Uses of Interface
psidev.psi.mi.jami.model.Organism
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Uses of Organism in psidev.psi.mi.jami.bridges.fetcher
Methods in psidev.psi.mi.jami.bridges.fetcher that return Organism Modifier and Type Method Description Organism
OrganismFetcher. fetchByTaxID(int taxID)
Finds the complete organism record matching the provided TaxID number.Methods in psidev.psi.mi.jami.bridges.fetcher that return types with arguments of type Organism Modifier and Type Method Description Collection<Organism>
OrganismFetcher. fetchByTaxIDs(Collection<Integer> taxIDs)
Finds the complete organism records matching the provided TaxID numbers. -
Uses of Organism in psidev.psi.mi.jami.bridges.fetcher.mock
Methods in psidev.psi.mi.jami.bridges.fetcher.mock that return Organism Modifier and Type Method Description Organism
FailingOrganismFetcher. fetchByTaxID(int taxID)
Finds the complete organism record matching the provided TaxID number.Organism
MockOrganismFetcher. fetchByTaxID(int taxID)
Finds the complete organism record matching the provided TaxID number.Methods in psidev.psi.mi.jami.bridges.fetcher.mock that return types with arguments of type Organism Modifier and Type Method Description Collection<Organism>
FailingOrganismFetcher. fetchByTaxIDs(Collection<Integer> taxIDs)
Finds the complete organism records matching the provided TaxID numbers.Collection<Organism>
MockOrganismFetcher. fetchByTaxIDs(Collection<Integer> taxIDs)
Finds the complete organism records matching the provided TaxID numbers. -
Uses of Organism in psidev.psi.mi.jami.bridges.uniprot.taxonomy
Methods in psidev.psi.mi.jami.bridges.uniprot.taxonomy that return Organism Modifier and Type Method Description Organism
CachedUniprotTaxonomyFetcher. fetchByTaxID(int taxID)
Finds the complete organism record matching the provided TaxID number.Organism
UniprotTaxonomyFetcher. fetchByTaxID(int taxID)
Finds the complete organism record matching the provided TaxID number.Methods in psidev.psi.mi.jami.bridges.uniprot.taxonomy that return types with arguments of type Organism Modifier and Type Method Description Collection<Organism>
CachedUniprotTaxonomyFetcher. fetchByTaxIDs(Collection<Integer> taxIDs)
Finds the complete organism records matching the provided TaxID numbers.Collection<Organism>
UniprotTaxonomyFetcher. fetchByTaxIDs(Collection<Integer> taxIDs)
Finds the complete organism records matching the provided TaxID numbers. -
Uses of Organism in psidev.psi.mi.jami.bridges.uniprot.util
Methods in psidev.psi.mi.jami.bridges.uniprot.util that return Organism Modifier and Type Method Description static Organism
UniprotUtils. createOrganismFromEntry(uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry entity)
createOrganismFromEntry. -
Uses of Organism in psidev.psi.mi.jami.crosslink.extension
Constructors in psidev.psi.mi.jami.crosslink.extension with parameters of type Organism Constructor Description CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)
Constructor for CsvExperimentalParticipantPool.CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, 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, Organism expressedIn, CvTerm participantIdentificationMethod)
Constructor for CsvExperimentalParticipantPool.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, Organism expressedIn, 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, Organism expressedIn, CvTerm participantIdentificationMethod)
Constructor for CsvParticipantEvidence.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, Organism organism)
Constructor for CsvProtein.CsvProtein(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for CsvProtein.CsvProtein(String name, Organism organism, Xref uniqueId)
Constructor for CsvProtein. -
Uses of Organism in psidev.psi.mi.jami.datasource
Methods in psidev.psi.mi.jami.datasource that return types with arguments of type Organism Modifier and Type Method Description Iterator<Organism>
OrganismStream. getOrganismsIterator()
The organisms iterator for this datasource. -
Uses of Organism in psidev.psi.mi.jami.enricher.impl.full
Methods in psidev.psi.mi.jami.enricher.impl.full with parameters of type Organism Modifier and Type Method Description void
FullFeatureEvidenceEnricher. onOrganismUpdate(Protein interactor, Organism o)
Listen to the event where the organism of a interactor has been initialised.void
FullFeatureEvidenceUpdater. onOrganismUpdate(Protein interactor, Organism o)
Listen to the event where the organism of a interactor has been initialised.void
FullFeatureUpdater. onOrganismUpdate(Protein interactor, Organism o)
Listen to the event where the organism of a interactor has been initialised.protected void
FullOrganismEnricher. processAliases(Organism organismToEnrich, Organism organismFetched)
processAliases.protected void
FullOrganismUpdater. processAliases(Organism organismToEnrich, Organism organismFetched)
processAliases.protected void
FullOrganismEnricher. processCellType(Organism entityToEnrich, Organism fetched)
processCellType.protected void
FullOrganismUpdater. processCellType(Organism entityToEnrich, Organism fetched)
processCellType.protected void
FullOrganismEnricher. processCompartment(Organism entityToEnrich, Organism fetched)
processCompartment.protected void
FullOrganismUpdater. processCompartment(Organism entityToEnrich, Organism fetched)
processCompartment.protected void
FullOrganismEnricher. processOtherProperties(Organism organismToEnrich, Organism organismFetched)
processOtherProperties.protected void
FullOrganismUpdater. processOtherProperties(Organism organismToEnrich, Organism organismFetched)
processOtherProperties.protected void
FullOrganismEnricher. processTissue(Organism entityToEnrich, Organism fetched)
processTissue.protected void
FullOrganismUpdater. processTissue(Organism entityToEnrich, Organism fetched)
processTissue. -
Uses of Organism in psidev.psi.mi.jami.enricher.impl.minimal
Methods in psidev.psi.mi.jami.enricher.impl.minimal that return Organism Modifier and Type Method Description Organism
MinimalOrganismEnricher. find(Organism objectToEnrich)
find.Methods in psidev.psi.mi.jami.enricher.impl.minimal with parameters of type Organism Modifier and Type Method Description void
MinimalOrganismEnricher. enrich(Organism organismToEnrich, Organism organismFetched)
enrich.Organism
MinimalOrganismEnricher. find(Organism objectToEnrich)
find.protected void
MinimalOrganismEnricher. onEnrichedVersionNotFound(Organism objectToEnrich)
onEnrichedVersionNotFound.void
MinimalFeatureEnricher. onOrganismUpdate(Protein interactor, Organism o)
Listen to the event where the organism of a interactor has been initialised.void
MinimalFeatureEvidenceUpdater. onOrganismUpdate(Protein interactor, Organism o)
Listen to the event where the organism of a interactor has been initialised.protected void
MinimalOrganismEnricher. processCommonName(Organism organismToEnrich, Organism organismFetched)
processCommonName.protected void
MinimalOrganismUpdater. processCommonName(Organism organismToEnrich, Organism organismFetched)
processCommonName.protected void
MinimalOrganismEnricher. processOtherProperties(Organism organismToEnrich, Organism organismFetched)
processOtherProperties.protected void
MinimalOrganismEnricher. processScientificName(Organism organismToEnrich, Organism organismFetched)
processScientificName.protected void
MinimalOrganismUpdater. processScientificName(Organism organismToEnrich, Organism organismFetched)
processScientificName.protected void
MinimalOrganismEnricher. processTaxid(Organism organismToEnrich, Organism organismFetched)
processTaxid.protected void
MinimalOrganismUpdater. processTaxid(Organism organismToEnrich, Organism organismFetched)
processTaxid. -
Uses of Organism in psidev.psi.mi.jami.enricher.listener.impl
Methods in psidev.psi.mi.jami.enricher.listener.impl with parameters of type Organism Modifier and Type Method Description void
OrganismEnricherListenerManager. onAddedAlias(Organism organism, Alias added)
Listen to the event where an alias has been added to the object aliases.void
OrganismEnricherListenerManager. onCellTypeUpdate(Organism organism, CvTerm oldType)
Listen to the event where the cell type has been initialised.void
OrganismEnricherListenerManager. onCommonNameUpdate(Organism organism, String oldCommonName)
Listen to the event where the commonName of an organism has been changed.void
OrganismEnricherListenerManager. onCompartmentUpdate(Organism organism, CvTerm oldType)
Listen to the event where the organism compartment has been initialised.void
ParticipantEvidenceEnricherListenerManager. onExpressedInUpdate(P participant, Organism oldOrganism)
onExpressedInUpdatevoid
ExperimentEnricherListenerManager. onHostOrganismUpdate(Experiment experiment, Organism oldOrganism)
onHostOrganismUpdatevoid
ComplexEnricherListenerManager. onOrganismUpdate(Complex interactor, Organism oldOrganism)
Listen to the event where the organism of a interactor has been initialised.void
InteractorEnricherListenerManager. onOrganismUpdate(T interactor, Organism org)
Listen to the event where the organism of a interactor has been initialised.void
OrganismEnricherListenerManager. onRemovedAlias(Organism organism, Alias removed)
Listen to the event where an alias has been removed from the object aliases.void
OrganismEnricherListenerManager. onScientificNameUpdate(Organism organism, String oldScientificName)
Listen to the event where the scientificName of an organism has been changed.void
OrganismEnricherListenerManager. onTaxidUpdate(Organism organism, String oldTaxid)
Listen to the event where the taxid of an organism has been changed.void
OrganismEnricherListenerManager. onTissueUpdate(Organism organism, CvTerm oldType)
Listen to the event where the organism tissue has been initialised. -
Uses of Organism in psidev.psi.mi.jami.enricher.listener.impl.log
Methods in psidev.psi.mi.jami.enricher.listener.impl.log with parameters of type Organism Modifier and Type Method Description void
OrganismEnricherLogger. onEnrichmentComplete(Organism organism, EnrichmentStatus status, String message)
onEnrichmentComplete.void
OrganismEnricherLogger. onEnrichmentError(Organism object, String message, Exception e)
onEnrichmentError. -
Uses of Organism in psidev.psi.mi.jami.enricher.listener.impl.writer
Methods in psidev.psi.mi.jami.enricher.listener.impl.writer with parameters of type Organism Modifier and Type Method Description void
OrganismEnricherStatisticsWriter. onAddedAlias(Organism organism, Alias added)
Listen to the event where an alias has been added to the object aliases.void
OrganismEnricherStatisticsWriter. onCellTypeUpdate(Organism organism, CvTerm oldType)
Listen to the event where the cell type has been initialised.void
OrganismEnricherStatisticsWriter. onCommonNameUpdate(Organism organism, String oldCommonName)
Listen to the event where the commonName of an organism has been changed.void
OrganismEnricherStatisticsWriter. onCompartmentUpdate(Organism organism, CvTerm oldType)
Listen to the event where the organism compartment has been initialised.void
ParticipantEvidenceEnricherStatisticsWriter. onExpressedInUpdate(P participant, Organism oldOrganism)
onExpressedInUpdatevoid
ExperimentEnricherStatisticsWriter. onHostOrganismUpdate(Experiment experiment, Organism oldOrganism)
onHostOrganismUpdatevoid
ComplexEnricherStatisticsWriter. onOrganismUpdate(Complex interactor, Organism oldOrganism)
Listen to the event where the organism of a interactor has been initialised.void
InteractorEnricherStatisticsWriter. onOrganismUpdate(T interactor, Organism organism)
Listen to the event where the organism of a interactor has been initialised.void
OrganismEnricherStatisticsWriter. onRemovedAlias(Organism organism, Alias removed)
Listen to the event where an alias has been removed from the object aliases.void
OrganismEnricherStatisticsWriter. onScientificNameUpdate(Organism organism, String oldScientificName)
Listen to the event where the scientificName of an organism has been changed.void
OrganismEnricherStatisticsWriter. onTaxidUpdate(Organism organism, String oldTaxid)
Listen to the event where the taxid of an organism has been changed.void
OrganismEnricherStatisticsWriter. onTissueUpdate(Organism organism, CvTerm oldType)
Listen to the event where the organism tissue has been initialised. -
Uses of Organism in psidev.psi.mi.jami.html
Methods in psidev.psi.mi.jami.html with parameters of type Organism Modifier and Type Method Description protected void
AbstractMIHtmlWriter. writeOrganism(String label, Organism organism)
writeOrganism -
Uses of Organism in psidev.psi.mi.jami.json.elements
Methods in psidev.psi.mi.jami.json.elements that return types with arguments of type Organism Modifier and Type Method Description JsonElementWriter<Organism>
SimpleJsonExperimentWriter. getHostOrganismWriter()
Getter for the fieldhostOrganismWriter
.JsonElementWriter<Organism>
SimpleJsonParticipantEvidenceWriter. getHostOrganismWriter()
Getter for the fieldhostOrganismWriter
.JsonElementWriter<Organism>
SimpleJsonInteractorWriter. getOrganismWriter()
Getter for the fieldorganismWriter
.JsonElementWriter<Organism>
SimpleJsonModelledInteractionWriter. getOrganismWriter()
Getter for the fieldorganismWriter
.Methods in psidev.psi.mi.jami.json.elements with parameters of type Organism Modifier and Type Method Description void
SimpleJsonOrganismWriter. write(Organism object)
write.protected void
SimpleJsonHostOrganismWriter. writeOtherProperties(Organism object)
writeOtherProperties.protected void
SimpleJsonOrganismWriter. writeOtherProperties(Organism object)
writeOtherProperties.Method parameters in psidev.psi.mi.jami.json.elements with type arguments of type Organism Modifier and Type Method Description void
SimpleJsonExperimentWriter. setHostOrganismWriter(JsonElementWriter<Organism> hostOrganismWriter)
Setter for the fieldhostOrganismWriter
.void
SimpleJsonParticipantEvidenceWriter. setHostOrganismWriter(JsonElementWriter<Organism> hostOrganismWriter)
Setter for the fieldhostOrganismWriter
.void
SimpleJsonInteractorWriter. setOrganismWriter(JsonElementWriter<Organism> organismWriter)
Setter for the fieldorganismWriter
.void
SimpleJsonModelledInteractionWriter. setOrganismWriter(JsonElementWriter<Organism> organismWriter)
Setter for the fieldorganismWriter
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Uses of Organism in psidev.psi.mi.jami.listener
Methods in psidev.psi.mi.jami.listener with parameters of type Organism Modifier and Type Method Description void
OrganismChangeListener. onCellTypeUpdate(Organism organism, CvTerm oldType)
Listen to the event where the cell type has been initialised.void
OrganismChangeListener. onCommonNameUpdate(Organism organism, String oldCommonName)
Listen to the event where the commonName of an organism has been changed.void
OrganismChangeListener. onCompartmentUpdate(Organism organism, CvTerm oldType)
Listen to the event where the organism compartment has been initialised.void
ParticipantEvidenceChangeListener. onExpressedInUpdate(F participant, Organism oldOrganism)
onExpressedInUpdatevoid
ExperimentChangeListener. onHostOrganismUpdate(Experiment experiment, Organism oldOrganism)
onHostOrganismUpdatevoid
InteractorChangeListener. onOrganismUpdate(T interactor, Organism oldOrganism)
Listen to the event where the organism of a interactor has been initialised.void
OrganismChangeListener. onScientificNameUpdate(Organism organism, String oldScientificName)
Listen to the event where the scientificName of an organism has been changed.void
OrganismChangeListener. onTaxidUpdate(Organism organism, String oldTaxid)
Listen to the event where the taxid of an organism has been changed.void
OrganismChangeListener. onTissueUpdate(Organism organism, CvTerm oldType)
Listen to the event where the organism tissue has been initialised. -
Uses of Organism in psidev.psi.mi.jami.listener.impl
Methods in psidev.psi.mi.jami.listener.impl with parameters of type Organism Modifier and Type Method Description void
OrganismChangeLogger. onAddedAlias(Organism organism, Alias added)
Listen to the event where an alias has been added to the object aliases.void
OrganismChangeLogger. onCellTypeUpdate(Organism organism, CvTerm oldType)
Listen to the event where the cell type has been initialised.void
OrganismChangeLogger. onCommonNameUpdate(Organism organism, String oldCommonName)
Listen to the event where the commonName of an organism has been changed.void
OrganismChangeLogger. onCompartmentUpdate(Organism organism, CvTerm oldType)
Listen to the event where the organism compartment has been initialised.void
ParticipantEvidenceChangeLogger. onExpressedInUpdate(T entity, Organism oldOrganism)
onExpressedInUpdatevoid
ExperimentChangeLogger. onHostOrganismUpdate(Experiment experiment, Organism oldOrganism)
onHostOrganismUpdatevoid
InteractorChangeLogger. onOrganismUpdate(T protein, Organism old)
Listen to the event where the organism of a interactor has been initialised.void
OrganismChangeLogger. onRemovedAlias(Organism organism, Alias removed)
Listen to the event where an alias has been removed from the object aliases.void
OrganismChangeLogger. onScientificNameUpdate(Organism organism, String oldScientificName)
Listen to the event where the scientificName of an organism has been changed.void
OrganismChangeLogger. onTaxidUpdate(Organism organism, String oldTaxid)
Listen to the event where the taxid of an organism has been changed.void
OrganismChangeLogger. onTissueUpdate(Organism organism, CvTerm oldType)
Listen to the event where the organism tissue has been initialised. -
Uses of Organism in psidev.psi.mi.jami.model
Methods in psidev.psi.mi.jami.model that return Organism Modifier and Type Method Description Organism
ParticipantEvidence. getExpressedInOrganism()
The organisms in which the participant has been expressed.Organism
Experiment. getHostOrganism()
The host organism where the interaction took place in this experiment.Organism
Interactor. getOrganism()
The original source organism for this interactor.Methods in psidev.psi.mi.jami.model with parameters of type Organism Modifier and Type Method Description void
ParticipantEvidence. setExpressedInOrganism(Organism organism)
Sets the expressed in organismvoid
Experiment. setHostOrganism(Organism organism)
Sets the host organism of an experimentvoid
Interactor. setOrganism(Organism organism)
Sets the source organism of this interactor -
Uses of Organism in psidev.psi.mi.jami.model.impl
Classes in psidev.psi.mi.jami.model.impl that implement Organism Modifier and Type Class Description class
DefaultOrganism
Default implementation for organism Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousOrganismComparatorMethods in psidev.psi.mi.jami.model.impl that return Organism Modifier and Type Method Description Organism
DefaultExperimentalParticipantPool. getExpressedInOrganism()
getExpressedInOrganismOrganism
DefaultParticipantEvidence. getExpressedInOrganism()
getExpressedInOrganismOrganism
DefaultExperiment. getHostOrganism()
Getter for the fieldhostOrganism
.Organism
DefaultInteractor. getOrganism()
Getter for the fieldorganism
.Methods in psidev.psi.mi.jami.model.impl with parameters of type Organism Modifier and Type Method Description void
DefaultExperimentalParticipantPool. setExpressedInOrganism(Organism organism)
Sets the expressed in organismvoid
DefaultParticipantEvidence. setExpressedInOrganism(Organism organism)
Sets the expressed in organismvoid
DefaultExperiment. setHostOrganism(Organism organism)
Sets the host organism of an experimentvoid
DefaultInteractor. setOrganism(Organism organism)
Sets the source organism of this interactorConstructors in psidev.psi.mi.jami.model.impl with parameters of type Organism Constructor Description 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, Organism organism)
Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, String fullName, Organism organism, String uniqueChebi)
Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, Organism organism, String uniqueChebi)
Constructor for DefaultBioactiveEntity.DefaultBioactiveEntity(String name, Organism organism, Xref uniqueId)
Constructor for DefaultBioactiveEntity.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, Organism organism)
Constructor for DefaultComplex.DefaultComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultComplex.DefaultComplex(String name, Organism organism, Xref uniqueId)
Constructor for DefaultComplex.DefaultExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for DefaultExperiment.DefaultExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)
Constructor for DefaultExperimentalParticipantPool.DefaultExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, 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, Organism expressedIn, CvTerm participantIdentificationMethod)
Constructor for DefaultExperimentalParticipantPool.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, Organism organism)
Constructor for DefaultGene.DefaultGene(String name, String fullName, Organism organism, String ensembl)
Constructor for DefaultGene.DefaultGene(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultGene.DefaultGene(String name, Organism organism, String ensembl)
Constructor for DefaultGene.DefaultGene(String name, Organism organism, Xref uniqueId)
Constructor for DefaultGene.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, Organism organism)
Constructor for DefaultInteractor.DefaultInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultInteractor.DefaultInteractor(String name, Organism organism, Xref uniqueId)
Constructor for DefaultInteractor.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, Organism organism)
Constructor for DefaultInteractorPool.DefaultInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultInteractorPool.DefaultInteractorPool(String name, Organism organism, Xref uniqueId)
Constructor for DefaultInteractorPool.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, Organism organism)
Constructor for DefaultMolecule.DefaultMolecule(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultMolecule.DefaultMolecule(String name, Organism organism, Xref uniqueId)
Constructor for DefaultMolecule.DefaultNamedExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for DefaultNamedExperiment.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, Organism expressedIn, 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, Organism expressedIn, CvTerm participantIdentificationMethod)
Constructor for DefaultNamedParticipantEvidence.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, Organism organism)
Constructor for DefaultNucleicAcid.DefaultNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultNucleicAcid.DefaultNucleicAcid(String name, Organism organism, Xref uniqueId)
Constructor for DefaultNucleicAcid.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, Organism expressedIn, 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, Organism expressedIn, CvTerm participantIdentificationMethod)
Constructor for DefaultParticipantEvidence.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, Organism organism)
Constructor for DefaultPolymer.DefaultPolymer(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultPolymer.DefaultPolymer(String name, Organism organism, Xref uniqueId)
Constructor for DefaultPolymer.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, Organism organism)
Constructor for DefaultProtein.DefaultProtein(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultProtein.DefaultProtein(String name, Organism organism, Xref uniqueId)
Constructor for DefaultProtein. -
Uses of Organism in psidev.psi.mi.jami.tab.extension
Classes in psidev.psi.mi.jami.tab.extension that implement Organism Modifier and Type Class Description class
MitabOrganism
Mitab extension of Organism.Constructors in psidev.psi.mi.jami.tab.extension with parameters of type Organism Constructor Description 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, Organism organism)
Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, String fullName, Organism organism, String uniqueChebi)
Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, Organism organism, String uniqueChebi)
Constructor for MitabBioactiveEntity.MitabBioactiveEntity(String name, Organism organism, Xref uniqueId)
Constructor for MitabBioactiveEntity.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, Organism organism)
Constructor for MitabComplex.MitabComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for MitabComplex.MitabComplex(String name, Organism organism, Xref uniqueId)
Constructor for MitabComplex.MitabExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for MitabExperiment.MitabGene(String name, String fullName, Organism organism)
Constructor for MitabGene.MitabGene(String name, String fullName, Organism organism, String ensembl)
Constructor for MitabGene.MitabGene(String name, String fullName, Organism organism, Xref uniqueId)
Constructor for MitabGene.MitabGene(String name, Organism organism)
Constructor for MitabGene.MitabGene(String name, Organism organism, String ensembl)
Constructor for MitabGene.MitabGene(String name, Organism organism, Xref uniqueId)
Constructor for MitabGene.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, Organism organism)
Constructor for MitabInteractor.MitabInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for MitabInteractor.MitabInteractor(String name, Organism organism, Xref uniqueId)
Constructor for MitabInteractor.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, Organism organism)
Constructor for MitabInteractorPool.MitabInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for MitabInteractorPool.MitabInteractorPool(String name, Organism organism, Xref uniqueId)
Constructor for MitabInteractorPool.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, Organism organism)
Constructor for MitabMolecule.MitabMolecule(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for MitabMolecule.MitabMolecule(String name, Organism organism, Xref uniqueId)
Constructor for MitabMolecule.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, Organism organism)
Constructor for MitabNucleicAcid.MitabNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for MitabNucleicAcid.MitabNucleicAcid(String name, Organism organism, Xref uniqueId)
Constructor for MitabNucleicAcid.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, Organism expressedIn, 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, Organism expressedIn, CvTerm participantIdentificationMethod)
Constructor for MitabParticipantEvidence.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, Organism organism)
Constructor for MitabPolymer.MitabPolymer(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for MitabPolymer.MitabPolymer(String name, Organism organism, Xref uniqueId)
Constructor for MitabPolymer.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, Organism organism)
Constructor for MitabProtein.MitabProtein(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for MitabProtein.MitabProtein(String name, Organism organism, Xref uniqueId)
Constructor for MitabProtein. -
Uses of Organism in psidev.psi.mi.jami.tab.io.writer.feeder
Methods in psidev.psi.mi.jami.tab.io.writer.feeder with parameters of type Organism Modifier and Type Method Description void
AbstractMitabColumnFeeder. writeOrganism(Organism organism)
Write an organism.void
MitabColumnFeeder. writeOrganism(Organism organism)
Write an organism. -
Uses of Organism in psidev.psi.mi.jami.utils
Methods in psidev.psi.mi.jami.utils that return Organism Modifier and Type Method Description static Organism
OrganismUtils. createChemicalSynthesisOrganism()
createChemicalSynthesisOrganismstatic Organism
OrganismUtils. createInSilicoOrganism()
createInSilicoOrganismstatic Organism
OrganismUtils. createInVitroOrganism()
createInVitroOrganismstatic Organism
OrganismUtils. createInVivoOrganism()
createInVivoOrganismstatic Organism
OrganismUtils. createSpecialistOrganism(int taxID)
If the TaxId is one of the reserved numbers (-5 to -1), it denotes a non-real organism.static Organism
OrganismUtils. createUnknownOrganism()
createUnknownOrganismMethods in psidev.psi.mi.jami.utils with parameters of type Organism Modifier and Type Method Description static NamedExperiment
ExperimentUtils. createExperiment(String name, String pubmedId, CvTerm interactionDetectionMethod, Organism hostOrganism)
createExperimentstatic Experiment
ExperimentUtils. createExperiment(String pubmedId, CvTerm interactionDetectionMethod, Organism hostOrganism)
createExperiment -
Uses of Organism in psidev.psi.mi.jami.utils.clone
Methods in psidev.psi.mi.jami.utils.clone with parameters of type Organism Modifier and Type Method Description static void
OrganismCloner. copyAndOverrideOrganismProperties(Organism source, Organism target)
This method will copy properties of organism source in organism target and will override all the other properties of Target organism. -
Uses of Organism in psidev.psi.mi.jami.utils.comparator.organism
Methods in psidev.psi.mi.jami.utils.comparator.organism with parameters of type Organism Modifier and Type Method Description static boolean
DefaultOrganismComparator. areEquals(Organism organism1, Organism organism2)
Use DefaultOrganismComparator to know if two organism are equals.static boolean
OrganismTaxIdComparator. areEquals(Organism organism1, Organism organism2)
Use OrganismTaxIdComparator to know if two organisms are equals.static boolean
UnambiguousOrganismComparator. areEquals(Organism organism1, Organism organism2)
Use UnambiguousOrganismComparator to know if two organism are equals.int
OrganismComparator. compare(Organism organism1, Organism organism2)
It will first look at the taxids.int
OrganismTaxIdComparator. compare(Organism organism1, Organism organism2)
Comparison is based on taxIds only.int
UnambiguousOrganismComparator. compare(Organism organism1, Organism organism2)
It will first look at the taxids.static int
OrganismTaxIdComparator. hashCode(Organism organism)
hashCodestatic int
UnambiguousOrganismComparator. hashCode(Organism organism)
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Uses of Organism in psidev.psi.mi.jami.xml.io.writer.elements
Methods in psidev.psi.mi.jami.xml.io.writer.elements that return types with arguments of type Organism Modifier and Type Method Description 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 PsiXmlElementWriter<Organism>
PsiXmlElementWriterFactory. createOrganismWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlElementWriter<Alias> aliasWriter, PsiXmlElementWriter<Annotation> annotationWriter, PsiXmlXrefWriter xrefWriter, PsiXmlVariableNameWriter<CvTerm> openCvWriter)
createOrganismWriter. -
Uses of Organism 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 Organism Modifier and Type Method Description PsiXmlElementWriter<Organism>
XmlInteractorWriter. getOrganismWriter()
Getter for the fieldorganismWriter
.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl with parameters of type Organism Modifier and Type Method Description protected void
XmlHostOrganismWriter. writeOtherProperties(Organism object)
writeOtherProperties.protected void
XmlOrganismWriter. writeOtherProperties(Organism object)
writeOtherProperties.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl with type arguments of type Organism Modifier and Type Method Description void
XmlInteractorWriter. setOrganismWriter(PsiXmlElementWriter<Organism> organismWriter)
Setter for the fieldorganismWriter
. -
Uses of Organism 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 types with arguments of type Organism Modifier and Type Method Description PsiXmlElementWriter<Organism>
AbstractXmlExperimentWriter. getHostOrganismWriter()
Getter for the fieldhostOrganismWriter
.PsiXmlElementWriter<Organism>
AbstractXmlParticipantEvidenceWriter. getHostOrganismWriter()
Getter for the fieldhostOrganismWriter
.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with parameters of type Organism Modifier and Type Method Description void
AbstractXmlOrganismWriter. write(Organism object)
write.protected abstract void
AbstractXmlOrganismWriter. writeOtherProperties(Organism object)
writeOtherProperties.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with type arguments of type Organism Modifier and Type Method Description void
AbstractXmlExperimentWriter. setHostOrganismWriter(PsiXmlElementWriter<Organism> hostOrganismWriter)
Setter for the fieldhostOrganismWriter
.void
AbstractXmlParticipantEvidenceWriter. setHostOrganismWriter(PsiXmlElementWriter<Organism> hostOrganismWriter)
Setter for the fieldhostOrganismWriter
. -
Uses of Organism 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 types with arguments of type Organism Modifier and Type Method Description PsiXmlElementWriter<Organism>
AbstractXmlModelledInteractionWriter. getOrganismWriter()
Getter for the fieldorganismWriter
.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30 with type arguments of type Organism Modifier and Type Method Description void
AbstractXmlModelledInteractionWriter. setOrganismWriter(PsiXmlElementWriter<Organism> organismWriter)
Setter for the fieldorganismWriter
. -
Uses of Organism 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 with parameters of type Organism Modifier and Type Method Description protected void
XmlHostOrganismWriter. writeOtherProperties(Organism object)
writeOtherProperties. -
Uses of Organism 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 with parameters of type Organism Modifier and Type Method Description protected void
XmlHostOrganismWriter. writeOtherProperties(Organism object)
writeOtherProperties. -
Uses of Organism 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 types with arguments of type Organism Modifier and Type Method Description PsiXmlElementWriter<Organism>
AbstractXmlModelledInteractionWriter. getOrganismWriter()
Getter for the fieldorganismWriter
.Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30 with parameters of type Organism Modifier and Type Method Description protected void
XmlHostOrganismWriter. writeOtherProperties(Organism object)
writeOtherProperties.Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30 with type arguments of type Organism Modifier and Type Method Description void
AbstractXmlModelledInteractionWriter. setOrganismWriter(PsiXmlElementWriter<Organism> organismWriter)
Setter for the fieldorganismWriter
. -
Uses of Organism in psidev.psi.mi.jami.xml.listener
Method parameters in psidev.psi.mi.jami.xml.listener with type arguments of type Organism Modifier and Type Method Description void
PsiXmlParserCompositeListener. onSeveralExpressedInOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralExpressedInOrganismFound.void
PsiXmlParserListener. onSeveralExpressedInOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralExpressedInOrganismFound.void
PsiXmlParserLogger. onSeveralExpressedInOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralExpressedInOrganismFound.void
PsiXmlParserCompositeListener. onSeveralHostOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralHostOrganismFound.void
PsiXmlParserListener. onSeveralHostOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralHostOrganismFound.void
PsiXmlParserLogger. onSeveralHostOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralHostOrganismFound. -
Uses of Organism in psidev.psi.mi.jami.xml.model.extension
Methods in psidev.psi.mi.jami.xml.model.extension that return Organism Modifier and Type Method Description Organism
AbstractBaseXmlInteractor. getOrganism()
Getter for the fieldorganism
.Methods in psidev.psi.mi.jami.xml.model.extension that return types with arguments of type Organism Modifier and Type Method Description List<Organism>
ExtendedPsiXmlExperiment. getHostOrganisms()
getHostOrganisms.List<Organism>
ExtendedPsiXmlParticipantEvidence. getHostOrganisms()
getHostOrganisms.Methods in psidev.psi.mi.jami.xml.model.extension with parameters of type Organism Modifier and Type Method Description void
AbstractBaseXmlInteractor. setJAXBOrganism(Organism organism)
setJAXBOrganism.void
AbstractBaseXmlInteractor. setOrganism(Organism organism)
Sets the source organism of this interactorConstructors in psidev.psi.mi.jami.xml.model.extension with parameters of type Organism Constructor Description 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, Organism organism)
Constructor for AbstractBaseXmlInteractor.AbstractBaseXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for AbstractBaseXmlInteractor.AbstractBaseXmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for AbstractBaseXmlInteractor. -
Uses of Organism in psidev.psi.mi.jami.xml.model.extension.binary.xml30
Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 that return Organism Modifier and Type Method Description Organism
XmlModelledBinaryInteraction. getOrganism()
The original source organism for this interactor.Organism
XmlModelledBinaryInteractionWrapper. getOrganism()
The original source organism for this interactor.Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 with parameters of type Organism Modifier and Type Method Description void
XmlModelledBinaryInteraction. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlModelledBinaryInteractionWrapper. setOrganism(Organism organism)
Sets the source organism of this interactor -
Uses of Organism in psidev.psi.mi.jami.xml.model.extension.datasource
Method parameters in psidev.psi.mi.jami.xml.model.extension.datasource with type arguments of type Organism Modifier and Type Method Description void
AbstractPsiXmlStream. onSeveralExpressedInOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralExpressedInOrganismFound.void
DefaultPsiXmlStreamSource. onSeveralExpressedInOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralExpressedInOrganismFound.void
AbstractPsiXmlStream. onSeveralHostOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralHostOrganismFound.void
DefaultPsiXmlStreamSource. onSeveralHostOrganismFound(Collection<Organism> organisms, FileSourceLocator locator)
onSeveralHostOrganismFound. -
Uses of Organism in psidev.psi.mi.jami.xml.model.extension.xml253
Classes in psidev.psi.mi.jami.xml.model.extension.xml253 that implement Organism Modifier and Type Class Description class
HostOrganism
The experiment/participant host organismclass
XmlOrganism
Xml implementation of an organismMethods in psidev.psi.mi.jami.xml.model.extension.xml253 that return Organism Modifier and Type Method Description Organism
XmlExperimentalParticipantPool. getExpressedInOrganism()
The organisms in which the participant has been expressed.Organism
XmlParticipantEvidence. getExpressedInOrganism()
getExpressedInOrganism.Organism
AbstractXmlExperiment. getHostOrganism()
getHostOrganism.Organism
AbstractXmlComplex. getOrganism()
The original source organism for this interactor.Organism
XmlBasicInteractionComplexWrapper. getOrganism()
The original source organism for this interactor.Organism
XmlInteractionEvidenceComplexWrapper. getOrganism()
The original source organism for this interactor.Organism
XmlModelledInteractionComplexWrapper. getOrganism()
The original source organism for this interactor.Methods in psidev.psi.mi.jami.xml.model.extension.xml253 that return types with arguments of type Organism Modifier and Type Method Description List<Organism>
AbstractXmlExperiment. getHostOrganisms()
getHostOrganisms.List<Organism>
XmlParticipantEvidence. getHostOrganisms()
getHostOrganisms.List<Organism>
AbstractXmlExperiment.JAXBHostOrganismWrapper. getJAXBHostOrganisms()
List<Organism>
XmlParticipantEvidence.JAXBHostOrganismWrapper. getJAXBHostOrganisms()
Methods in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Organism Modifier and Type Method Description void
XmlExperimentalParticipantPool. setExpressedInOrganism(Organism organism)
Sets the expressed in organismvoid
XmlParticipantEvidence. setExpressedInOrganism(Organism organism)
Sets the expressed in organismvoid
AbstractXmlExperiment. setHostOrganism(Organism organism)
Sets the host organism of an experimentvoid
AbstractXmlComplex. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlBasicInteractionComplexWrapper. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlInteractionEvidenceComplexWrapper. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlModelledInteractionComplexWrapper. setOrganism(Organism organism)
Sets the source organism of this interactorConstructors in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Organism Constructor Description 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, Organism organism)
Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, Organism organism, Xref uniqueId)
Constructor for AbstractXmlComplex.AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for AbstractXmlExperiment.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, Organism organism)
Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for AbstractXmlInteractor.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, Organism organism)
Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, Organism organism, Xref uniqueId)
Constructor for DefaultXmlComplex.DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for DefaultXmlExperiment.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, Organism organism)
Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for DefaultXmlInteractor.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, Organism organism)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, Organism organism, String uniqueChebi)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, Organism organism, String uniqueChebi)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, Organism organism, Xref uniqueId)
Constructor for XmlBioactiveEntity.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, Organism organism)
Constructor for XmlComplex.XmlComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlComplex.XmlComplex(String name, Organism organism, Xref uniqueId)
Constructor for XmlComplex.XmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for XmlExperiment.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, Organism organism)
Constructor for XmlGene.XmlGene(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlGene.XmlGene(String name, Organism organism, Xref uniqueId)
Constructor for XmlGene.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, Organism organism)
Constructor for XmlInteractor.XmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlInteractor.XmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for XmlInteractor.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, Organism organism)
Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlInteractorPool.XmlInteractorPool(String name, Organism organism, Xref uniqueId)
Constructor for XmlInteractorPool.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, Organism organism)
Constructor for XmlMolecule.XmlMolecule(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlMolecule.XmlMolecule(String name, Organism organism, Xref uniqueId)
Constructor for XmlMolecule.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, Organism organism)
Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, Organism organism, Xref uniqueId)
Constructor for XmlNucleicAcid.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, Organism organism)
Constructor for XmlPolymer.XmlPolymer(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlPolymer.XmlPolymer(String name, Organism organism, Xref uniqueId)
Constructor for XmlPolymer.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, Organism organism)
Constructor for XmlProtein.XmlProtein(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlProtein.XmlProtein(String name, Organism organism, Xref uniqueId)
Constructor for XmlProtein. -
Uses of Organism in psidev.psi.mi.jami.xml.model.extension.xml254
Classes in psidev.psi.mi.jami.xml.model.extension.xml254 that implement Organism Modifier and Type Class Description class
HostOrganism
The experiment/participant host organismclass
XmlOrganism
Xml implementation of an organismMethods in psidev.psi.mi.jami.xml.model.extension.xml254 that return Organism Modifier and Type Method Description Organism
XmlExperimentalParticipantPool. getExpressedInOrganism()
The organisms in which the participant has been expressed.Organism
XmlParticipantEvidence. getExpressedInOrganism()
getExpressedInOrganism.Organism
AbstractXmlExperiment. getHostOrganism()
getHostOrganism.Organism
AbstractXmlComplex. getOrganism()
The original source organism for this interactor.Organism
XmlBasicInteractionComplexWrapper. getOrganism()
The original source organism for this interactor.Organism
XmlInteractionEvidenceComplexWrapper. getOrganism()
The original source organism for this interactor.Organism
XmlModelledInteractionComplexWrapper. getOrganism()
The original source organism for this interactor.Methods in psidev.psi.mi.jami.xml.model.extension.xml254 that return types with arguments of type Organism Modifier and Type Method Description List<Organism>
AbstractXmlExperiment. getHostOrganisms()
getHostOrganisms.List<Organism>
XmlParticipantEvidence. getHostOrganisms()
getHostOrganisms.List<Organism>
AbstractXmlExperiment.JAXBHostOrganismWrapper. getJAXBHostOrganisms()
List<Organism>
XmlParticipantEvidence.JAXBHostOrganismWrapper. getJAXBHostOrganisms()
Methods in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Organism Modifier and Type Method Description void
XmlExperimentalParticipantPool. setExpressedInOrganism(Organism organism)
Sets the expressed in organismvoid
XmlParticipantEvidence. setExpressedInOrganism(Organism organism)
Sets the expressed in organismvoid
AbstractXmlExperiment. setHostOrganism(Organism organism)
Sets the host organism of an experimentvoid
AbstractXmlComplex. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlBasicInteractionComplexWrapper. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlInteractionEvidenceComplexWrapper. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlModelledInteractionComplexWrapper. setOrganism(Organism organism)
Sets the source organism of this interactorConstructors in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Organism Constructor Description 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, Organism organism)
Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, Organism organism, Xref uniqueId)
Constructor for AbstractXmlComplex.AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for AbstractXmlExperiment.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, Organism organism)
Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for AbstractXmlInteractor.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, Organism organism)
Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, Organism organism, Xref uniqueId)
Constructor for DefaultXmlComplex.DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for DefaultXmlExperiment.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, Organism organism)
Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for DefaultXmlInteractor.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, Organism organism)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, Organism organism, String uniqueChebi)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, Organism organism, String uniqueChebi)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, Organism organism, Xref uniqueId)
Constructor for XmlBioactiveEntity.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, Organism organism)
Constructor for XmlComplex.XmlComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlComplex.XmlComplex(String name, Organism organism, Xref uniqueId)
Constructor for XmlComplex.XmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for XmlExperiment.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, Organism organism)
Constructor for XmlGene.XmlGene(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlGene.XmlGene(String name, Organism organism, Xref uniqueId)
Constructor for XmlGene.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, Organism organism)
Constructor for XmlInteractor.XmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlInteractor.XmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for XmlInteractor.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, Organism organism)
Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlInteractorPool.XmlInteractorPool(String name, Organism organism, Xref uniqueId)
Constructor for XmlInteractorPool.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, Organism organism)
Constructor for XmlMolecule.XmlMolecule(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlMolecule.XmlMolecule(String name, Organism organism, Xref uniqueId)
Constructor for XmlMolecule.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, Organism organism)
Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, Organism organism, Xref uniqueId)
Constructor for XmlNucleicAcid.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, Organism organism)
Constructor for XmlPolymer.XmlPolymer(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlPolymer.XmlPolymer(String name, Organism organism, Xref uniqueId)
Constructor for XmlPolymer.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, Organism organism)
Constructor for XmlProtein.XmlProtein(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlProtein.XmlProtein(String name, Organism organism, Xref uniqueId)
Constructor for XmlProtein. -
Uses of Organism in psidev.psi.mi.jami.xml.model.extension.xml300
Classes in psidev.psi.mi.jami.xml.model.extension.xml300 that implement Organism Modifier and Type Class Description class
HostOrganism
The experiment/participant host organismclass
XmlOrganism
Xml implementation of an organismMethods in psidev.psi.mi.jami.xml.model.extension.xml300 that return Organism Modifier and Type Method Description Organism
XmlExperimentalParticipantPool. getExpressedInOrganism()
The organisms in which the participant has been expressed.Organism
XmlParticipantEvidence. getExpressedInOrganism()
getExpressedInOrganism.Organism
AbstractXmlExperiment. getHostOrganism()
getHostOrganism.Organism
AbstractXmlComplex. getOrganism()
The original source organism for this interactor.Organism
XmlBasicInteractionComplexWrapper. getOrganism()
The original source organism for this interactor.Organism
XmlInteractionEvidenceComplexWrapper. getOrganism()
The original source organism for this interactor.Organism
XmlModelledInteraction. getOrganism()
The original source organism for this interactor.Organism
XmlModelledInteractionComplexWrapper. getOrganism()
The original source organism for this interactor.Methods in psidev.psi.mi.jami.xml.model.extension.xml300 that return types with arguments of type Organism Modifier and Type Method Description List<Organism>
AbstractXmlExperiment. getHostOrganisms()
getHostOrganisms.List<Organism>
XmlParticipantEvidence. getHostOrganisms()
getHostOrganisms.List<Organism>
AbstractXmlExperiment.JAXBHostOrganismWrapper. getJAXBHostOrganisms()
List<Organism>
XmlParticipantEvidence.JAXBHostOrganismWrapper. getJAXBHostOrganisms()
Methods in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Organism Modifier and Type Method Description void
XmlExperimentalParticipantPool. setExpressedInOrganism(Organism organism)
Sets the expressed in organismvoid
XmlParticipantEvidence. setExpressedInOrganism(Organism organism)
Sets the expressed in organismvoid
AbstractXmlExperiment. setHostOrganism(Organism organism)
Sets the host organism of an experimentvoid
AbstractXmlComplex. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlBasicInteractionComplexWrapper. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlInteractionEvidenceComplexWrapper. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlModelledInteraction. setOrganism(Organism organism)
Sets the source organism of this interactorvoid
XmlModelledInteractionComplexWrapper. setOrganism(Organism organism)
Sets the source organism of this interactorConstructors in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Organism Constructor Description 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, Organism organism)
Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for AbstractXmlComplex.AbstractXmlComplex(String name, Organism organism, Xref uniqueId)
Constructor for AbstractXmlComplex.AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for AbstractXmlExperiment.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, Organism organism)
Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for AbstractXmlInteractor.AbstractXmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for AbstractXmlInteractor.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, Organism organism)
Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultXmlComplex.DefaultXmlComplex(String name, Organism organism, Xref uniqueId)
Constructor for DefaultXmlComplex.DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for DefaultXmlExperiment.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, Organism organism)
Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for DefaultXmlInteractor.DefaultXmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for DefaultXmlInteractor.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, Organism organism)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, Organism organism, String uniqueChebi)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, Organism organism, String uniqueChebi)
Constructor for XmlBioactiveEntity.XmlBioactiveEntity(String name, Organism organism, Xref uniqueId)
Constructor for XmlBioactiveEntity.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, Organism organism)
Constructor for XmlComplex.XmlComplex(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlComplex.XmlComplex(String name, Organism organism, Xref uniqueId)
Constructor for XmlComplex.XmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)
Constructor for XmlExperiment.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, Organism organism)
Constructor for XmlGene.XmlGene(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlGene.XmlGene(String name, Organism organism, Xref uniqueId)
Constructor for XmlGene.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, Organism organism)
Constructor for XmlInteractor.XmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlInteractor.XmlInteractor(String name, Organism organism, Xref uniqueId)
Constructor for XmlInteractor.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, Organism organism)
Constructor for XmlInteractorPool.XmlInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlInteractorPool.XmlInteractorPool(String name, Organism organism, Xref uniqueId)
Constructor for XmlInteractorPool.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, Organism organism)
Constructor for XmlMolecule.XmlMolecule(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlMolecule.XmlMolecule(String name, Organism organism, Xref uniqueId)
Constructor for XmlMolecule.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, Organism organism)
Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlNucleicAcid.XmlNucleicAcid(String name, Organism organism, Xref uniqueId)
Constructor for XmlNucleicAcid.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, Organism organism)
Constructor for XmlPolymer.XmlPolymer(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlPolymer.XmlPolymer(String name, Organism organism, Xref uniqueId)
Constructor for XmlPolymer.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, Organism organism)
Constructor for XmlProtein.XmlProtein(String name, String fullName, Organism organism, Xref uniqueId)
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, Organism organism)
Constructor for XmlProtein.XmlProtein(String name, Organism organism, Xref uniqueId)
Constructor for XmlProtein. -
Uses of Organism in psidev.psi.mi.jami.xml.model.reference.xml253
Methods in psidev.psi.mi.jami.xml.model.reference.xml253 that return Organism Modifier and Type Method Description Organism
AbstractExperimentRef. getHostOrganism()
getHostOrganism.Organism
AbstractInteractorRef. getOrganism()
getOrganism.Methods in psidev.psi.mi.jami.xml.model.reference.xml253 that return types with arguments of type Organism Modifier and Type Method Description List<Organism>
AbstractExperimentRef. getHostOrganisms()
getHostOrganisms.Methods in psidev.psi.mi.jami.xml.model.reference.xml253 with parameters of type Organism Modifier and Type Method Description void
AbstractExperimentRef. setHostOrganism(Organism organism)
Sets the host organism of an experimentvoid
AbstractInteractorRef. setOrganism(Organism organism)
Sets the source organism of this interactor -
Uses of Organism in psidev.psi.mi.jami.xml.model.reference.xml254
Methods in psidev.psi.mi.jami.xml.model.reference.xml254 that return Organism Modifier and Type Method Description Organism
AbstractExperimentRef. getHostOrganism()
getHostOrganism.Organism
AbstractInteractorRef. getOrganism()
getOrganism.Methods in psidev.psi.mi.jami.xml.model.reference.xml254 that return types with arguments of type Organism Modifier and Type Method Description List<Organism>
AbstractExperimentRef. getHostOrganisms()
getHostOrganisms.Methods in psidev.psi.mi.jami.xml.model.reference.xml254 with parameters of type Organism Modifier and Type Method Description void
AbstractExperimentRef. setHostOrganism(Organism organism)
Sets the host organism of an experimentvoid
AbstractInteractorRef. setOrganism(Organism organism)
Sets the source organism of this interactor -
Uses of Organism in psidev.psi.mi.jami.xml.model.reference.xml300
Methods in psidev.psi.mi.jami.xml.model.reference.xml300 that return Organism Modifier and Type Method Description Organism
AbstractExperimentRef. getHostOrganism()
getHostOrganism.Organism
AbstractInteractorRef. getOrganism()
getOrganism.Methods in psidev.psi.mi.jami.xml.model.reference.xml300 that return types with arguments of type Organism Modifier and Type Method Description List<Organism>
AbstractExperimentRef. getHostOrganisms()
getHostOrganisms.Methods in psidev.psi.mi.jami.xml.model.reference.xml300 with parameters of type Organism Modifier and Type Method Description void
AbstractExperimentRef. setHostOrganism(Organism organism)
Sets the host organism of an experimentvoid
AbstractInteractorRef. setOrganism(Organism organism)
Sets the source organism of this interactor
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