AbstractXmlPosition.DefaultXmlAnnotation(CvTerm topic)Constructor for DefaultXmlAnnotation.DefaultXmlAnnotation(CvTerm topic, String value)Constructor for DefaultXmlAnnotation.DefaultXmlBasicInteraction(String shortName, CvTerm type)Constructor for DefaultXmlBasicInteraction.DefaultXmlComplex(String name, String fullName, CvTerm type)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type, Organism organism)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, CvTerm type, Xref uniqueId)Constructor for DefaultXmlComplex.DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for DefaultXmlExperiment.DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for DefaultXmlExperiment.DefaultXmlInteractionEvidence(String shortName, CvTerm type)Constructor for DefaultXmlInteractionEvidence.DefaultXmlInteractor(String name, String fullName, CvTerm type)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type, Organism organism)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for DefaultXmlInteractor.DefaultXmlModelledInteraction(String shortName, CvTerm type)Constructor for DefaultXmlModelledInteraction.HostOrganism(int taxId, String commonName, String scientificName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for HostOrganism.HostOrganism(int taxId, String commonName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for HostOrganism.HostOrganism(int taxId, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for HostOrganism.XmlAlias(String name, CvTerm type)Constructor for XmlAlias.XmlAllostery(CvTerm outcome)Constructor for XmlAllostery.XmlAllostery(CvTerm outcome, CvTerm response)Constructor for XmlAllostery.XmlAnnotation(CvTerm topic)Constructor for XmlAnnotation.XmlAnnotation(CvTerm topic, String value)Constructor for XmlAnnotation.XmlBasicInteraction(String shortName, CvTerm type)Constructor for XmlBasicInteraction.XmlBioactiveEntity(String name, String fullName, CvTerm type)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, String uniqueChebi)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, String uniqueChebi)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Organism organism)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Organism organism, String uniqueChebi)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, CvTerm type, Xref uniqueId)Constructor for XmlBioactiveEntity.XmlCausalRelationship(CvTerm relationType, Participant target)Constructor for XmlCausalRelationship.XmlComplex(String name, String fullName, CvTerm type)Constructor for XmlComplex.XmlComplex(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlComplex.XmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlComplex.XmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlComplex.XmlComplex(String name, CvTerm type)Constructor for XmlComplex.XmlComplex(String name, CvTerm type, Organism organism)Constructor for XmlComplex.XmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlComplex.XmlComplex(String name, CvTerm type, Xref uniqueId)Constructor for XmlComplex.XmlConfidence(CvTerm type, String value)Constructor for XmlConfidence.XmlExperiment(Publication publication, CvTerm interactionDetectionMethod)Constructor for XmlExperiment.XmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)Constructor for XmlExperiment.XmlFeature(String shortName, String fullName, CvTerm type)Constructor for XmlFeature.XmlFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for XmlFeature.XmlFeature(CvTerm type)Constructor for XmlFeature.XmlFeature(CvTerm type, String interpro)Constructor for XmlFeature.XmlFeatureEvidence(String shortName, String fullName, CvTerm type)Constructor for XmlFeatureEvidence.XmlFeatureEvidence(String shortName, String fullName, CvTerm type, String interpro)Constructor for XmlFeatureEvidence.XmlFeatureEvidence(CvTerm type)Constructor for XmlFeatureEvidence.XmlFeatureEvidence(CvTerm type, String interpro)Constructor for XmlFeatureEvidence.XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref ensembl)Constructor for XmlGene.XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlGene(String name, String fullName, CvTerm type, Xref ensembl)Constructor for XmlGene.XmlGene(String name, String fullName, CvTerm type, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Organism organism, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Xref ensembl)Constructor for XmlGene.XmlGene(String name, CvTerm type, Xref uniqueId, Xref ensembl)Constructor for XmlGene.XmlInteractionEvidence(String shortName, CvTerm type)Constructor for XmlInteractionEvidence.XmlInteractor(String name, String fullName, CvTerm type)Constructor for XmlInteractor.XmlInteractor(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlInteractor.XmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractor.XmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type, Organism organism)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractor.XmlInteractor(String name, CvTerm type, Xref uniqueId)Constructor for XmlInteractor.XmlInteractorPool(String name, String fullName, CvTerm type)Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type, Organism organism)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlInteractorPool.XmlInteractorPool(String name, CvTerm type, Xref uniqueId)Constructor for XmlInteractorPool.XmlInterval(CvTerm status, boolean positionUndetermined)Constructor for XmlInterval.XmlInterval(CvTerm status, long start, long end, boolean positionUndetermined)Constructor for XmlInterval.XmlModelledFeature(String shortName, String fullName, CvTerm type)Constructor for XmlModelledFeature.XmlModelledFeature(String shortName, String fullName, CvTerm type, String interpro)Constructor for XmlModelledFeature.XmlModelledFeature(CvTerm type)Constructor for XmlModelledFeature.XmlModelledFeature(CvTerm type, String interpro)Constructor for XmlModelledFeature.XmlModelledInteraction(String shortName, CvTerm type)Constructor for XmlModelledInteraction.XmlModelledParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty, CvTerm unit)Constructor for XmlModelledParameter.XmlModelledParticipant(Interactor interactor, CvTerm bioRole)Constructor for XmlModelledParticipant.XmlModelledParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for XmlModelledParticipant.XmlMolecule(String name, String fullName, CvTerm type)Constructor for XmlMolecule.XmlMolecule(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlMolecule.XmlMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlMolecule.XmlMolecule(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type, Organism organism)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlMolecule.XmlMolecule(String name, CvTerm type, Xref uniqueId)Constructor for XmlMolecule.XmlNucleicAcid(String name, String fullName, CvTerm type)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type, Organism organism)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, CvTerm type, Xref uniqueId)Constructor for XmlNucleicAcid.XmlOrganism(int taxId, String commonName, String scientificName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for XmlOrganism.XmlOrganism(int taxId, String commonName, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for XmlOrganism.XmlOrganism(int taxId, CvTerm cellType, CvTerm tissue, CvTerm compartment)Constructor for XmlOrganism.XmlParameter(CvTerm type, ParameterValue value, BigDecimal uncertainty, CvTerm unit)Constructor for XmlParameter.XmlParticipant(Interactor interactor, CvTerm bioRole)Constructor for XmlParticipant.XmlParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for XmlParticipant.XmlParticipantEvidence(Interactor interactor, CvTerm bioRole)Constructor for XmlParticipantEvidence.XmlParticipantEvidence(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)Constructor for XmlParticipantEvidence.XmlPolymer(String name, String fullName, CvTerm type)Constructor for XmlPolymer.XmlPolymer(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlPolymer.XmlPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlPolymer.XmlPolymer(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type, Organism organism)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlPolymer.XmlPolymer(String name, CvTerm type, Xref uniqueId)Constructor for XmlPolymer.XmlPosition(CvTerm status, boolean positionUndetermined)Constructor for XmlPosition.XmlPosition(CvTerm status, long pos, boolean positionUndetermined)Constructor for XmlPosition.XmlPreAssembly(CvTerm outcome)Constructor for XmlPreAssembly.XmlPreAssembly(CvTerm outcome, CvTerm response)Constructor for XmlPreAssembly.XmlProtein(String name, String fullName, CvTerm type)Constructor for XmlProtein.XmlProtein(String name, String fullName, CvTerm type, Organism organism)Constructor for XmlProtein.XmlProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlProtein.XmlProtein(String name, String fullName, CvTerm type, Xref uniqueId)Constructor for XmlProtein.XmlProtein(String name, CvTerm type)Constructor for XmlProtein.XmlProtein(String name, CvTerm type, Organism organism)Constructor for XmlProtein.XmlProtein(String name, CvTerm type, Organism organism, Xref uniqueId)Constructor for XmlProtein.XmlProtein(String name, CvTerm type, Xref uniqueId)Constructor for XmlProtein.XmlVariableParameter(String description, CvTerm unit)Constructor for XmlVariableParameter.XmlVariableParameter(String description, Experiment experiment, CvTerm unit)Constructor for XmlVariableParameter.XmlXref(CvTerm database, String id)Constructor for XmlXref.XmlXref(CvTerm database, String id, String version)Constructor for XmlXref.XmlXref(CvTerm database, String id, String version, CvTerm qualifier)Constructor for XmlXref.XmlXref(CvTerm database, String id, CvTerm qualifier)Constructor for XmlXref. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.reference
Methods in psidev.psi.mi.jami.xml.model.reference that return CvTerm Modifier and Type Method Description CvTermAbstractFeatureRef. getRole()getRole.CvTermAbstractFeatureRef. getType()getType.Methods in psidev.psi.mi.jami.xml.model.reference with parameters of type CvTerm Modifier and Type Method Description voidAbstractFeatureRef. setRole(CvTerm effect)Sets the interaction effect/role for this feature.voidAbstractFeatureRef. setType(CvTerm type)Sets the feature type. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.reference.xml253
Methods in psidev.psi.mi.jami.xml.model.reference.xml253 that return CvTerm Modifier and Type Method Description CvTermAbstractParticipantRef. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermAbstractParticipantRef. getBiologicalRole()getBiologicalRole.CvTermAbstractComplexRef. getEvidenceType()The evidence type for this modelled interactions.CvTermAbstractExperimentRef. getFeatureDetectionMethod()getFeatureDetectionMethod.CvTermAbstractExperimentRef. getInteractionDetectionMethod()getInteractionDetectionMethod.CvTermAbstractComplexRef. getInteractionType()getInteractionType.CvTermAbstractInteractorRef. getInteractorType()getInteractorType.CvTermAbstractExperimentRef. getParticipantIdentificationMethod()getParticipantIdentificationMethod.Methods in psidev.psi.mi.jami.xml.model.reference.xml253 that return types with arguments of type CvTerm Modifier and Type Method Description List<CvTerm>AbstractComplexRef. getInteractionTypes()getInteractionTypes.Methods in psidev.psi.mi.jami.xml.model.reference.xml253 with parameters of type CvTerm Modifier and Type Method Description voidAbstractParticipantRef. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidAbstractParticipantRef. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidAbstractComplexRef. setEvidenceType(CvTerm eco)voidAbstractExperimentRef. setFeatureDetectionMethod(CvTerm method)setFeatureDetectionMethod.voidAbstractExperimentRef. setInteractionDetectionMethod(CvTerm term)Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).voidAbstractComplexRef. setInteractionType(CvTerm term)Sets the interaction type.voidAbstractInteractorRef. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidAbstractExperimentRef. setParticipantIdentificationMethod(CvTerm method)setParticipantIdentificationMethod. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.reference.xml254
Methods in psidev.psi.mi.jami.xml.model.reference.xml254 that return CvTerm Modifier and Type Method Description CvTermAbstractParticipantRef. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermAbstractParticipantRef. getBiologicalRole()getBiologicalRole.CvTermAbstractComplexRef. getEvidenceType()The evidence type for this modelled interactions.CvTermAbstractExperimentRef. getFeatureDetectionMethod()getFeatureDetectionMethod.CvTermAbstractExperimentRef. getInteractionDetectionMethod()getInteractionDetectionMethod.CvTermAbstractComplexRef. getInteractionType()getInteractionType.CvTermAbstractInteractorRef. getInteractorType()getInteractorType.CvTermAbstractExperimentRef. getParticipantIdentificationMethod()getParticipantIdentificationMethod.Methods in psidev.psi.mi.jami.xml.model.reference.xml254 that return types with arguments of type CvTerm Modifier and Type Method Description List<CvTerm>AbstractComplexRef. getInteractionTypes()getInteractionTypes.Methods in psidev.psi.mi.jami.xml.model.reference.xml254 with parameters of type CvTerm Modifier and Type Method Description voidAbstractParticipantRef. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidAbstractParticipantRef. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidAbstractComplexRef. setEvidenceType(CvTerm eco)voidAbstractExperimentRef. setFeatureDetectionMethod(CvTerm method)setFeatureDetectionMethod.voidAbstractExperimentRef. setInteractionDetectionMethod(CvTerm term)Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).voidAbstractComplexRef. setInteractionType(CvTerm term)Sets the interaction type.voidAbstractInteractorRef. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidAbstractExperimentRef. setParticipantIdentificationMethod(CvTerm method)setParticipantIdentificationMethod. -
Uses of CvTerm in psidev.psi.mi.jami.xml.model.reference.xml300
Methods in psidev.psi.mi.jami.xml.model.reference.xml300 that return CvTerm Modifier and Type Method Description CvTermAbstractParticipantRef. getBiologicalEffect()The biological effect of the participant in a causal interaction.CvTermAbstractParticipantRef. getBiologicalRole()getBiologicalRole.CvTermAbstractComplexRef. getEvidenceType()The evidence type for this modelled interactions.CvTermAbstractExperimentRef. getFeatureDetectionMethod()getFeatureDetectionMethod.CvTermAbstractExperimentRef. getInteractionDetectionMethod()getInteractionDetectionMethod.CvTermAbstractComplexRef. getInteractionType()getInteractionType.CvTermAbstractInteractorRef. getInteractorType()getInteractorType.CvTermAbstractExperimentRef. getParticipantIdentificationMethod()getParticipantIdentificationMethod.Methods in psidev.psi.mi.jami.xml.model.reference.xml300 that return types with arguments of type CvTerm Modifier and Type Method Description List<CvTerm>AbstractComplexRef. getInteractionTypes()getInteractionTypes.Methods in psidev.psi.mi.jami.xml.model.reference.xml300 with parameters of type CvTerm Modifier and Type Method Description voidAbstractParticipantRef. setBiologicalEffect(CvTerm biologicalEffect)Sets the biological effect of the participant in a causal interaction.voidAbstractParticipantRef. setBiologicalRole(CvTerm bioRole)Sets the biological role.voidAbstractComplexRef. setEvidenceType(CvTerm eco)voidAbstractExperimentRef. setFeatureDetectionMethod(CvTerm method)setFeatureDetectionMethod.voidAbstractExperimentRef. setInteractionDetectionMethod(CvTerm term)Set the interaction detection method for this experiment If term is null, this method will set the interaction detection method to 'unspecified method' (MI:0686).voidAbstractComplexRef. setInteractionType(CvTerm term)Sets the interaction type.voidAbstractInteractorRef. setInteractorType(CvTerm type)Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)voidAbstractExperimentRef. setParticipantIdentificationMethod(CvTerm method)setParticipantIdentificationMethod.
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